21738389|t|A novel DFNB31 mutation associated with Usher type 2 syndrome showing variable degrees of auditory loss in a consanguineous Portuguese family.
21738389|a|PURPOSE: To identify the genetic defect of a consanguineous Portuguese family with rod-cone dystrophy and varying degrees of decreased audition. METHODS: A detailed ophthalmic and auditory examination was performed on a Portuguese patient with severe autosomal recessive rod-cone dystrophy. Known genetic defects were excluded by performing autosomal recessive retinitis pigmentosa (arRP) genotyping microarray analysis and by Sanger sequencing of the coding exons and flanking intronic regions of eyes shut homolog-drosophila (EYS) and chromosome 2 open reading frame 71 (C2orf71). Subsequently, genome-wide homozygosity mapping was performed in DNA samples from available family members using a 700K single nucleotide polymorphism (SNP) microarray. Candidate genes present in the significantly large homozygous regions were screened for mutations using Sanger sequencing. RESULTS: The largest homozygous region (~11 Mb) in the affected family members was mapped to chromosome 9, which harbors deafness, autosomal recessive 31 (DFNB31; a gene previously associated with Usher syndrome). Mutation analysis of DFNB31 in the index patient identified a novel one-base-pair deletion (c.737delC), which is predicted to lead to a truncated protein (p.Pro246HisfsX13) and co-segregated with the disease in the family. Ophthalmic examination of the index patient and the affected siblings showed severe rod-cone dystrophy. Pure tone audiometry revealed a moderate hearing loss in the index patient, whereas the affected siblings were reported with more profound and early onset hearing impairment. CONCLUSIONS: We report a novel truncating mutation in DFNB31 associated with severe rod-cone dystrophy and varying degrees of hearing impairment in a consanguineous family of Portuguese origin. This is the second report of DFNB31 implication in Usher type 2.
21738389	1323	1332	c.737delC	DNAMutation	c|DEL|737|C
21738389	1386	1402	p.Pro246HisfsX13	ProteinMutation	p|P|246|H|FSX|13

22051099|t|Variation in the CXCR1 gene (IL8RA) is not associated with susceptibility to chronic periodontitis.
22051099|a|BACKGROUND: The chemokine receptor 1 CXCR-1 (or IL8R-alpha) is a specific receptor for the interleukin 8 (IL-8), which is chemoattractant for neutrophils and has an important role in the inflammatory response. The polymorphism rs2234671 at position Ex2+860G>C of the CXCR1 gene causes a conservative amino acid substitution (S276T). This single nucleotide polymorphism (SNP) seemed to be functional as it was associated with decreased lung cancer risk. Previous studies of our group found association of haplotypes in the IL8 and in the CXCR2 genes with the multifactorial disease chronic periodontitis. In this study we investigated the polymorphism rs2234671 in 395 Brazilian subjects with and without chronic periodontitis. FINDINGS: Similar distribution of the allelic and genotypic frequencies were observed between the groups (p>0.05). CONCLUSIONS: The polymorphism rs2234671 in the CXCR1 gene was not associated with the susceptibility to chronic periodontitis in the studied Brazilian population.
22051099	327	336	rs2234671	SNP	rs2234671
22051099	349	359	Ex2+860G>C	DNAMutation	c|G|Ex2+860|C
22051099	425	430	S276T	ProteinMutation	p|S|276|T
22051099	751	760	rs2234671	SNP	rs2234671
22051099	972	981	rs2234671	SNP	rs2234671

22188495|t|A case of Werner syndrome without metabolic abnormality: implications for the early pathophysiology.
22188495|a|Werner syndrome (WS) is an autosomal recessive progeroid disorder caused by mutations in the WRN DNA helicase. It is characterized by the graying and loss of hair, juvenile cataracts, sclerosis and ulceration of skin, insulin-resistant diabetes mellitus, dyslipidemia, abdominal adiposity, osteoporosis, atherosclerosis, and malignant neoplasm. Patients are usually diagnosed in their 30s or 40s, but the early pathophysiology of the syndrome is still not fully understood. Here we report a 29-year-old female patient who displayed cataracts, hair graying, and tendinous calcinosis. Her parents were first cousins. Interestingly, the patient lacked the metabolic signs typical for WS, including glucose intolerance, dyslipidemia, and visceral fat accumulation. A hyperinsulinemic response at 30 min was observed in an oral glucose tolerance test. Mutational analysis for the WRN gene revealed a homozygous nucleotide substitution 3190C>T in exon 24, resulting in a protein product with replacement of an arginine residue at position 573 by termination codon (Arg987Ter). The mutated WRN protein was unable to translocate into the nucleus in an in vitro cell assay. A WS patient with an Arg987Ter mutation has been previously reported in Switzerland, the present case is the first to be identified in Asia. This case demonstrates the early clinical features of WS and suggests that metabolic abnormality, including insulin resistance, is not an essential component of WS at disease onset. Moreover, a follow-up study of such case would be useful to understand how the various clinical symptoms in WS develop and progress over the years.
22188495	1031	1038	3190C>T	DNAMutation	g|C|3190|T
22188495	1160	1169	Arg987Ter	ProteinMutation	p|R|987|X
22188495	1287	1296	Arg987Ter	ProteinMutation	p|R|987|X

21881116|t|Enhanced replication of hepatitis B virus with frameshift in the precore region found in fulminant hepatitis patients.
21881116|a|BACKGROUND: The genotype B of hepatitis B virus (HBV) was reported to associate with fulminant hepatitis (FH). We aimed to clarify the characteristics of HBV obtained from FH patients in an area of Japan where genotype B HBV is prevalent. METHODS: Using serum samples of 16 HBV-associated FH patients, partial HBV sequences were determined. The effects of HBV mutation/insertion/deletion were evaluated using an in vitro HBV replication system. RESULTS: Of the 16 HBV isolates, 31% belonged to subgenotype B1/Bj, 38% were subgenotype B2/Ba, and 31% were subgenotype C2/Ce. Notably, the single nucleotide insertion/deletion that resulted in a frameshift of the precore protein was found exclusively in 60% of B1/Bj strains. An in vitro study showed that all of the frameshift mutants had significantly higher amounts of HBV DNA than did the wild type. One of the isolates had a novel insertion of A between nucleotides 1900 and 1901, which resulted in a 3-nucleotide change within the Kozak sequence of the core protein and enhanced the core protein expression in vitro. CONCLUSIONS: The frameshift insertion/deletion in the precore region enhanced HBV replication and might be associated with the development of FH by the subgenotype B1/Bj HBV.

21559944|t|A complete deficiency of Hyaluronoglucosaminidase 1 (HYAL1) presenting as familial juvenile idiopathic arthritis.
21559944|a|We describe a single consanguineous family with three affected children exhibiting knee and/or hip pain associated with swelling. Detailed clinical evaluation demonstrated diffuse joint involvement with an unusual proliferative synovitis on MRI. Synovial biopsies were notable for an infiltration of macrophages with abundant cytoplasm filled with faintly basophilic vacuoles. We used homozygosity mapping with a panel of 262,000 single nucleotide polymorphism markers to identify a homozygous stretch of 40.52  Mb on chromosome 3p22.3 - 3p13 that segregated with the arthropathy in the family. Of the 378 genes in the interval, the three hyaluronoglucosaminidase genes were considered good candidates based on the phenotype. Dideoxy sequencing identified a homozygous deletion in HYAL1, c.104delT, resulting in a premature termination codon, p.Val35AlafsX25, found in all three affected children. Enzymatic analysis confirmed total HYAL1 deficiency in the three affected children. This confirms the diagnosis of Mucopolysaccharidosis IX (MPS IX) which has only been described in a single patient to date. In contrast to the previously described MPS IX patient, our three patients display a phenotype limited to the joints, suggesting that this is the primary manifestation of HYAL1 deficiency.
21559944	902	911	c.104delT	DNAMutation	c|DEL|104|T
21559944	957	972	p.Val35AlafsX25	ProteinMutation	p|V|35|A|FSX|25

21798259|t|WT1 mutations and polymorphisms in Southeast Asian acute myeloid leukemia.
21798259|a|Genomic alterations of the Wilms' Tumor 1 (WT1) gene have been reported to occur in patients with acute myeloid leukemia (AML). No data presently exists regarding the frequency of WT1 mutations in the Southeast Asian AML population. This study focused on WT1 exons 7-10 mutations and their correlation with other molecular markers and patients' characteristics. The zinc finger domain of WT1 gene covering exons 7-10 was directly sequenced. Six types of mutations were identified among 49 cases (12.24%); 4 localized on exon 7 and 2 on exon 9. Two novel mutations were identified including the insertion within codon 313 and codon 314. Patients harboring WT1 mutations seemed to have a younger age (29.5 vs 45.4 years), a higher white blood cell count (120.3 vs 19.8 10(9)/L), and a lower platelet count (54.2 vs 104.3 10(9)/L) as compared to those without the mutations although statistical differences could not be demonstrated. All exon 7 mutations were frameshift mutations and had NRAS mutation while exon 9 mutations were base substitutions and had FLT3-ITD mutation. Interestingly, the major allele for rs16754 single nucleotide polymorphism was G (25-homozygous and 6-heterozygous) which was in contrast to A in the Western reports. The frequency of WT1 mutation in the Southeast Asian AML was thus comparable to the figures reported from the West although the designated major allele for rs16754 polymorphism was different.
21798259	1185	1192	rs16754	SNP	rs16754
21798259	1472	1479	rs16754	SNP	rs16754

21897748|t|A recurrent missense mutation in GJA3 associated with autosomal dominant cataract linked to chromosome 13q.
21897748|a|PURPOSE: To map and identify the genetic defect underlying autosomal dominant cataract segregating in a 5-generation Caucasian American family. METHODS: Genomic DNA was prepared from blood leukocytes, genotyping was performed using microsatellite markers, and logarithm of the odds (LOD) scores were calculated using the LINKAGE programs. Mutation profiling was performed using direct exon cycle-sequencing and restriction fragment analysis. Protein function effects were evaluated using in silico prediction algorithms. RESULTS: Significant evidence of linkage was obtained at marker D13S175 (maximum LOD score [Z(max)]=3.67; maximum recombination fraction [  (max)]=0.04) and D13S1316 (Z(max)=2.80,   (max)=0.0). Haplotyping indicated that the disease lay in the ~170 Kb physical interval between D13S1316 and D13S175, which contained the gene for gap-junction protein alpha-3 (GJA3) or connexin-46. Sequencing of GJA3 detected a heterozygous transition (c.130G>A) in exon-2 that resulted in gain of an Hsp92 II restriction site. Allele-specific PCR amplification and restriction analysis confirmed that the novel Hsp92 II site co-segregated with cataract in the family but was not detected in 192 normal unrelated individuals. The c.130G>A transition was predicted to result in a non-conservative substitution of valine-to-methionine at codon 44 (p.V44M) with damaging effects on protein function. CONCLUSIONS: These data confirm GJA3 as one of the most frequently mutated genes that underlie autosomal dominant cataract in humans, and further emphasize the importance of connexin function in maintaining lens transparency.
21897748	1065	1073	c.130G>A	DNAMutation	c|G|130|A
21897748	1342	1350	c.130G>A	DNAMutation	c|G|130|A
21897748	1458	1464	p.V44M	ProteinMutation	p|V|44|M

21911891|t|Plasminogen activator inhibitor type 1 serum levels and 4G/5G gene polymorphism in morbidly obese Hispanic patients with non-alcoholic fatty liver disease.
21911891|a|BACKGROUND: The plasminogen activator inhibitor type-1 (PAI-1) has been implicated in the regulation of fibrinolysis and extracellular matrix components. The single base pair guanine insertion/deletion polymorphism (4G/5G) within the promoter region of the PAI-1 gene influences PAI-1 synthesis and may modulate hepatic fibrogenesis. AIM: To evaluate the influence of PAI-1 serum levels and 4G/5G polymorphism on the risk of liver fibrosis associated to non-alcoholic fatty liver disease (NAFLD) in morbidly obese patients. MATERIAL AND METHODS: Case-control study of 50 obese patients undergoing bariatric surgery and 71 non-obese subjects matched by age and sex. Anthropometric and biochemical measurements were performed, including PAI-1 serum levels. Genomic DNA was obtained to assess the presence of 4G/5G polymorphism. RESULTS: BMI, insulinemia, triglycerides, HOMA-IR, hypertension and diabetes were significantly higher in obese patients compared to control subjects. PAI-1 serum levels observed in obese patients were significantly lower (10.63    4.82) compared to controls (14.26    11.4; p < 0.05). No differences were observed in the PAI-1 4G/5G promoter genotypes frequencies (p = 0.12). No differences were observed in PAI-1 plasma levels among obese patients with liver fibrosis (10.64    4.35) compared to patients without liver fibrosis (10.61    5.2; p = 0.985). PAI-1 4G/5G promoter genotypes frequencies were similar in patients with or without liver fibrosis associated to NASH (p = 0.6). CONCLUSIONS: Morbidly obese patients had significantly lower PAI-1 serum levels with similar PAI-1 4G/5G genotypes frequencies compared to non-obese subjects. The frequency of 4G/5G genotypes in Chilean Hispanic healthy subjects was similar to that described in other populations. No association was found between PAI-1 serum levels or 4G/5G genotype with liver fibrosis in obese patients.

21757944|t|A 13-bp deletion in the 3' untranslated region of the b-globin gene causes b-thalassemia major in compound heterozygosity with IVSII-1 mutation.
21757944|a|OBJECTIVE: To describe hematological and molecular features of a 13-bp deletion in the 3' untranslated region(3' UTR) of the b-globin gene in carrier individuals and a compound heterozygous patient. SUBJECTS AND METHODS: Five members of an Iranian family of Persian ethnic origin were studied. Red blood cell indices and hemoglobin analysis were carried out according to standard methods. Genomic DNA was obtained from peripheral blood cells by salting-out procedures. b-Globin gene amplification and DNA sequencing were performed. RESULTS: One patient had a 13-bp deletion in the 3' UTR of the b-globin gene that causes the b-thalassemia phenotype in combination with the IVSII-1 (G > A) mutation. The patient had inherited the IVSII-1 (G > A) mutation from his mother, while the second b-globin gene (inherited paternally) had a 13-bp deletion at nucleotide 90 downstream of the termination codon (CD +90 del 13 bp).The patient's father and paternal grandmother, who are carriers of this deletion, had no hematological abnormalities. CONCLUSION: This case showed a patient with a 13-bp deletion in the 3' UTR of b-globin gene that could cause a slight decrease in the stability of the mRNA, but did not have a hematological effect in the heterozygotes. The 13-bp deletion could be clinically important only in situations where b-chain synthesis in trans is compromised.
21757944	818	833	IVSII-1 (G > A)	DNAMutation	c|G|IVS2-1|A
21757944	874	889	IVSII-1 (G > A)	DNAMutation	c|G|IVS2-1|A
21757944	1045	1061	CD +90 del 13 bp	DNAMutation	c|DEL|CD+90|13

22129472|t|The Arabic allele: a single base pair substitution activates a 10-base downstream cryptic splice acceptor site in exon 12 of LDLR and severely decreases LDLR expression in two unrelated Arab families with familial hypercholesterolemia.
22129472|a|Familial hypercholesterolemia (FH) is a monogenic autosomal dominant disorder caused by defects in LDLR. Few reports describe FH mutations among Arabs. We describe a mutation in LDLR of two unrelated Arab families. We investigated 19 patients using DNA sequencing, RFLP, and real-time (RT) PCR. DNA sequencing showed a base pair substitution (c.1706-2 A>T) in the splice acceptor site of LDLR intron 11. Our results were confirmed by RFLP on 2% agarose gel. In silico analysis predicted a new cryptic splice site downstream of the original position generating a 10-base deletion from the beginning of exon 12; (c.1706-1715del.ATCTCCTCAG). cDNA sequencing of exon 12 confirmed the computational analysis. The deletion was visualized on 4% agarose gel. The deletion generates a frameshift and a premature termination codon (c.1991-1993; p.(Asp569Valfs*93). RT-PCR revealed that LDLR mRNA is 9.3%  6.5 and 17.9%  8.0 for FH homozygote and heterozygote individuals respectively, compared to a healthy family control. We predict a class II LDLR mutation that leads to a truncated receptor missing exons 14-18. We called this mutation "the Arabic allele". We expect a significant contribution of this mutation to the prevalence of FH among Arabs. Also, we propose that the severe down regulation of LDLR mRNA expression is due to nonsense-mediated-decay.
22129472	579	591	c.1706-2 A>T	DNAMutation	c|A|1706-2|T
22129472	847	872	c.1706-1715del.ATCTCCTCAG	DNAMutation	c|DEL|1706_1715|ATCTCCTCAG
22129472	1071	1089	p.(Asp569Valfs*93)	ProteinMutation	p|D|569|V|FSX|93

21682595|t|XRCC1 Arg399Gln gene polymorphism and the risk of systemic lupus erythematosus in the Polish population.
21682595|a|It has been shown that DNA repair is reduced in patients with systemic lupus erythematosus (SLE) and that the X-ray repair cross-complementing (XRCC1) Arg399Gln (rs25487) polymorphism may contribute to DNA repair. We evaluated the frequency of the XRCC1 Arg399Gln substitution in patients with SLE (n=265) and controls (n=360) in a sample of the Polish population. The odds ratio (OR) for SLE patients with the Gln/Gln versus Gln/Arg or Arg/Arg genotypes was 1.553 (95% confidence interval [CI]=0.9573-2.520; p=0.0729). OR for the Gln/Gln or Gln/Arg versus Arg/Arg genotype was 1.551 (95% CI=1.122-2.144, p=0.0077). The OR for the 399 Gln allele in patients with SLE was 1.406 (95% CI=1.111-1.779, p=0.0045). There was also a statistically significant p-value of the   (2) test for the trend observed in the XRCC1 Arg399Gln polymorphism (ptrend=0.0048). We also found a significant contribution of the Gln/Gln or Arg/Gln versus Arg/Arg genotype to the presence of either the malar rash or photosensitivity manifestations of SLE OR=2.241 (1.328-3.781, p=0.0023, pcorr=0.0414). Moreover, the meta-analysis of Taiwanese Han Chinese, Brazilian, and Polish populations showed that the Gln/Gln or Gln/Arg genotype and Gln allele were associated with SLE incidence. OR for the Gln/Gln or Gln/Arg versus Arg/Arg genotype was 1.440 (95% CI=1.15-1.80, p=0.0019) and OR for the Gln allele was 1.27 (95% CI=1.08-1.51, p=0.0051). Our studies may confirm that the XRCC1 Arg399Gln polymorphism may increase the risk of incidence of SLE and the occurrence of some SLE manifestations.
21682595	6	15	Arg399Gln	ProteinMutation	p|R|399|Q
21682595	256	265	Arg399Gln	ProteinMutation	p|R|399|Q
21682595	267	274	rs25487	SNP	rs25487
21682595	359	368	Arg399Gln	ProteinMutation	p|R|399|Q
21682595	919	928	Arg399Gln	ProteinMutation	p|R|399|Q
21682595	1561	1570	Arg399Gln	ProteinMutation	p|R|399|Q

21054465|t|Mutational analysis of CYP2C8 in hypertensive patients using denaturing high performance liquid chromatography.
21054465|a|WHAT IS KNOWN AND OBJECTIVE: CYP2C8 is involved in the cytochrome P450 (CYP) epoxygenase pathway. Arachidonic acid metabolites such as epoxyeicosatrienenoic acids and hydroxyeicosatetrenoic acids, produced may have a role in hypertension. We aimed to develop a medium through-put method for screening samples of known and new mutations of CYP2C8 using denaturing high performance liquid chromatography (DHPLC). METHODS: DNA samples from 200 subjects (hypertensive patients and healthy controls) were screened for SNPs in CYP2C8 using DHPLC. Genotypes and allelic frequencies of CYP2C8 between the healthy controls and patients with hypertension were compared. RESULTS AND DISCUSSIONS: Six variants were detected and two were new; T deletion at 5063 and substitution of C to T at 33468 in exon 8. Differences in variant frequencies were detected between the controls and hypertensive patients. The controls have significantly higher prevalence of C35322C compared to the patients. The functional significance of the SNP at 35322 requires further study. Having homozygous C35322C could be a protective factor for hypertension. WHAT IS NEW AND CONCLUSION: Denaturing high performance liquid chromatography is useful for population screening to identify new and existing SNPs. A higher frequency of the C35322T SNP was observed among hypertensive patients than control subjects. This potentially important observation requires confirmation and the clinical significance assessed.

20648600|t|High frequency of lamivudine resistance mutations in Brazilian patients co-infected with HIV and hepatitis B.
20648600|a|This study analyzed the genotype distribution and frequency of lamivudine (LAM) and tenofovir (TDF) resistance mutations in a group of patients co-infected with HIV and hepatitis B virus (HBV). A cross-sectional study of 847 patients with HIV was conducted. Patients provided blood samples for HBsAg detection. The load of HBV was determined using an "in-house" real-time polymerase chain reaction. HBV genotypes/subgenotypes, antiviral resistance, basal core promoter (BCP), and precore mutations were detected by DNA sequencing. Twenty-eight patients with co-infection were identified. The distribution of HBV genotypes among these patients was A (n = 9; 50%), D (n = 4; 22.2%), G (n = 3; 16.7%), and F (n = 2; 11.1%). Eighteen patients were treated with LAM and six patients were treated with LAM plus TDF. The length of exposure to LAM and TDF varied from 4 to 216 months. LAM resistance substitutions (rtL180M + rtM204V) were detected in 10 (50%) of the 20 patients with viremia. This pattern and an accompanying rtV173L mutation was found in four patients. Three patients with the triple polymerase substitution pattern (rtV173L + rtL180M + rtM204V) had associated changes in the envelope gene (sE164D + sI195M). Mutations in the BCP region (A1762T, G1764A) and in the precore region (G1896A, G1899A) were also found. No putative TDF resistance substitution was detected. The data suggest that prolonged LAM use is associated with the emergence of particular changes in the HBV genome, including substitutions that may elicit a vaccine escape phenotype. No putative TDF resistance change was detected after prolonged use of TDF.
20648600	1019	1024	L180M	ProteinMutation	p|L|180|M
20648600	1029	1034	M204V	ProteinMutation	p|M|204|V
20648600	1130	1135	V173L	ProteinMutation	p|V|173|L
20648600	1239	1244	V173L	ProteinMutation	p|V|173|L
20648600	1249	1254	L180M	ProteinMutation	p|L|180|M
20648600	1259	1264	M204V	ProteinMutation	p|M|204|V
20648600	1312	1317	E164D	ProteinMutation	p|E|164|D
20648600	1321	1326	I195M	ProteinMutation	p|I|195|M
20648600	1358	1364	A1762T	DNAMutation	g|A|1762|T
20648600	1366	1372	G1764A	DNAMutation	g|G|1764|A
20648600	1401	1407	G1896A	DNAMutation	g|G|1896|A
20648600	1409	1415	G1899A	DNAMutation	g|G|1899|A

20846357|t|A novel mutation in the connexin 26 gene (GJB2) in a child with clinical and histological features of keratitis-ichthyosis-deafness (KID) syndrome.
20846357|a|BACKGROUND: Keratitis-ichthyosis-deafness (KID) syndrome is a rare congenital ectodermal disorder, caused by heterozygous missense mutation in GJB2, encoding the gap junction protein connexin 26. The commonest mutation is the p.Asp50Asn mutation, and only a few other mutations have been described to date. AIM: To report the fatal clinical course and characterize the genetic background of a premature male neonate with the clinical and histological features of KID syndrome. METHODS: Genomic DNA was extracted from peripheral blood and used for PCR amplification of the GJB2 gene. Direct sequencing was used for mutation analysis. RESULTS: The clinical features included hearing impairment, ichthyosiform erythroderma with hyperkeratotic plaques, palmoplantar keratoderma, alopecia of the scalp and eyelashes, and a thick vernix caseosa-like covering of the scalp. On histological analysis, features characteristic of KID syndrome, such as acanthosis and papillomatosis of the epidermis with basket-weave hyperkeratosis, were seen. The skin symptoms were treated successfully with acitretin 0.5 mg/kg. The boy developed intraventricular and intracerebral haemorrhage, leading to hydrocephalus. His condition was further complicated by septicaemia and meningitis caused by infection with extended-spectrum beta-lactamase-producing Klebsiella pneumoniae. Severe respiratory failure followed, and the child died at 46 weeks of gestational age (13 weeks postnatally). Sequencing of the GJB2 gene showed that the child was heterozygous for a novel nucleotide change, c.263C>T, in exon 2, leading to a substitution of alanine for valine at position 88 (p.Ala88Val). CONCLUSIONS: This study has identified a new heterozygous de novo mutation in the Cx26 gene (c.263C>T; p.Ala88Val) leading to KID syndrome.
20846357	374	384	p.Asp50Asn	ProteinMutation	p|D|50|N
20846357	1712	1720	c.263C>T	DNAMutation	c|C|263|T
20846357	1797	1807	p.Ala88Val	ProteinMutation	p|A|88|V
20846357	1903	1911	c.263C>T	DNAMutation	c|C|263|T
20846357	1913	1923	p.Ala88Val	ProteinMutation	p|A|88|V

21445905|t|Analysis of a SNP linked to lactase persistence: An exercise for teaching molecular biology techniques to undergraduates.
21445905|a|Recent experimental evidence indicates that the ability of adults to tolerate milk, cheese, and other lactose-containing dairy products is an autosomal dominant trait that co-evolved with dairy farming in Central Europe about 7,500 years ago. Among persons of European descent, this trait is strongly associated with a C to T substitution at a polymorphic site 13,910 bp upstream of the lactase gene. This mutation results in the persistent expression of lactase into adulthood enabling individuals carrying a T(-13,910) allele to digest lactose as adults. In this report, we describe a laboratory exercise for an undergraduate molecular biology course in which students determine their own genotype at the -13,910 polymorphic site and correlate this with their ability to tolerate dairy products. The exercise is used as a tool to teach basic molecular biology procedures such as agarose gel electrophoresis, PCR1, and DNA sequencing. Students are actively engaged in the learning process, not only by analyzing their own DNA but also by applying their knowledge and skills to answer an authentic question. The exercise is also integrated with lecture material on the control of gene expression at the transcriptional level, in particular, how transcription factors can influence the activity of a promoter by binding to cis-acting DNA regulatory elements located within the proximal promoter of a gene or distant enhancer regions.

21343167|t|The distribution of human endogenous retrovirus K-113 in health and autoimmune diseases in Poland.
21343167|a|OBJECTIVE: During the evolution of the human genome, a number of retroviral integrations have occurred creating a group of human endogenous retroviruses (HERVs). As of now several studies have pointed to the association of HERVs with certain autoimmune diseases such as RA, SLE, multiple sclerosis (MS) and SS as well as various neoplasms. In this study, we investigated the prevalence of HERV-K113 in patients with RA, SLE and in healthy subjects in the Polish population. METHODS: Genomic DNA samples from 155 RA patients, 139 SLE patients and 261 newborns (as controls) were tested for the presence of the HERV-K113 allele using PCR. Each individual's DNA was genotyped for null, homozygous or heterozygous insertion of HERV-K113. RESULTS: Our data revealed statistically significant differences in the insertion frequencies of HERV-K113 between the groups of RA and SLE patients vs healthy controls (provirus DNA was found in 14.19, 15.11 and 8.05% of individuals, respectively). No homozygous individuals for the K113 allele were found in each of the groups. There was no evidence for HERV-K113 association with clinical features in either group. CONCLUSION: Our study-the first such performed for the Polish population-provides a consistent observation with previous reports on the genetic association of HERV-K113 integrations in autoimmune disorders. Here, we found that the prevalence of insertionally polymorphic HERV-K113 was significantly increased in Polish patients with SLE and RA.

21133595|t|Association of GSTM1 and GSTT1 gene deletions with risk of head and neck cancer in Pakistan: a case control study.
21133595|a|Polymorphic deletions of GSTM1 and GSTT1 genes involved in the detoxification of potentially carcinogenic agents may be risk factors for various cancers, including head and neck cancer (HNC). In the present case-control study we aimed to access possible associations of HNC with GSTM1 and GSTT1 null genotypes in a Pakistani population. DNA was extracted from leukocytes of 388 cancer patients and 150 healthy controls by phenol-chloroform procedure. GSTM1 and GSTT1 deletion variants were genotyped by multiplex PCR assay with CYP1A1 as an internal control and further analyzed by primer specific PCR assay and sequencing. Mean age of cases and controls was 48 (  16.6) years with a male to female ratio of 1:1. Cancer of the oral cavity (57%) was most prevalent in the sampled population followed by pharynx and larynx (30% and 13% respectively). A statistically significant (P<0.05) association was observed for both null genotypes in contribution to HNC as compared with the controls. The odds ratio (OR) for the GSTM1 null genotype was 2.3 with a 95% CI of 1.5-5.5 and for GSTT1 OR was 2.04 with 95% CI of 1.3-3.1. These results suggest that the GSTM1 and GSTT1 null genotypes are risk factors for HNC development among the Pakistani population.

21325775|t|A novel apolipoprotein E mutation, ApoE Osaka (Arg158 Pro), in a dyslipidemic patient with lipoprotein glomerulopathy.
21325775|a|Lipoprotein glomerulopathy (LPG) is a rare disease characterized by the presence of thrombuslike deposition in markedly dilated glomerular capillaries and is often accompanied by an increased serum apolipoprotein E (apoE) level. Several gene mutations of apoE have been reported to be associated with LPG. In the current study, we report an LPG patient with a novel apoE mutation, apoE Osaka. The patient was a 45-year-old man who was hospitalized due to nephrotic syndrome. Light and electron microscopic observations of renal biopsy clearly showed characteristic findings of LPG, including lamellate thrombi in the lumen of dilated glomerular capillaries. His apoE phenotype was apoE3/2 and he had mild dyslipidemia with a mid-band on polyacrylamide gel electrophoresis. It is intriguing that the serum apoE level was within normal limits. We determined the sequence of the apoE gene using direct sequencing of the polymerase chain reaction (PCR) products. ApoE gene analysis showed a nucleotide substitution of G to C at codon 158 of exon 4. This mutation denoted an amino acid substitution of arginine residue for the proline residue at position 158 of apoE. The result of PCR associated with restriction fragment length polymorphism analysis also suggested that this mutation is heterozygous. It is possible that apoE Osaka mutation causes a conformational change of apoE protein and affects the interaction between abnormal apoE-containing lipoproteins and the endothelial cells of glomerular capillaries. The precise mechanism of LPG related with apoE Osaka, however, remains to be elucidated.
21325775	47	57	Arg158 Pro	ProteinMutation	p|R|158|P

21108633|t|PAX2 gene mutations in pediatric and young adult transplant recipients: kidney and urinary tract malformations without ocular anomalies.
21108633|a|Heterozygous humans for PAX2 mutations show autosomal dominant papillorenal syndrome (PRS), consisting of ocular colobomas, renal hypo/dysplasia and progressive renal failure in childhood. PAX2 mutations have also been identified in patients with isolated renal hypo/dysplasia. Twenty unrelated children and young adults with kidney and urinary tract malformations and no ocular abnormalities were retrospectively recruited for PAX2 mutational analysis. All patients had undergone renal transplantation after end-stage renal disease. We identified two new sequence variations: (i) a deletion causing a frameshift (c.69delC) and (ii) a nucleotide substitution determining a splice site mutation (c.410+5 G/A) by predictive analysis. Therefore, we suggest PAX2 molecular analysis to be extended to all patients with congenital malformations of kidney and urinary tract (CAKUT).
21108633	751	759	c.69delC	DNAMutation	c|DEL|69|C
21108633	832	843	c.410+5 G/A	DNAMutation	c|G|410+5|A

20884631|t|Acquired TNFRSF14 mutations in follicular lymphoma are associated with worse prognosis.
20884631|a|Clinical correlative studies have linked 1p36 deletions with worse prognosis in follicular lymphoma (FL). In this study, we sought to identify the critical gene(s) in this region that is responsible for conferring inferior prognosis. BAC array technology applied to 141 FL specimens detected a minimum region of deletion (MRD) of    97 kb within 1p36.32 in 20% of these cases. Frequent single-nucleotide polymorphism-detected copy-neutral loss of heterozygosity was also found in this region. Analysis of promoter CpGs in the MRD did not reveal differential patterns of DNA methylation in samples that differed in 1p36 status. Exon sequencing of MRD genes identified somatic alterations in the TNFRSF14 gene in 3 of 11 selected cases with matching normal DNA. An expanded cohort consisting of 251 specimens identified 46 cases (18.3%) with nonsynonymous mutations affecting TNFRSF14. Overall survival (OS) and disease-specific survival (DSS) were associated with the presence of TNFRSF14 mutation in patients whose overall treatment included rituximab. We further showed that inferior OS and DSS were most pronounced in patients whose lymphomas contained both TNFRSF14 mutations and 1p36 deletions after adjustment for the International Prognostic Index [hazard ratios of 3.65 (95% confidence interval, 1.35-9.878, P=0.011) and 3.19 (95% confidence interval, 1.06-9.57, P=0.039), respectively]. Our findings identify TNFRSF14 as a candidate gene associated with a subset of FL, based on frequent occurrence of acquired mutations and their correlation with inferior clinical outcomes.

21099701|t|Familial pycnodysostosis: identification of a novel mutation in the CTSK gene (cathepsin K).
21099701|a|BACKGROUND: Pycnodysostosis, an autosomal recessive skeletal dysplasia, is characterized by short stature, osteosclerosis, delayed cranial suture closure, hypoplastic mandible, acro-osteolysis, hypoplastic clavicle, and dental anomalies. The disorder is caused by CTSK gene defects, a gene localized on 1q21. PURPOSE: To describe the clinical, radiological, and molecular findings in a family with pycnodysostosis. METHODS: The CTSK gene was analyzed from genomic DNA in a nonconsanguinity Mexican family with 3 affected members with pycnodysostosis and 100 healthy controls. RESULTS AND INTERPRETATION: We identified the novel homozygous mutation c.908G>A within exon 8 of the CTSK gene. This missense mutation leads to the substitution of the amino acid glycine at position 303 by glutamic acid (G303E) in cathepsin K protease. No genotype/phenotype correlation was present in affected members of the family with pycnodysostosis.
21099701	741	749	c.908G>A	DNAMutation	c|G|908|A
21099701	891	896	G303E	ProteinMutation	p|G|303|E

20738799|t|Ankyloblepharon-ectodermal dysplasia-clefting syndrome: a novel p63 mutation associated with generalized neonatal erosions.
20738799|a|Ankyloblepharon-ectodermal dysplasia-clefting (AEC) syndrome is a rare disorder characterized by ankyloblepharon (congenital adhesions of the eyelids), ectodermal dysplasia, and orofacial clefts. Here, we report the case of an infant born with severe ectodermal dysplasia including generalized neonatal erosions with scalp involvement, facial clefting but notably without ankyloblepharon. Mutational analysis of the p63 gene showed a novel heterozygous T>C nucleotide substitution on exon 14 (I597T). To our knowledge, this is a novel mutation that has not previously been reported in the pathogenesis of AEC, or other p63-related syndromes. This case further highlights the clinical and genetic heterogeneity of p63 syndromes.
20738799	577	580	T>C	DNAMutation	|T||C
20738799	617	622	I597T	ProteinMutation	p|I|597|T

20801104|t|Association study of polymorphisms in the promoter region of DRD4 with schizophrenia, depression, and heroin addiction.
20801104|a|This study investigated the possible association between three functional polymorphisms in the promoter region of the dopamine D4 receptor (DRD4) gene and schizophrenia, depression, and heroin addiction. Genomic DNA was isolated from the venous blood leukocytes of 322 unrelated patients with schizophrenia, 156 patients with depression, 300 patients with heroin addiction, and 300 healthy unrelated individuals. Polymorphisms in the promoter region of DRD4 (-120 bp duplication, -616C/G, and -521C/T) were genotyped using allele-specific polymerase chain reaction analysis. Genotype and allele were analyzed using SPSS 11.5 software. Results of this analysis indicated that there is a strong finding of -120 bp duplication allele frequencies with schizophrenia (p=0.008) and weak finding with -1240 L/S and for paranoid schizophrenia (p=0.022). Interestingly, there is a stronger finding with -521 C/T allele frequencies with heroin dependence (p=0.0002). These observations strongly suggest that the -120-bp duplication polymorphism of DRD4 is associated with schizophrenia and that the -521 C/T polymorphism is associated with heroin addiction.
20801104	600	607	-616C/G	DNAMutation	c|C|-616|G
20801104	613	620	-521C/T	DNAMutation	c|C|-521|T
20801104	914	923	-1240 L/S	ProteinMutation	p|L|-1240|S
20801104	1014	1022	-521 C/T	DNAMutation	c|C|-521|T
20801104	1209	1217	-521 C/T	DNAMutation	c|C|-521|T

21127202|t|Mutations in the sarcomere gene MYH7 in Ebstein anomaly.
21127202|a|BACKGROUND: Ebstein anomaly is a rare congenital heart malformation characterized by adherence of the septal and posterior leaflets of the tricuspid valve to the underlying myocardium. An association between Ebstein anomaly with left ventricular noncompaction (LVNC) and mutations in MYH7 encoding b-myosin heavy chain has been shown; in this report, we have screened for MYH7 mutations in a cohort of probands with Ebstein anomaly in a large population-based study. METHODS AND RESULTS: Mutational analysis in a cohort of 141 unrelated probands with Ebstein anomaly was performed by next-generation sequencing and direct DNA sequencing of MYH7. Heterozygous mutations were identified in 8 of 141 samples (6%). Seven distinct mutations were found; 5 were novel and 2 were known to cause hypertrophic cardiomyopathy. All mutations except for 1 3-bp deletion were missense mutations; 1 was a de novo change. Mutation-positive probands and family members showed various congenital heart malformations as well as LVNC. Among 8 mutation-positive probands, 6 had LVNC, whereas among 133 mutation-negative probands, none had LVNC. The frequency of MYH7 mutations was significantly different between probands with and without LVNC accompanying Ebstein anomaly (P<0.0001). LVNC segregated with the MYH7 mutation in the pedigrees of 3 of the probands, 1 of which also included another individual with Ebstein anomaly. CONCLUSIONS: Ebstein anomaly is a congenital heart malformation that is associated with mutations in MYH7. MYH7 mutations are predominantly found in Ebstein anomaly associated with LVNC and may warrant genetic testing and family evaluation in this subset of patients.

21135151|t|Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models.
21135151|a|The interplay between C-C chemokine receptor type 5 (CCR5) host genetic background, disease progression, and intrahost HIV-1 evolutionary dynamics remains unclear because differences in viral evolution between hosts limit the ability to draw conclusions across hosts stratified into clinically relevant populations. Similar inference problems are proliferating across many measurably evolving pathogens for which intrahost sequence samples are readily available. To this end, we propose novel hierarchical phylogenetic models (HPMs) that incorporate fixed effects to test for differences in dynamics across host populations in a formal statistical framework employing stochastic search variable selection and model averaging. To clarify the role of CCR5 host genetic background and disease progression on viral evolutionary patterns, we obtain gp120 envelope sequences from clonal HIV-1 variants isolated at multiple time points in the course of infection from populations of HIV-1-infected individuals who only harbored CCR5-using HIV-1 variants at all time points. Presence or absence of a CCR5 wt//\32 genotype and progressive or long-term nonprogressive course of infection stratify the clinical populations in a two-way design. As compared with the standard approach of analyzing sequences from each patient independently, the HPM provides more efficient estimation of evolutionary parameters such as nucleotide substitution rates and d(N)/d(S) rate ratios, as shown by significant shrinkage of the estimator variance. The fixed effects also correct for nonindependence of data between populations and results in even further shrinkage of individual patient estimates. Model selection suggests an association between nucleotide substitution rate and disease progression, but a role for CCR5 genotype remains elusive. Given the absence of clear d(N)/d(S) differences between patient groups, delayed onset of AIDS symptoms appears to be solely associated with lower viral replication rates rather than with differences in selection on amino acid fixation.
21135151	14	21	delta32	DNAMutation	|DEL||32

21070631|t|The dopamine b-hydroxylase -1021C/T polymorphism is associated with the risk of Alzheimer's disease in the Epistasis Project.
21070631|a|BACKGROUND: The loss of noradrenergic neurones of the locus coeruleus is a major feature of Alzheimer's disease (AD). Dopamine b-hydroxylase (DBH) catalyses the conversion of dopamine to noradrenaline. Interactions have been reported between the low-activity -1021T allele (rs1611115) of DBH and polymorphisms of the pro-inflammatory cytokine genes, IL1A and IL6, contributing to the risk of AD. We therefore examined the associations with AD of the DBH -1021T allele and of the above interactions in the Epistasis Project, with 1757 cases of AD and 6294 elderly controls. METHODS: We genotyped eight single nucleotide polymorphisms (SNPs) in the three genes, DBH, IL1A and IL6. We used logistic regression models and synergy factor analysis to examine potential interactions and associations with AD. RESULTS: We found that the presence of the -1021T allele was associated with AD: odds ratio = 1.2 (95% confidence interval: 1.06-1.4, p = 0.005). This association was nearly restricted to men < 75 years old: odds ratio = 2.2 (1.4-3.3, 0.0004). We also found an interaction between the presence of DBH -1021T and the -889TT genotype (rs1800587) of IL1A: synergy factor = 1.9 (1.2-3.1, 0.005). All these results were consistent between North Europe and North Spain. CONCLUSIONS: Extensive, previous evidence (reviewed here) indicates an important role for noradrenaline in the control of inflammation in the brain. Thus, the -1021T allele with presumed low activity may be associated with misregulation of inflammation, which could contribute to the onset of AD. We suggest that such misregulation is the predominant mechanism of the association we report here.
21070631	27	35	-1021C/T	DNAMutation	c|C|-1021|T
21070631	400	409	rs1611115	SNP	rs1611115
21070631	1261	1270	rs1800587	SNP	rs1800587

21405999|t|Mutation screening of the GUCA1B gene in patients with autosomal dominant cone and cone rod dystrophy.
21405999|a|Background: Heterozygous mutations in GUCA1A (MIM # 600364) have been identified to cause autosomal dominantly inherited cone dystrophy, cone rod dystrophy and macular dystrophy. However, the role of GUCA1B gene mutations in inherited retinal disease has been controversial. We therefore performed a mutation analysis of the GUCA1B gene in a clinically well characterized group of patients of European and North-American geographical origin with autosomal dominantly inherited cone dystrophy and cone rod dystrophy. Material and Methods: Twenty-four unrelated patients diagnosed with cone dystrophy or cone rod dystrophy according to standard diagnostic criteria and a family history consistent with an autosomal dominant mode of inheritance were included in the study. Mutation analysis of all coding exons of the GUCA1B gene was performed by polymerase chain reaction amplification of genomic DNA and subsequent DNA sequencing. Results: Three different sequence variants, c.-17T>C, c.171T>C, c.465G>T were identified. The sequence variant c.465G>T encodes a conservative amino acid substitution, p.Glu155Asp, located in EF-hand 4, the calcium binding site of GCAP2 protein. All sequence variants were previously reported in healthy subjects. Conclusion: The absence of clearly pathogenic mutations in the selected patient group suggests that the GUCA1B gene is a minor cause for retinal degenerations in Europeans or North-Americans.
21405999	1077	1085	c.-17T>C	DNAMutation	c|T|-17|C
21405999	1087	1095	c.171T>C	DNAMutation	c|T|171|C
21405999	1097	1105	c.465G>T	DNAMutation	c|G|465|T
21405999	1144	1152	c.465G>T	DNAMutation	c|G|465|T
21405999	1201	1212	p.Glu155Asp	ProteinMutation	p|E|155|D

21112374|t|AluYb8 insertion in the MUTYH gene is related to increased 8-OHdG in genomic DNA and could be a risk factor for type 2 diabetes in a Chinese population.
21112374|a|The Mutyh DNA glycosylase is involved in the repair of oxidized DNA bases. Because oxidative stress may contribute to increased diabetes risk, the common variant of the MUTYH gene (AluYb8MUTYH) was investigated for its possible role in type 2 diabetes mellitus (T2DM). A total of 565 T2DM patients and 565 healthy subjects from China were enrolled in a case-control study. The distribution of AluYb8MUTYH differed in diabetic patients from controls, with a moderately increased percentage of the mutant allele (P) (44.7% versus 40.3%, P = 0.033, OR = 1.199). However, this distribution was similar between the diabetic early-onset and late-onset subgroups. Another 66 T2DM patients were further evaluated for 8-hydroxy-2'deoxyguanosine (8-OHdG) levels in leukocytic DNA. The average value of 8-OHdG/10(6) dG was 10.4 in patients with the wild-type genotype, 15.9 in heterozygotes, and 22.3 in homozygotes with the variation (P < 0.001, compared with the wild-type). Therefore, the AluYb8MUTYH polymorphism could be a novel genetic risk factor for T2DM, and accumulated 8-OHdG could contribute to this disease.

20709368|t|The fibrinogen gamma 10034C>T polymorphism is not associated with Peripheral Arterial Disease.
20709368|a|Conversion of fibrinogen to fibrin plays an essential role in hemostasis and results in stabilization of the fibrin clot. Fibrinogen consists of three pairs of non-identical polypeptide chains, encoded by different genes (fibrinogen alpha [FGA], fibrinogen beta [FGB] and fibrinogen gamma [FGG]). A functional single nucleotide polymorphism (SNP) in the 3' untranslated region of the FGG gene (FGG 10034C>T, rs2066865) has been associated with deep venous thrombosis and myocardial infarction. Aim of the present study was to analyze the role of this polymorphism in peripheral arterial disease (PAD). The study was designed as case-control study including 891 patients with documented PAD and 777 control subjects. FGG genotypes were determined by exonuclease (TaqMan) assays. FGG genotype frequencies were not significantly different between PAD patients (CC: 57.3%, CT: 36.7%, TT: 5.8%) and control subjects (CC: 60.9%, CT: 33.5%, TT 5.6%; p=0.35). In a multivariate logistic regression analysis including age, sex, smoking, diabetes, arterial hypertension and hypercholesterolemia, the FGG 10034 T variant was not significantly associated with the presence of PAD (Odds ratio 1.07, 95% confidence interval 0.84 - 1.37; p = 0.60). The FGG 10034C>T polymorphism was furthermore not associated with age at onset of PAD. We conclude that the thrombophilic FGG 10034 T gene variant does not contribute to the genetic susceptibility to PAD.
20709368	21	29	10034C>T	DNAMutation	|C|10034|T
20709368	493	501	10034C>T	DNAMutation	|C|10034|T
20709368	503	512	rs2066865	SNP	rs2066865
20709368	1337	1345	10034C>T	DNAMutation	|C|10034|T

21493871|t|Multilocus association of genetic variants in MLL, CREBBP, EP300, and TOP2A with childhood acute lymphoblastic leukemia in Hispanics from Texas.
21493871|a|BACKGROUND: Hispanic children have both a higher incidence and a poorer outcome in acute lymphoblastic leukemia (ALL). Moreover, a higher incidence for therapy-related acute myeloid leukemia with 11q23 translocations after treatment with topoisomerase II (topo II) inhibitors has been observed in Hispanic children with ALL. We sought to determine the potential role of genetic variants within the topoisomerase IIa gene (TOP2A), within the mixed lineage leukemia gene (MLL) and two of its translocation partners, cyclin AMP response element-binding protein gene (CREBBP) and E1A binding protein gene (EP300) in the increased sensitivity of Hispanic children with ALL to topo II inhibitors. METHODS: Fifty-two tagged single nucleotide polymorphisms (SNP) covering the four genes were genotyped in 241 samples (66 children with ALL and 175 age matched controls) of self-identified Hispanic origin. RESULTS: Two SNPs within MLL (rs525549 and rs6589664) and three SNPs within EP300 (rs5758222, rs7286979, and rs20551) were significantly associated with ALL (P = 0.001-0.04). A significant gene-dosage effect for increasing numbers of potential high-risk genotypes (OR = 16.66; P = 2   10(-5)) and a major haplotype significantly associated with ALL (OR = 5.68; P = 2   10(-6)) were found. Replication in a sample of 137 affected White children and 239 controls showed that only rs6589664 (MLL) was significantly associated in this ethnic group. CONCLUSIONS: Our findings indicate that the association between ALL and common genetic variants within MLL and EP300 is population specific. IMPACT: Replication of our findings in independent Hispanic populations is warranted to elucidate the role of these variants in ALL susceptibility and define their importance in the ethnic specific differences in ALL risk.
21493871	1072	1080	rs525549	SNP	rs525549
21493871	1085	1094	rs6589664	SNP	rs6589664
21493871	1125	1134	rs5758222	SNP	rs5758222
21493871	1136	1145	rs7286979	SNP	rs7286979
21493871	1151	1158	rs20551	SNP	rs20551
21493871	1520	1529	rs6589664	SNP	rs6589664

21138945|t|Homozygous loss of ADAM3A revealed by genome-wide analysis of pediatric high-grade glioma and diffuse intrinsic pontine gliomas.
21138945|a|Overall, pediatric high-grade glioma (pHGG) has a poor prognosis, in part due to the lack of understanding of the underlying biology. High-resolution 244 K oligo array comparative genomic hybridization (CGH) was used to analyze DNA from 38 formalin-fixed paraffin-embedded predominantly pretreatment pHGG samples, including 13 diffuse intrinsic pontine gliomas (DIPGs). The patterns of gains and losses were distinct from those seen in HGG arising in adults. In particular, we found 1q gain in up to 27% of our cohort compared with 9% reported in adults. A total of 13% had a balanced genetic profile with no large-scale copy number alterations. Homozygous loss at 8p12 was seen in 6 of 38 (16%) cases of pHGG. This novel deletion, which includes the ADAM3A gene, was confirmed by quantitative real-time PCR (qPCR). Loss of CDKN2A/CDKN2B in 4 of 38 (10%) samples by oligo array CGH was confirmed by fluorescent in situ hybridization on tissue microarrays and was restricted to supratentorial tumors. Only    50% of supratentorial tumors were positive for CDKN2B expression by immunohistochemistry (IHC), while    75% of infratentorial tumors were positive for CDKN2B expression (P = 0.03). Amplification of the 4q11-13 region was detected in 8% of cases and included PDGFRA and KIT, and subsequent qPCR analysis was consistent with the amplification of PDGFRA. MYCN amplification was seen in 5% of samples being significantly associated with anaplastic astrocytomas (P= 0.03). Overall, DIPG shared similar spectrum of changes to supratentorial HGG with some notable differences, including high-frequency loss of 17p and 14q and lack of CDKN2A/CDKN2B deletion. Informative genetic data providing insight into the underlying biology and potential therapeutic possibilities can be generated from archival tissue and typically small biopsies from DIPG. Our findings highlight the importance of obtaining pretreatment samples.

20801540|t|Hepatic but not brain iron is rapidly chelated by deferasirox in aceruloplasminemia due to a novel gene mutation.
20801540|a|BACKGROUND _#38; AIMS: Aceruloplasminemia is a rare autosomal recessive neurodegenerative disease associated with brain and liver iron accumulation which typically presents with movement disorders, retinal degeneration, and diabetes mellitus. Ceruloplasmin is a multi-copper ferroxidase that is secreted into plasma and facilitates cellular iron export and iron binding to transferrin. RESULTS: A novel homozygous ceruloplasmin gene mutation, c.2554+1G>T, was identified as the cause of aceruloplasminemia in three affected siblings. Two siblings presented with movement disorders and diabetes. Complementary DNA sequencing showed that this mutation causes skipping of exon 14 and deletion of amino acids 809-852 while preserving the open reading frame. Western blotting of liver extracts and sera of affected patients showed retention of the abnormal protein in the liver. Aceruloplasminemia was associated with severe brain and liver iron overload, where hepatic mRNA expression of the iron hormone hepcidin was increased, corresponding to the degree of iron overload. Hepatic iron concentration normalized after 3 and 5months of iron chelation therapy with deferasirox, which was also associated with reduced insulin demands. During short term treatment there was no clinical or imaging evidence for significant effects on brain iron overload. CONCLUSIONS: Aceruloplasminemia can show an incomplete clinical penetrance but is invariably associated with iron accumulation in the liver and in the brain. Iron accumulation in aceruloplasminemia is a result of defective cellular iron export, where hepcidin regulation is appropriate for the degree of iron overload. Iron chelation with deferasirox was effective in mobilizing hepatic iron but has no effect on brain iron.
20801540	557	568	c.2554+1G>T	DNAMutation	c|G|2554+1|T

20555334|t|A genome-wide analysis of loss of heterozygosity and chromosomal copy number variation in Proteus syndrome using high-density SNP microarrays.
20555334|a|Excessive cell proliferation and genetic changes such as loss of an allele (loss of heterozygosity (LOH)) or amplifications or deletions of parts of chromosomes (copy number variations (CNV)) are common findings in cancers. It is unknown whether these changes are also present in patients with overgrowth syndromes, although the presence of small-scale CNVs (such as duplication of 11p15 in Beckwith-Wiedemann syndrome), excessive cell proliferation and an increased frequency of tumors have all been reported in these patients. We present results of a genome-wide scan for LOH and CNV in Proteus syndrome (PS), a severely disfiguring overgrowth syndrome. We investigated CNV and LOH in DNA derived from affected and normal tissue samples from six PS patients using Affymetrix GeneChip Mapping 250   K Nsp high-density single-nucleotide polymorphism microarrays. Analysis revealed that LOH and CNVs were not common in PS. We attempted to validate selected CNVs detected by microarray analysis using quantitative genomic PCR, but the observed changes were not confirmed. These results suggest that large-scale genome-wide CNVs and LOH as seen in cancer syndromes are not characteristic findings in PS, although we cannot rule out the possibility that newer arrays with a higher number of probes could uncover smaller CNVs not detected in this study.

20512659|t|Mutation and association analysis of GEN1 in breast cancer susceptibility.
20512659|a|GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene mutational analysis of GEN1 in 176 BRCA1/2-negative familial breast cancer samples and 159 controls. We genotyped six SNPs tagging the 30 common variants in the transcribed region of GEN1 in 3,750 breast cancer cases and 4,907 controls. Mutation analysis revealed one truncating variant, c.2515_2519delAAGTT, which was present in 4% of cases and 4% of controls. We identified control individuals homozygous for the deletion, demonstrating that the last 69 amino acids of GEN1 are dispensable for its function. We identified 17 other variants, but their frequency did not significantly differ between cases and controls. Analysis of 3,750 breast cancer cases and 4,907 controls demonstrated no evidence of significant association with breast cancer for six SNPs tagging the 30 common GEN1 variants. These data indicate that although it also plays a key role in double-strand DNA break repair, GEN1 does not make an appreciable contribution to breast cancer susceptibility by acting as a high- or intermediate-penetrance breast cancer predisposition gene like BRCA1, BRCA2, CHEK2, ATM, BRIP1 and PALB2 and that common GEN1 variants do not act as low-penetrance susceptibility alleles analogous to SNPs in FGFR2. Furthermore, our analyses demonstrate the importance of undertaking appropriate genetic investigations, typically full gene screening in cases and controls together with large-scale case-control association analyses, to evaluate the contribution of genes to cancer susceptibility.
20512659	722	741	c.2515_2519delAAGTT	DNAMutation	c|DEL|2515_2519|AAGTT

20454699|t|Identification and characterization of a novel TACSTD2 mutation in gelatinous drop-like corneal dystrophy.
20454699|a|PURPOSE: To study the clinical, histological, in vivo confocal microscopic, and molecular profile in a family with gelatinous drop-like corneal dystrophy (GDLD) from north India. METHODS: Two siblings from a consanguineous family presented with clinical features analogous to GDLD. Detailed clinical evaluations were performed for all the available affected and unaffected members of this family. In vivo confocal microscopy and histology was done wherever necessary. DNA isolated from peripheral blood samples was subjected to polymerase chain reaction (PCR) followed by direct sequencing to detect mutations in the tumor-associated calcium signal transducer 2 (TACSTD2) gene. Protein modeling studies were done to asses the effect of the mutation on the protein structure. RESULTS: The diagnosis of GDLD was established in the patient and the affected sibling on slit-lamp examinations, which revealed mulberry-like opacities in the subepithelium and anterior stroma that were confirmed on histopathology. The findings of the in vivo confocal microscopy were consistent with those reported in previous reports. Sequencing TACSTD2 revealed a novel homozygous missense mutation c.356G>A, leading to amino acid substitution C119Y in the two affected siblings. The mutation was found to be pathogenic on Sorting Intolerant From Tolerant (SIFT) analysis and was not found in normal controls and unaffected individuals of the family. A synonymous, previously reported, single nucleotide polymorphism (SNP; rs13267) was also seen in all the individuals of the family. Protein modeling studies involving wild-type and mutant protein indicated an exposed cysteine residue in the mutant protein. CONCLUSIONS: A novel TACSTD2 C119Y mutation leading to an amino acid substitution was identified in two affected siblings of a family. Protein modeling studies revealed an exposed cysteine residue, which might cause interchain disulfide bond formation and protein aggregation leading to disturbed cell junctions of the corneal epithelium.
20454699	1285	1293	c.356G>A	DNAMutation	c|G|356|A
20454699	1330	1335	C119Y	ProteinMutation	p|C|119|Y
20454699	1609	1616	rs13267	SNP	rs13267
20454699	1824	1829	C119Y	ProteinMutation	p|C|119|Y

20367983|t|Mutation analysis in a Chinese family with multiple endocrine neoplasia type 1.
20367983|a|BACKGROUND: Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant cancer syndrome which is caused by germline mutations of the tumor suppressor gene MEN1. This study aimed to identify mutations in a Chinese pedigree with MEN1. METHODS: A large Chinese family with MEN1 was collected. All of the coded regions and their adjacent sequences of the MEN1 gene were amplified and sequenced. RESULTS: In this family, a heterozygous cytosine insertion in exon 10 (c.1546_1547insC) inducing a frame shift mutation of MEN1 was found in the proband and the other two suffering members of his family. This mutation was linked to a novel single nucleotide polymorphism (SNP) in intron 3 (IVS3 + 18C > T). CONCLUSIONS: The mutation in exon 10 of MEN1 gene might induce development of parathyroid hyperplasia and pituitary adenoma and cosegregate with MEN1 syndrome. The significance of the new found IVS3 + 18C > T of MEN1 needs a further investigation.
20367983	550	565	c.1546_1547insC	DNAMutation	c|INS|1546_1547|C
20367983	769	783	IVS3 + 18C > T	DNAMutation	c|C|IVS3+18|T
20367983	980	994	IVS3 + 18C > T	DNAMutation	c|C|IVS3+18|T

20335448|t|A novel point mutation in helix 10 of the human glucocorticoid receptor causes generalized glucocorticoid resistance by disrupting the structure of the ligand-binding domain.
20335448|a|CONTEXT: Generalized glucocorticoid resistance syndrome is a rare familial or sporadic condition characterized by partial insensitivity to glucocorticoids, caused by mutations in the glucocorticoid receptor (GR) gene. Most of the reported cases are adults, demonstrating symptoms associated with mineralocorticoid and/or adrenal androgen excess caused by compensatively increased secretion of the adrenocorticotropic hormone. PATIENT: We identified a new 2-yr-old female case of generalized glucocorticoid resistance syndrome. The patient (TJ) presented with a generalized seizure associated with hypoglycemia and hypokalemia. She also had hypertension and premature pubarche, whereas dexamethasone effectively suppressed these clinical manifestations. RESULTS: The patient's GR gene had a heterozygotic mutation (G-->A) at nucleotide position 2141 (exon 8), which resulted in substitution of arginine by glutamine at amino acid position 714 in the ligand-binding domain (LBD) of the GR alpha. Molecular analysis revealed that the mutant receptor had significantly impaired transactivation activity with a 2-fold reduction in affinity to ligand. It showed attenuated transactivation of the activation function (AF)-2 and reduced binding to a p160 nuclear receptor coactivator. Computer-based structural analysis revealed that replacement of arginine by glutamine at position 714 transmitted a conformational change to the LBD and the AF-2 transactivation surface, resulting in a decreased binding affinity to ligand and to the LXXLL coactivator motif. CONCLUSIONS: Dexamethasone treatment is effective in controlling the premature pubarche, hypoglycemia, hypertension, and hypokalemia in this child case, wherein arginine 714 plays a key role in the proper formation of the ligand-binding pocket and the AF-2 surface of the GR alpha LBD.
20335448	988	1023	(G-->A) at nucleotide position 2141	DNAMutation	c|G|2141|A

20331852|t|Mutation analysis of the LCE3B/LCE3C genes in Psoriasis.
20331852|a|BACKGROUND: An association between a common deletion comprising the late cornified envelope LCE3B and LCE3C genes (LCE3C_LCE3B-del) and Psoriasis (Ps) has been reported. The expression of these LCE genes was induced after skin barrier disruption and was also strong in psoriatic lesions. The damage to the skin barrier could trigger an epidermal response that includes the expression of genes involved in the formation of skin barrier. METHODS: We determined the LCE3C_LCE3B-del genotype in 405 Ps patients and 400 healthy controls from a Northern Spain region (Asturias). These patients and controls were also genotyped for the rs4112788 single nucleotide polymorphism, in strong linkage disequilibrium with the LCE3C_B cluster. The LCE3B and LCE3C gene variant was determined in the patients through SSCA, DHPLC, and direct sequencing. RESULTS: Allele and genotype frequencies did not differ between patients and controls for the rs4112788 and LCE3C_LCE3B-del polymorphisms. However, del/del homozygotes were significantly higher among patients with chronic plaque type Ps who did not develop arthritis (p = 0.03; OR = 1.4; 95%CI = 1.03-1.92). The analysis of the coding sequence of LCE3B and LCE3C in the patients who had at least one copy of this showed that only one patient has a no previously reported LCE3B variant (R68C). CONCLUSION: Our work suggested that homozygosity for a common LCE3C_LCE3B deletion contributes to the risk of developing chronic plaque type Ps without psoriatic arthritis. Our work confirmed previous reports that described an association of this marker with only skin manifestations, and supported the concept of different genetic risk factors contributing to skin and joint disease.
20331852	686	695	rs4112788	SNP	rs4112788
20331852	989	998	rs4112788	SNP	rs4112788
20331852	1381	1385	R68C	ProteinMutation	p|R|68|C

20300861|t|Loss of heterozygosity of the tumor suppressor gene Tg737 in the side population cells of hepatocellular carcinomas is associated with poor prognosis.
20300861|a|Analysis of loss of heterozygosity (LOH) is a useful method for finding genetic alterations in tumor and precancerous lesion tissues. In this study, we analyzed LOH of the tumor suppressor gene Tg737 in side population cells of human hepatocellular carcinomas. Side population cells were sorted and identification by flow cytometry from suspensions of hepatocarcinoma or normal liver cells generated from 95 hepatocellular carcinoma and normal tissues, respectively. DNA was extracted from the two groups of side population cells and peripheral blood specimens. Five microsatellite markers on the Tg737 gene were used to analyze the frequency of loss of heterozygosity in the side population cells of the hepatocellular carcinoma. Twenty-four (25.30%) tumor samples had a large deletion in more than three microsatellite markers. The highest frequency of loss of heterozygosity was observed with the G64212 marker (78.75%) and the SHGC-57879 marker (75.95%). Statistical analysis of the correlation between loss of heterozygosity of Tg737 and clinicopathological features indicated a strong correlation between the two markers associated with the highest frequency of loss of heterozygosity and survival. The results indicate that loss of heterozygosity of the tumor suppressor gene Tg737 may play an important role in the carcinogenetic mechanism of liver cancer stem cells. In addition, the independent association between loss of heterozygosity at the SHGC-57879 and G64212 markers and worsened short-term survival in patients could be used as a novel prognostic predictor. Further studies of side population cells may contribute to the establishment of novel therapeutic strategies for hepatocellular carcinoma.

20154289|t|Molecular diversity of hemoglobin H disease in India.
20154289|a|This study was undertaken to evaluate the variable clinical expression of hemoglobin (Hb) H disease in India. For the study, alpha genotyping was done in 8 patients with Hb H disease using multiplex polymerase chain reaction and DNA sequencing. The study revealed that 4 genotypes (- -(SEA)/ -alpha(3.7), - -(SA)/-alpha(3.7), - -(SEA)/-alpha(3.7 Sallanches), - -alpha(3.7)/-alpha(3.7 Sallanches)) were responsible for Hb H disease, the alpha+ thalassemia mutation (-alpha(3.7) deletion) being the most common defect. The nondeletional mutation Hb Sallanches (alpha 2 codon 104 G --> A) was seen in 3 cases. Two unique and novel genotypes leading to Hb H disease were characterized (- -(SEA)/-alpha(3.7 Sallanches) and -alpha(3.7)/-alpha(3.7 Sallanches)). Because a majority of patients with Hb H disease do not have severe manifestations, prenatal diagnosis is usually unwarranted in India.
20154289	621	638	codon 104 G --> A	DNAMutation	|G|CODON104|A

20080916|t|Promoter insertion/deletion in the IRF5 gene is highly associated with susceptibility to systemic lupus erythematosus in distinct populations, but exerts a modest effect on gene expression in peripheral blood mononuclear cells.
20080916|a|OBJECTIVE: We examined the genetic association of the promoter insertion/deletion (indel) in IRF5 gene with systemic lupus erythematosus (SLE) in distinct populations and assessed its role in gene expression. METHODS: Four IRF5 polymorphisms were genotyped in 1488 SLE patients and 1466 controls. Gene expression was analyzed by quantitative real-time PCR using RNA from peripheral blood mononuclear cells (PBMC). RESULTS: The promoter indel and rs2070197 had independent genetic effects, which accounted for the association of rs2004640 and rs10954213. Gene expression analysis revealed that rs10954213 exerted the greatest influence on IRF5 transcript levels. CONCLUSION: We corroborated the association of the promoter indel with SLE in 5 different populations and revealed that rs10954213 is the main single-nucleotide polymorphism responsible for altered IRF5 expression in PBMC.
20080916	674	683	rs2070197	SNP	rs2070197
20080916	756	765	rs2004640	SNP	rs2004640
20080916	770	780	rs10954213	SNP	rs10954213
20080916	821	831	rs10954213	SNP	rs10954213
20080916	1010	1020	rs10954213	SNP	rs10954213

20019594|t|Novel mutations identification in exon 4 of LDLR gene in patients with moderate hypercholesterolemia in a Venezuelan population.
20019594|a|Familial hypercholesterolemia (FH) is an autosomal dominant disease characterized by increase in low-density lipoprotein (LDL) cholesterol levels and premature coronary artery disease. In Venezuela, the molecular basis of FH has not been characterized, thus, the aim of this study was to investigate mutations in the exon 4 of the LDLR (LDL-receptor) gene in 225 Venezuelan mixed race individuals (65 hypercholesterolemic and 160 normolipidemic). The exon 4 of the LDLR gene was screened by polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) analysis and DNA sequencing. Additionally, ApoB-100 gene mutations were investigated. Different LDLR gene mutations were identified in 5 hypercholesterolemic patients (7.7%), 3 missense mutations (4.6%), and 2 frameshift mutations (3%). All mutations were heterozygous. The missense mutations included the amino acid substitution p.E180K, p.R194S, and p.C152G. The frameshift mutations are caused by insertions resulting in the creation of stop codons: p.D157fsX158 and p.S173fsX174, which could code for truncated LDLR of 157 and 173 amino acids, respectively. The apoB gene mutations were not detected in any of our patients and to our knowledge 4 mutations identified in this study have not been reported previously, this study being the first comprehensive mutation analysis of the LDLR causing FH in our region. The early identification of individuals at risk allows changes in lifestyle, including dietary intervention, followed by drug treatment.
20019594	1029	1036	p.E180K	ProteinMutation	p|E|180|K
20019594	1038	1045	p.R194S	ProteinMutation	p|R|194|S
20019594	1051	1058	p.C152G	ProteinMutation	p|C|152|G
20019594	1152	1164	p.D157fsX158	ProteinMutation	p|D|157||FSX|158
20019594	1169	1181	p.S173fsX174	ProteinMutation	p|S|173||FSX|174

19881468|t|hOGG1 Ser326Cys polymorphism and risk of lung cancer by histological type.
19881468|a|Human 8-oxoguanine DNA glycosylase 1 (hOGG1) has a major role in the repair of 8-hydroxyguanine, a major promutagenic DNA lesion. The genetic polymorphism rs1052133, which leads to substitution of the amino acid at codon 326 from Ser to Cys, shows functional differences, namely a decrease in enzyme activity in hOGG1-Cys326. Although several studies have investigated the association between rs1052133 and lung cancer susceptibility, the effect of this locus on lung cancer according to histology remains unclear. We therefore conducted a case-control study with 515 incident lung cancer cases and 1030 age- and sex-matched controls without cancer, and further conducted a meta-analysis. In overall analysis, the homozygous Cys/Cys genotype showed a significant association with lung cancer compared to Ser allele carrier status (odds ratio (OR)=1.31, 95% confidence interval (CI)=1.02-1.69). By histology-based analysis, the Cys/Cys genotype showed a significantly positive association with small-cell carcinoma (OR=2.40, 95% CI=1.32-4.49) and marginally significant association with adenocarcinoma (OR=1.32, 95% CI=0.98-1.77). A meta-analysis of previous and our present study revealed that this polymorphism is positively associated with adenocarcinoma, although suggestive associations were also found for squamous- and small-cell lung cancers. These results indicate that rs1052133 contributes to the risk of adenocarcinoma of lung.
19881468	6	15	Ser326Cys	ProteinMutation	p|S|326|C
19881468	230	239	rs1052133	SNP	rs1052133
19881468	468	477	rs1052133	SNP	rs1052133
19881468	1453	1462	rs1052133	SNP	rs1052133

19880293|t|Polymorphisms in the FOXP3 gene in Han Chinese psoriasis patients.
19880293|a|BACKGROUND: Psoriasis is a common dermatological disorder, in which autoimmunity plays an important role. CD4(+)CD25(+) regulatory T cells (T-regs) have been suggested to be involved in the pathogenesis of some autoimmune diseases. T-regs express the fork head/winged helix transcription factor, FOXP3, which appears to be of key importance in the development and function of T-regs. Studies have found that single-nucleotide polymorphisms (SNPs) in the FOXP3 gene contribute to susceptibility to some autoimmune disorders. However, information about FOXP3 gene in psoriasis is limited. OBJECTIVE: This study evaluated the association between FOXP3 gene SNPs and susceptibility to psoriasis in a Han Chinese population. METHODS: In a hospital-based case-control study, 524 patients with psoriasis and 549 psoriasis-free controls were recruited according to age and gender. We investigated four SNPs in the FOXP3 gene (-6054, deletion/ATT; -3279, A/C; -924, A/G; IVS9+459, A/G) in psoriatic patients, and assessed allele and genotype frequencies in psoriatic patients (237 females, 287 males) and normal controls (272 females, 277 males). The polymorphisms were genotyped using the PCR sequence-specific primer (PCR-SSP) technique and PCR-restriction fragment length polymorphism (RFLP) analysis. RESULTS: We found that increased risk of psoriasis was associated with the FOXP3 -3279 AC genotype (adjusted OR, 1.32; 95% CI, 1.01-1.74) and the combined AC+AA genotype (adjusted OR, 1.38; 95% CI, 1.07-1.78), compared with the -3279 CC genotype. We also found that an increased risk of psoriasis was associated with the FOXP3 IVS9+459 GG genotype (adjusted OR, 2.24; 95% CI, 1.41-3.58). However, the combined GA+GG genotype showed no such tendency (adjusted OR=1.28; 95% CI, 1.00-1.64), compared with the IVS9+459 AA genotype. There was no evidence of an increased risk associated with the FOXP3-6054 deletion/ATT or FOXP3-924 A/G genotype. In combined genotype analyses, the FOXP3-3279 AC+AA genotype was more obviously associated in males (adjusted OR=1.60, 95% CI=1.11-2.31) and severe psoriasis patients (PASI score >20; adjusted OR=1.97, 95% CI=1.41-2.75). Meanwhile, the FOXP3 IVS9+459 GA+GG genotype was also associated with severe psoriasis patients (adjusted OR=1.69, 95% CI=1.21-2.36). CONCLUSIONS: FOXP3 polymorphisms appear to contribute to the risk of psoriasis in a Han Chinese population. Larger studies are needed to confirm these findings.
19880293	985	1004	-6054, deletion/ATT	DNAMutation	c|DEL|-6054|ATT
19880293	1006	1016	-3279, A/C	DNAMutation	c|A|-3279|C
19880293	1018	1027	-924, A/G	DNAMutation	c|A|-924|G
19880293	1029	1042	IVS9+459, A/G	DNAMutation	c|A|IVS9+459|G
19880293	1959	1977	-6054 deletion/ATT	DNAMutation	c|DEL|-6054|ATT
19880293	1986	1994	-924 A/G	DNAMutation	c|A|-924|G

19823838|t|TNF receptor-associated periodic fever syndrome caused by sequence alterations in exonic splicing enhancers: comment on the article by Tr  benbach et al.
19823838|a|Tumor necrosis factor receptor-associated periodic syndrome (TRAPS), an autosomal disease belonging to human autoinflammatory syndromes, is caused by mutations in Tumor Necrosis Factor Receptor Superfamily Member 1A (TNFRSF1A) gene. Tr  benbach and colleagues described a patient with two heterozygotic nucleotide transversions in exon 4 of TNFRSF1A gene: the first is a substitution from guanine to cytosine at position 263 of the nucleotide sequence (c.263 G>C); the second is a substitution from cytosine to adenine at position 264 (c.264 C>A); the two mutations affect the amino acid number 88 of the protein. To date, this was the first report of a double monoallelic mutation in a gene related to autoinflammatory syndromes. Using two web interfaces (ESEfinder and RESCUE-ESE), we provide evidence that the double nucleotide change may affect an exonic splicing enhancer (ESE), a sequence element distinct from the canonical splice sites that are needed for normal splicing. ESEs are short and degenerate sequences found within coding exons and required for efficient splicing and splice site recognition. In order to verify if these changes really affect an ESE, it would be useful to analyze the described index case TNFRSF1A cDNA, because if this analysis will evidence an exon skipping in the TNFRSF1A coding sequence, it would then represent the first mutation in autoinflammatory syndromes demonstrated to be caused by ESE elements alteration.
19823838	607	616	c.263 G>C	DNAMutation	c|G|263|C
19823838	690	699	c.264 C>A	DNAMutation	c|C|264|A

19781362|t|Mutation analysis of p63 gene in the first Chinese family with ADULT syndrome.
19781362|a|BACKGROUND: ADULT syndrome (acro-dermato-ungual-lacrimal-tooth syndrome) is a rare ectodermal dysplasia disorder known as autosomal dominant inheritance. Recent studies have linked p63 gene mutation to the development of this disease. However, the genetic characteristics of ADULT syndrome were still not well understood. METHODS: Mutation analysis of p63 gene in the first Chinese ADULT syndrome family was performed using direct DNA sequencing. RESULTS: The sequence analysis of exon 8 of p63 gene disclosed a heterozygous G>A substitution at nucleotide 893 (R298Q) in the proband. In addition, a single nucleotide polymorphism (SNP) rs16864880 in the downstream flanking region (DFR) of p63 exon 8 was also identified in this family. The proband and the paternal side including her father exhibited the C/G genotype at this position. The C/G variant frequency in the paternal was significantly higher as compared with the maternal (6/10 vs 0/6, P = 0.034). CONCLUSIONS: ADULT syndrome may be caused by the p63 gene mutation, and it might have closer genetic association with the paternal side in this family.
19781362	604	638	G>A substitution at nucleotide 893	DNAMutation	c|G|893|A
19781362	640	645	R298Q	ProteinMutation	p|R|298|Q
19781362	715	725	rs16864880	SNP	rs16864880

19686598|t|New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.
19686598|a|BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary renal disease. The disease is caused by mutations of the PKD1 (affecting roughly 85% of ADPKD patients) and PKD2 (affecting roughly 14% of ADPKD patients) genes, although in several ADPKD families, the PKD1 and/or PKD2 linkage was not found. Mutation analysis of the PKD1 gene is complicated by the presence of highly homologous genomic duplications of the first two thirds of the gene. METHODS: The direct detection of mutations in the non-duplicated region of the PKD1 gene was performed in 90 unrelated individuals, consisting of 58 patients with end-stage renal failure (manifesting before their 50th year of life) and 32 individuals from families where the disease was clearly linked to the PKD1 gene. Mutation screening was performed using denaturing gradient gel electrophoresis (DGGE). DNA fragments showing an aberrant electrophoretic banding pattern were sequenced. RESULTS: In the non-duplicated region of the PKD1 gene, 19 different likely pathogenic germline sequence changes were identified in 19 unrelated families/individuals. Fifteen likely pathogenic sequence changes are unique for the Czech population. The following probable mutations were identified: 9 nonsense mutations, 6 likely pathogenic missense mutations, 2 frameshifting mutations, one in-frame deletion and probable splice site mutation. In the non-duplicated region of the PKD1 gene, 16 different polymorphisms or unclassified variants were detected. CONCLUSION: Twenty probable mutations of the PKD1 gene in 90 Czech individuals (fifteen new probable mutations) were detected. The establishment of localization and the type of causal mutations and their genotype phenotype correlation in ADPKD families will improve DNA diagnosis and could help in the assessment of the clinical prognosis of ADPKD patients.

19624920|t|Clusters of multidrug-resistant Mycobacterium tuberculosis cases, Europe.
19624920|a|Molecular surveillance of multidrug-resistant tuberculosis (MDR TB) was implemented in Europe as case reporting in 2005. For all new MDR TB cases detected from January 2003 through June 2007, countries reported case-based epidemiologic data and DNA fingerprint patterns of MDR TB strains when available. International clusters were detected and analyzed. From 2003 through mid-2007 in Europe, 2,494 cases of MDR TB were reported from 24 European countries. Epidemiologic and molecular data were linked for 593 (39%) cases, and 672 insertion sequence 6110 DNA fingerprint patterns were reported from 19 countries. Of these patterns, 288 (43%) belonged to 18 European clusters; 7 clusters (242/288 cases, 84%) were characterized by strains of the Beijing genotype family, including the largest cluster (175/288 cases, 61%). Both clustering and the Beijing genotype were associated with strains originating in eastern European countries. Molecular cluster detection contributes to identification of transmission profile, risk factors, and control measures.

19624485|t|The HLA-G 14 bp insertion/deletion polymorphism is a putative susceptible factor for active human cytomegalovirus infection in children.
19624485|a|Human leukocyte antigen-G (HLA-G) expression is a potential factor for the pathogenesis of virus infection. A 14 bp insertion/deletion polymorphism (rs16375) in the 3'-untranslated region of the HLA-G gene is involved in the stability of HLA-G mRNA and HLA-G protein expression. Therefore, the HLA-G 14 bp polymorphism might be involved in human cytomegalovirus (hCMV) infection. To test a possible association between the HLA-G 14 bp deletion/insertion polymorphism and the active hCMV infection, in this study, a total of 54 patients with active hCMV infection and 165 age- and sex-matched, unrelated, normal Chinese Han population were genotyped for the 14 bp insertion/deletion polymorphism. Association of 14 bp polymorphism with hCMV urine DNA copies and the odds ratio (OR) of the polymorphism as a risk factor for active hCMV infection were analyzed. Our results showed that the prevalence of -14 bp/ -14 bp genotype in active hCMV patients was markedly increased [P(c) = 0.00034, OR = 3.31, 95% confidence interval (CI): 1.77-6.18], and similar significance was also observed for the frequency of -14 bp allele (P c = 0.0023, OR = 2.24, 95% CI: 1.38-3.64) when compared with that of healthy controls. Furthermore, urine hCMV DNA copies in patients with the -14 bp/ -14 bp genotype were significantly higher than those in patients with the +14 bp/ +14 bp genotype (P = 0.041). Our findings support a potential role of HLA-G 14 bp insertion/deletion polymorphism as a susceptible factor for the active hCMV infection.
19624485	286	293	rs16375	SNP	rs16375

19565319|t|Adenosine A(2A) receptor gene (ADORA2A) variants may increase autistic symptoms and anxiety in autism spectrum disorder.
19565319|a|Autism spectrum disorders (ASDs) are heterogeneous disorders presenting with increased rates of anxiety. The adenosine A(2A) receptor gene (ADORA2A) is associated with panic disorder and is located on chromosome 22q11.23. Its gene product, the adenosine A(2A) receptor, is strongly expressed in the caudate nucleus, which also is involved in ASD. As autistic symptoms are increased in individuals with 22q11.2 deletion syndrome, and large 22q11.2 deletions and duplications have been observed in ASD individuals, in this study, 98 individuals with ASD and 234 control individuals were genotyped for eight single-nucleotide polymorphisms in ADORA2A. Nominal association with the disorder was observed for rs2236624-CC, and phenotypic variability in ASD symptoms was influenced by rs3761422, rs5751876 and rs35320474. In addition, association of ADORA2A variants with anxiety was replicated for individuals with ASD. Findings point toward a possible mediating role of ADORA2A variants on phenotypic expression in ASD that need to be replicated in a larger sample.
19565319	825	834	rs2236624	SNP	rs2236624
19565319	900	909	rs3761422	SNP	rs3761422
19565319	911	920	rs5751876	SNP	rs5751876
19565319	925	935	rs35320474	SNP	rs35320474

19561170|t|Protein kinase C gamma, a protein causative for dominant ataxia, negatively regulates nuclear import of recessive-ataxia-related aprataxin.
19561170|a|Spinocerebellar ataxia type 14 (SCA14) is an autosomal dominant disease caused by mutations in the gene encoding protein kinase C gamma (PKC gamma). We report an SCA14 family with a novel deletion of a termination-codon-containing region, resulting in a missense change and a C-terminal 13-amino-acid extension with increased kinase activity. Notably, one patient with a severe phenotype is the first homozygote for the mutation causing SCA14. We show the novel molecular consequences of increased kinase activities of mutants: aprataxin (APTX), a DNA repair protein causative for autosomal recessive ataxia, was found to be a preferential substrate of mutant PKC gamma, and phosphorylation inhibited its nuclear entry. The phosphorylated residue was Thr111, located adjacent to the nuclear localization signal, and disturbed interactions with importin alpha, a nuclear import adaptor. Decreased nuclear APTX increased oxidative stress-induced DNA damage and cell death. Phosphorylation-resistant APTX, kinase inhibitors, and antioxidants may be therapeutic options for SCA14.

19537956|t|CYP1A1 genotype modifies the impact of smoking on effectiveness of HAART among women.
19537956|a|We have recently shown that cigarette smoking is associated with lesser responses to potent antiretroviral therapies. Certain Cytochrome P-450 enzymes activate compounds derived from tobacco smoke into toxic forms that may promote HIV-1 gene expression through promotion of DNA-adduct formation by the oxidation of chemical constituents of cigarette smoke, such as polyaromatic hydrocarbons and dioxins. To explore the association between environmental and genetic factors to viral replication in women who smoke and receive highly active anti-retroviral therapy (HAART), we assessed the impact of polymorphisms in a panel of four Cytochrome P-450 genes (CYP1A1, CYP2A6, CYP2D6, and CYP2E1) and two Glutathione S-transferase genes (GSTM1 and GSST1) in 924 participants of the Women's Interagency HIV Study (WIHS). Our findings showed that GSTM1 and GSST1 deletions were not associated with HAART effectiveness. By contrast, homozygosity for the CYP1A1-m1 polymorphism, was associated with impaired viral response to treatment among smokers (relative hazard (RH) = 0.54; 95% confidence interval = 0.31-0.94) after adjustment for pretreament viral load, CD4 count, age, hepatitis C infection, prior HAART therapy and race, although it had no effect among nonsmokers. We conclude that the association of the CPY1A1-m1 variant with a reduced response to HAART therapy in HIV infected smokers is consistent with this enzyme's role in the metabolic conversion of environmental toxins to DNA adducts, which may directly promote HIV-1 gene expression.

19429592|t|RPGR ORF15 genotype and clinical variability of retinal degeneration in an Australian population.
19429592|a|BACKGROUND: Mutations in the retinitis pigmentosa GTPase regulator gene (RPGR) are estimated to cause up to 20% of all Caucasian retinitis pigmentosa and up to 75% of cases of X-Linked RP (XLRP). Exon open reading frame 15 (ORF15) is a purine-rich mutation hotspot. Mutations in RPGR ORF15 have also been documented to cause X linked cone-rod dystrophy (XLCORD) and atrophic macular degeneration at an unknown frequency. METHODS: From a hospital clinic population, probands with probable XLRP and XLCORD were screened for RPGR ORF15 mutations and fully phenotyped. RESULTS: Four different RPGR ORF15 mutations were found in four probands. All mutations in the ORF15 exon resulted in premature truncation of the RPGR protein. Three were nonsense mutations: c.507G>T (p.E169stop), c.867G>T (p.G289stop), c.897G>T (p.E299stop) and the fourth a single nucleotide insertion c.1558-1559insA (p.S522fs 525stop). One family exhibited typical XLRP, two XLCORD and one a combination of the phenotypes. CONCLUSION: RPGR ORF15 mutations produce intrafamilial and interfamilial clinical variability with varying degrees of cone degeneration. In an Australian clinic population RPGR ORF15 mutations cause XLCORD in addition to XLRP.
19429592	854	862	c.507G>T	DNAMutation	c|G|507|T
19429592	864	874	p.E169stop	ProteinMutation	p|E|169|X
19429592	877	885	c.867G>T	DNAMutation	c|G|867|T
19429592	887	897	p.G289stop	ProteinMutation	p|G|289|X
19429592	900	908	c.897G>T	DNAMutation	c|G|897|T
19429592	910	920	p.E299stop	ProteinMutation	p|E|299|X
19429592	967	982	c.1558-1559insA	DNAMutation	c|INS|1558_1559|A
19429592	984	1000	p.S522fs 525stop	ProteinMutation	p|S|522||FSX|525

19340305|t|Somatic LKB1 mutations promote cervical cancer progression.
19340305|a|Human Papilloma Virus (HPV) is the etiologic agent for cervical cancer. Yet, infection with HPV is not sufficient to cause cervical cancer, because most infected women develop transient epithelial dysplasias that spontaneously regress. Progression to invasive cancer has been attributed to diverse host factors such as immune or hormonal status, as no recurrent genetic alterations have been identified in cervical cancers. Thus, the pressing question as to the biological basis of cervical cancer progression has remained unresolved, hampering the development of novel therapies and prognostic tests. Here we show that at least 20% of cervical cancers harbor somatically-acquired mutations in the LKB1 tumor suppressor. Approximately one-half of tumors with mutations harbored single nucleotide substitutions or microdeletions identifiable by exon sequencing, while the other half harbored larger monoallelic or biallelic deletions detectable by multiplex ligation probe amplification (MLPA). Biallelic mutations were identified in most cervical cancer cell lines; HeLa, the first human cell line, harbors a homozygous 25 kb deletion that occurred in vivo. LKB1 inactivation in primary tumors was associated with accelerated disease progression. Median survival was only 13 months for patients with LKB1-deficient tumors, but >100 months for patients with LKB1-wild type tumors (P = 0.015, log rank test; hazard ratio = 0.25, 95% CI = 0.083 to 0.77). LKB1 is thus a major cervical tumor suppressor, demonstrating that acquired genetic alterations drive progression of HPV-induced dysplasias to invasive, lethal cancers. Furthermore, LKB1 status can be exploited clinically to predict disease recurrence.

19223935|t|Novel promoter and exon mutations of the BMPR2 gene in Chinese patients with pulmonary arterial hypertension.
19223935|a|Pulmonary arterial hypertension (PAH), which is clinically characterized by a sustained elevation in mean pulmonary artery pressure leading to significant morbidity and mortality, is caused by intense remodeling of small pulmonary arteries by endothelial and smooth muscle proliferation. Genetic studies in familial PAH (FPAH) have revealed heterozygous germline mutations in the bone morphogenetic protein type II receptor (BMPR2), a receptor for the transforming growth factor (TGF)-beta/BMP superfamily. In this study, we conducted mutation screening in the promoter region and the entire coding regions as well as the intron/exon boundaries of the BMPR2 gene in 20 Chinese patients with either idiopathic or FPAH. All novel detected mutations were excluded by their presence in a panel of 200 chromosomes from normal individuals. A novel mutation, G-669A, in the promoter sequence of the BMPR2 gene was identified in one patient with FPAH, and no exonic mutations were detected in the proband. This mutation abolished a potential specificity protein 3 (sp3) transcription factor-binding site, and a dual luciferase assay showed that the promoter carrying the -669A allele had significantly decreased transcriptional activity compared with -669G allele. Of the other 19 patients, three novel heterozygous exonic mutations were identified: a frame shift mutation with deletion of TG at the nucleotide position 608-609 in exon 5 (Leu203fsX15), a nonsense mutation at the nucleotide position 292 in exon 3 (Glu98X) and a missense single nucleotide substitution in exon 12 (Ser863Asn).
19223935	962	968	G-669A	DNAMutation	c|G|-669|A
19223935	1541	1552	Leu203fsX15	ProteinMutation	p|L|203||FSX|15
19223935	1617	1623	Glu98X	ProteinMutation	p|E|98|X
19223935	1683	1692	Ser863Asn	ProteinMutation	p|S|863|N

19196567|t|Relation between angiotensin-converting enzyme I/D gene polymorphism and pulse pressure in patients with a first anterior acute myocardial infarction.
19196567|a|OBJECTIVE: Evidence shows that an elevated pulse pressure (PP) may lead to an increased risk of cardiovascular morbidity and mortality. The aim of the present study was to determine the effects of polymorphism of the angiotensin-converting enzyme (ACE) gene on the PP after a first anterior acute myocardial infarction (AMI). METHODS: Overall 116 patients with a first anterior AMI were included in this cross-sectional study. DNA was isolated from peripheral leukocytes. The ID status was determined by polymerase chain reaction by a laboratory staff member who was unaware of the clinical details. Based on the polymorphism of the ACE gene, they were classified into 3 groups: Deletion/Deletion (DD) genotype (Group 1, n=45), Insertion/Deletion (ID) genotype (Group 2, n=58), Insertion/Insertion (II) genotype (Group 3, n=13). Blood pressure measurements were performed in all patients within 10 minutes admitted to coronary care unit. The PP was calculated by subtraction of diastolic blood pressure (DBP) from systolic blood pressure (SBP). Echocardiographic examinations were performed using the parasternal longitudinal axis and apical 4-chamber windows in accordance with the recommendations of the American Echocardiography Committee. One-way analysis of variance (ANOVA) and Chi-square analyses were used to compare differences among subjects with different genotypes. RESULTS: There were no significant differences among clinical parameters of patients. Pulse pressure was significantly higher in patients who have ACE DD and ID genotypes than in patients who have ACE II genotype (47+/- 16, 47+/- 14 and 39+/- 12, F=3.4, p<0.05). But SBP, DBP and heart rate were not significantly different among ACE DD, ACE ID and ACE II genotypes. CONCLUSION: Our results suggested that, ACE Gene I/D polymorphism D allele may affect PP in patients with a first anterior AMI.

19137569|t|Identification of microdeletions in candidate genes for cleft lip and/or palate.
19137569|a|BACKGROUND: Genome-wide association studies are now used routinely to identify genes implicated in complex traits. The panels used for such analyses can detect single nucleotide polymorphisms and copy number variants, both of which may help to identify small deleted regions of the genome that may contribute to a particular disease. METHODS: We performed a candidate gene analysis involving 1,221 SNPs in 333 candidate genes for orofacial clefting, using 2,823 samples from 725 two- and three-generation families with a proband having cleft lip with or without cleft palate. We used SNP genotyping, DNA sequencing, high-resolution DNA microarray analysis, and long-range PCR to confirm and characterize the deletion events. RESULTS: This dataset had a high duplicate reproducibility rate (99.98%), high Mendelian consistency rate (99.93%), and low missing data rate (0.55%), which provided a powerful opportunity for deletion detection. Apparent Mendelian inconsistencies between parents and children suggested deletion events in 15 individuals in 11 genomic regions. We confirmed deletions involving CYP1B1, FGF10, SP8, SUMO1, TBX1, TFAP2A, and UGT7A1, including both de novo and familial cases. Deletions of SUMO1, TBX1, and TFAP2A are likely to be etiologic. CONCLUSIONS: These deletions suggest the potential roles of genes or regulatory elements contained within deleted regions in the etiology of clefting. Our analysis took advantage of genotypes from a candidate-gene-based SNP survey and proved to be an efficient analytical approach to interrogate genes potentially involved in clefting. This can serve as a model to find genes playing a role in complex traits in general.

19067809|t|Hemodynamic parameters and heart rate variability during a tilt test in relation to gene polymorphism of renin-angiotensin and serotonin system.
19067809|a|PURPOSE: The aim of the study was to evaluate the renin-angiotensin system and serotonin transporter gene polymorphisms in relation to hemodynamic parameters and heart rate variability during a head-up tilt test (HUT) in patients with vasovagal syncope. METHODS: DNA was collected from 191 patients (mean age 44+/-18 years, 61 men, 130 women). The following gene polymorphisms were determined in genomic DNA: angiotensin-converting enzyme insertion/deletion polymorphism (I/D ACE), angiotensinogen gene polymorphism (M 235), angiotensin II receptor type 1 (ATR1) polymorphism (A 11666C), and polymorphism of serotonin transporter gene (5HTTLPR).Heart rate variability during HUT was assessed in 5-minute intervals by low frequency, high frequency, standard deviation of the normal-to-normal (SDNN), and root mean square successive difference parameters. RESULTS: AA genotype of A 1166C polymorphism was associated with lower minimal systolic blood pressure (SBP) and diastolic blood pressure (DBP) during HUT compared with other genotypes (minimal SBP: AA 59.6+/-21,8, AC 79.9+/-22.7, CC 65.4+/-22.7 mmHg, P=0.007), (minimal DBP: AA 36.4+/-22.7, AC 52.3+/-22.9, CC 45.4+/-19.5 mmHg, P=0.007).AA genotype was also associated with higher SDNN compared to other genotypes in the early phase of HUT (SDNN in 5 minutes of tilt: AA 59.7+/-24.6, AC 50.6+/-20.6, CC 46.0+/-13.2, P=0.01) and at syncope occurrence (SDNN: AA 71.0+/-20.9, AC 58.2+/-17.9, CC 58+/-10, P=0.04) CONCLUSION: AA genotype of A 1166C polymorphism in the ATR1 gene may be associated with hypotension and decline in sympathetic tone during HUT. Its role in genetic predisposition to vasovagal syncope cannot be excluded.
19067809	722	730	A 11666C	DNAMutation	|A|11666|C
19067809	1023	1030	A 1166C	DNAMutation	|A|1166|C
19067809	1636	1643	A 1166C	DNAMutation	|A|1166|C

18945288|t|R58fs mutation in the HGD gene in a family with alkaptonuria in the UAE.
18945288|a|This study was conducted to determine the prevalence of alkaptonuria in the UAE population and to identify the genotype of affected individuals. In a 3 stage sampling technique 2981 pupils from Government schools in Al Ain and private schools in Dubai were selected to take part in the study, of whom 2857 provided urine samples. Urine collected was analysed for homogentisic acid by gas chromatography-mass spectrometry. Genomic DNA was isolated from the white blood cells of all family members of the affected case following standard established protocols. Specific PRC primers were designed to amplify all 14 exons of the HGD gene with the flanking intronic sequences including the splice site sequences. 2857 children returned a viable urine sample, of which one was highly positive for homogentisic acid. All 12 members of this girl's family were studied and one, a 22 year old brother, was found to excrete HGA. Another, a sister who had not provided a urine sample, was discovered by genetic testing. There were no complaints of joint pain or other symptoms in any member of this family. Parents were first cousins. We found a single nucleotide deletion c.342delA, located in exon 3, which resulted in a frameshift at amino acid position 58 (p.Arg58fs or p.R58fs). Alkaptonuria may be more common than it is thought to be with an allele prevalence estimated at 0.0107 (95% CI 0.000392-0.03473). The R58fs mutation is old, perhaps having occurred several thousand years ago, and has spread over a large geographical area.
18945288	0	5	R58fs	ProteinMutation	p|R|58||FS
18945288	1234	1243	c.342delA	DNAMutation	c|DEL|342|A
18945288	1322	1331	p.Arg58fs	ProteinMutation	p|R|58||FS
18945288	1335	1342	p.R58fs	ProteinMutation	p|R|58||FS
18945288	1479	1484	R58fs	ProteinMutation	p|R|58||FS

18759095|t|Peters plus syndrome.
18759095|a|A 10-year-old boy, issue of unrelated parents presented with visual impairment, short stature and mental retardation. The presence of a Peters' anomaly, mental retardation, disproportionate short stature, skeletal abnormalities and distinctive facial features (broad forehead, telecanthus, cupid bow shaped upper lip) established the diagnosis of Peters' plus syndrome. Analysis of his genomic DNA revealed a homozygous deletion in the beta1,3-galactosyltransferase-like gene (B3GALTL), a recently identified gene.

18726896|t|Expression of TSLC1, a candidate tumor suppressor gene mapped to chromosome 11q23, is downregulated in unfavorable neuroblastoma without promoter hypermethylation.
18726896|a|Although it has been well documented that loss of human chromosome 11q is frequently observed in primary neuroblastomas, the smallest region of overlap (SRO) has not yet been precisely identified. Previously, we performed array-comparative genomic hybridization (array-CGH) analysis for 236 primary neuroblastomas to search for genomic aberrations with high-resolution. In our study, we have identified the SRO of deletion (10-Mb or less) at 11q23. Within this region, there exists a TSLC1/IGSF4/CADM1 gene (Tumor suppressor in lung cancer 1/Immunoglobulin superfamily 4/Cell adhesion molecule 1), which has been identified as a putative tumor suppressor gene for lung and some other cancers. Consistent with previous observations, we have found that 35% of primary neuroblastomas harbor loss of heterozygosity (LOH) on TSLC1 locus. In contrast to other cancers, we could not detect the hypermethylation in its promoter region in primary neuroblastomas as well as neuroblastoma-derived cell lines. The clinicopathological analysis demonstrated that TSLC1 expression levels significantly correlate with stage, Shimada's pathological classification, MYCN amplification status, TrkA expression levels and DNA index in primary neuroblastomas. The immunohistochemical analysis showed that TSLC1 is remarkably reduced in unfavorable neuroblastomas. Furthermore, decreased expression levels of TSLC1 were significantly associated with a poor prognosis in 108 patients with neuroblastoma. Additionally, TSLC1 reduced cell proliferation in human neuroblastoma SH-SY5Y cells. Collectively, our present findings suggest that TSLC1 acts as a candidate tumor suppressor gene for neuroblastoma.

18699851|t|Integrated genomic and expression profiling in mantle cell lymphoma: identification of gene-dosage regulated candidate genes.
18699851|a|Mantle cell lymphoma (MCL) is characterized by the t(11;14)(q13;q32) translocation and several other cytogenetic aberrations, including heterozygous loss of chromosomal arms 1p, 6q, 11q and 13q and/or gains of 3q and 8q. The common intervals of chromosomal imbalance have been narrowed down using array-comparative genomic hybridization (CGH). However, the chromosomal intervals still contain many genes potentially involved in MCL pathogeny. Combined analysis of tiling-resolution array-CGH with gene expression profiling on 11 MCL tumours enabled the identification of genomic alterations and their corresponding gene expression profiles. Only subsets of genes located within given cytogenetic anomaly-intervals showed a concomitant change in mRNA expression level. The genes that showed consistent correlation between DNA copy number and RNA expression levels are likely to be important in MCL pathology. Besides several 'anonymous genes', we also identified various fully annotated genes, whose gene products are involved in cyclic adenosine monophosphate-regulated pathways (PRKACB), DNA damage repair, maintenance of chromosome stability and prevention of rereplication (ATM, ERCC5, FBXO5), energy metabolism (such as genes that are involved in the synthesis of proteins encoded by the mitochondrial genome) and signal transduction (ARHGAP29). Deregulation of these gene products may interfere with the signalling pathways that are involved in MCL tumour development and maintenance.

18694509|t|Association of TMPRSS2-ERG gene fusion with clinical characteristics and outcomes: results from a population-based study of prostate cancer.
18694509|a|BACKGROUND: The presence of the TMPRSS2-ERG fusion gene in prostate tumors has recently been associated with an aggressive phenotype, as well as recurrence and death from prostate cancer. These associations suggest the hypothesis that the gene fusion may be used as a prognostic indicator for prostate cancer. METHODS: In this study, fluorescent in situ hybridization (FISH) assays were used to assess TMPRSS2-ERG fusion status in a group of 214 prostate cancer cases from two population-based studies. The FISH assays were designed to detect both fusion type (deletion vs. translocation) and the number of fusion copies (single vs. multiple). Genotyping of four ERG and one TMPRSS2 SNPs using germline DNA was also performed in a sample of the cases (n = 127). RESULTS: Of the 214 tumors scored for the TMPRSS2-ERG fusion, 64.5% were negative and 35.5% were positive for the fusion. Cases with the TMPRSS2-ERG fusion did not exhibit reduced prostate cancer survival (HR = 0.92, 95% CI = 0.22-3.93), nor was there a significant difference in cause-specific survival when stratifying by translocation or deletion (HR = 0.84, 95% CI = 0.23-3.12) or by the number of retained fusion copies (HR = 1.22, 95% CI = 0.45-3.34). However, evidence for reduced prostate cancer-specific survival was apparent in those cases whose tumor had multiple copies of the fusion. The variant T allele of the TMPRSS2 SNP, rs12329760, was positively associated with TMPRSS2-ERG fusion by translocation (p = 0.05) and with multiple copies of the gene fusion (p = 0.03). CONCLUSION: If replicated, the results presented here may provide insight into the mechanism by which the TMPRSS2-ERG gene fusion arises and also contribute to diagnostic evaluations for determining the subset of men who will go on to develop metastatic prostate cancer.
18694509	1541	1551	rs12329760	SNP	rs12329760

18672102|t|GATA4 mutations in 486 Chinese patients with congenital heart disease.
18672102|a|Recent studies have reported germline mutations in GATA4 gene in some types of congenital heart disease (CHD). However, the prevalence of GATA4 mutations in CHD and the correlation between the GATA4 genotype and CHD phenotype have not been extensively studied. We screened germline mutations in the coding exons and the flanking intron sequences of the GATA4 gene in 486 CHD patients by denaturing high-performance liquid chromatography (DHPLC), and confirmed the mutations by sequencing. Nine distinct mutations including one small deletion mutation (46delS), two small insertion mutations (118-119insA and 125-126insAA), and six non-synonymous mutations (A6V, P163S, E359K, P407Q, S429T and A442V) were identified in 12 of the 486 patients (nine with ventricular septal defect, two with Tetralogy of Fallot, and one with endocardial cushion defect). Of them, two patients carrying E359K mutation were from two generations in one family with ventricular septal defect (VSD). Interestingly, a nucleotide insertion of c.1146+25insA in exon 6 was detected in five VSD patients, but not in 486 normal healthy controls. Our findings are useful in understanding the prevalence of GATA4 mutations and the correlation between the GATA4 genotype and the CHD phenotype in Chinese patients.
18672102	623	629	46delS	DNAMutation	|DEL|46|S
18672102	663	674	118-119insA	DNAMutation	|INS|118_119|A
18672102	679	691	125-126insAA	DNAMutation	|INS|125_126|AA
18672102	728	731	A6V	ProteinMutation	p|A|6|V
18672102	733	738	P163S	ProteinMutation	p|P|163|S
18672102	740	745	E359K	ProteinMutation	p|E|359|K
18672102	747	752	P407Q	ProteinMutation	p|P|407|Q
18672102	754	759	S429T	ProteinMutation	p|S|429|T
18672102	764	769	A442V	ProteinMutation	p|A|442|V
18672102	954	959	E359K	ProteinMutation	p|E|359|K
18672102	1088	1101	c.1146+25insA	DNAMutation	c|INS|1146+25|A

18622266|t|Chromosome 17: association of a large inversion polymorphism with corticosteroid response in asthma.
18622266|a|A 900-kb inversion exists within a large region of conserved linkage disequilibrium (LD) on chromosome 17. CRHR1 is located within the inversion region and associated with inhaled corticosteroid response in asthma. We hypothesized that CRHR1 variants are in LD with the inversion, supporting a potential role for natural selection in the genetic response to corticosteroids. We genotyped six single nucleotide polymorphisms (SNPs) spanning chromosome 17: 40,410,565-42,372,240, including four SNPs defining inversion status. Similar allele frequencies and strong LD were noted between the inversion and a CRHR1 SNP previously associated with lung function response to inhaled corticosteroids. Each inversion-defining SNP was strongly associated with inhaled corticosteroid response in adult asthma (P values 0.002-0.005). The CRHR1 response to inhaled corticosteroids may thus be explained by natural selection resulting from inversion status or by long-range LD with another gene. Additional pharmacogenetic investigations into regions of chromosomal diversity, including copy number variation and inversions, are warranted.

18606230|t|Premature stop codons in a facilitating EF-hand splice variant of CaV2.1 cause episodic ataxia type 2.
18606230|a|Premature stop codons in CACNA1A, which encodes the alpha(1A) subunit of neuronal P/Q-type (Ca(V)2.1) Ca(2+) channels, cause episodic ataxia type 2 (EA2). CACNA1A undergoes extensive alternative splicing, which contributes to the pharmacological and kinetic heterogeneity of Ca(V)2.1-mediated Ca(2+) currents. We identified three novel heterozygous stop codon mutations associated with EA2 in an alternately spliced exon (37A), which encodes part of an EF-hand motif required for Ca(2+)-dependent facilitation. One family had a C to G transversion (Y1854X). A dinucleotide deletion results in the same premature stop codon in a second family, and a further single nucleotide change leads to a different truncation (R1858X) in a de novo case of EA2. Expression studies of the Y1854X mutation revealed loss of Ca(V)2.1-mediated current. Because these mutations do not affect the alternate exon 37B, these findings reveal unexpected dependence of cerebellar function on intact exon 37A-containing Ca(V)2.1 channels.
18606230	652	658	Y1854X	ProteinMutation	p|Y|1854|X
18606230	818	824	R1858X	ProteinMutation	p|R|1858|X
18606230	878	884	Y1854X	ProteinMutation	p|Y|1854|X

18559591|t|A metastasis modifier locus on human chromosome 8p in uveal melanoma identified by integrative genomic analysis.
18559591|a|PURPOSE: To identify genes that modify metastatic risk in uveal melanoma, a type of cancer that is valuable for studying metastasis because of its remarkably consistent metastatic pattern and well-characterized gene expression signature associated with metastasis. EXPERIMENTAL DESIGN: We analyzed 53 primary uveal melanomas by gene expression profiling, array-based comparative genomic hybridization, array-based global DNA methylation profiling, and single nucleotide polymorphism-based detection of loss of heterozygosity to identify modifiers of metastatic risk. A candidate gene, leucine zipper tumor suppressor-1 (LZTS1), was examined for its effect on proliferation, migration, and motility in cultured uveal melanoma cells. RESULTS: In metastasizing primary uveal melanomas, deletion of chromosome 8p12-22 and DNA hypermethylation of the corresponding region of the retained hemizygous 8p allele were associated with more rapid metastasis. Among the 11 genes located within the deleted region, LZTS1 was most strongly linked to rapid metastasis. LZTS1 was silenced in rapidly metastasizing and metastatic uveal melanomas but not in slowly metastasizing and nonmetastasizing uveal melanomas. Forced expression of LZTS1 in metastasizing uveal melanoma cells inhibited their motility and invasion, whereas depletion of LZTS1 increased their motility. CONCLUSIONS: We have described a metastatic modifier locus on chromosome 8p and identified LZTS1 as a potential metastasis suppressor within this region. This study shows the utility of integrative genomic methods for identifying modifiers of metastatic risk in human cancers and may suggest new therapeutic targets in metastasizing tumor cells.

18492086|t|Variable phenotypic expression of homozygous familial hypobetalipoproteinaemia due to novel APOB gene mutations.
18492086|a|Homozygous familial hypobetalipoproteinaemia (Ho-FHBL) is a rare co-dominant disorder characterized by extremely low levels of low-density lipoprotein cholesterol (LDL-C) and apolipoprotein B (apoB). Most patients with Ho-FHBL have mutations in APOB gene resulting in truncated apoBs. Some patients are asymptomatic, while others have fatty liver, intestinal fat malabsorption and neurological dysfunctions. We investigated three adult subjects with severe hypobetalipoproteinaemia and a family history of FHBL. Proband FHBL-47 had liver cirrhosis with hepatocarcinoma and a renal carcinoma but no clinical manifestations related to FHBL. He was a compound heterozygote for a 7-bp deletion in exon 21 and a base insertion in exon 26 resulting in truncated apoBs (apoB-22.46/apoB-66.51). Proband FHBL-53, with severe hepatic steatosis and fibrosis, had a nonsense mutation in exon 19 resulting in a truncated apoB (apoB-20.61) and a rare nucleotide substitution in intron 14 (c.2068-4T>A). The latter was also present in her daughter, found to have low plasma LDL-C and apoB. Proband FHBL-82 had chronic diarrhoea and steatorrhoea. She was found to be homozygous for a nonsense mutation in exon 24 resulting in a truncated apoB (apoB-26.65). In adult subjects, the presence of chronic liver disease and chronic diarrhoea, when associated with severe hypobetalipoproteinaemia, may lead to the diagnosis of Ho-FHBL.
18492086	1088	1099	c.2068-4T>A	DNAMutation	c|T|2068-4|A

18397285|t|L1503R is a member of group I mutation and has dominant-negative effect on secretion of full-length VWF multimers: an analysis of two patients with type 2A von Willebrand disease.
18397285|a|Type 2A von Willebrand disease (VWD) is characterized by decreased platelet-dependent function of von Willebrand factor (VWF); this in turn is associated with an absence of high-molecular-weight multimers. Sequence analysis of the VWF gene from two unrelated type 2A VWD patients showed an identical, novel, heterozygous T-->G transversion at nucleotide 4508, resulting in the substitution of L1503R in the VWF A2 domain. This substitution, which was not found in 60 unrelated normal individuals, was introduced into a full-length VWF cDNA and subsequently expressed in 293T cells. Only trace amount of the mutant VWF protein was secreted but most of the same was retained in 293T cells. Co-transfection experiment of both wild-type and mutant plasmids indicated the dominant-negative mechanism of disease development; as more of mutant DNA was transfected, VWF secretion was impaired in the media, whereas more of VWF was stored in the cell lysates. Molecular dynamic simulations of structural changes induced by L1503R indicated that the mean value of all-atom root-mean-squared-deviation was shifted from those with wild type or another mutation L1503Q that has been reported to be a group II mutation, which is susceptible to ADAMTS13 proteolysis. Protein instability of L1503R may be responsible for its intracellular retention and perhaps the larger VWF multimers, containing more mutant VWF subunits, are likely to be mal-processed and retained within the cell.
18397285	0	6	L1503R	ProteinMutation	p|L|1503|R
18397285	501	538	T-->G transversion at nucleotide 4508	DNAMutation	c|T|4508|G
18397285	573	579	L1503R	ProteinMutation	p|L|1503|R
18397285	1194	1200	L1503R	ProteinMutation	p|L|1503|R
18397285	1329	1335	L1503Q	ProteinMutation	p|L|1503|Q
18397285	1455	1461	L1503R	ProteinMutation	p|L|1503|R

18372165|t|Molecular and clinical characterization in Japanese and Korean patients with Hailey-Hailey disease: six new mutations in the ATP2C1 gene.
18372165|a|BACKGROUND: The autosomal dominant disorder Hailey-Hailey disease (HHD) results from mutations in the ATP2C1 gene, which encodes the human secretory pathway Ca2+/Mn2+ -ATPase protein 1. To date, over 90 pathological mutations scattered throughout ATP2C1 have been described with no indication of mutational hotspots or clustering of mutations. No paradigm for genotype-phenotype correlation has emerged. OBJECTIVES: To determine the pathogenic ATP2C1 abnormality in additional patients with HHD in order to provide further contributions to the understanding of the molecular basis of this disorder and to add the data to the known mutation database. METHODS: In this study, we investigated eight unrelated Japanese and Korean patients with HHD. We performed direct nucleotide sequencing of the ATP2C1 gene in all patients and RT-PCR analysis, using RNA extracted from a skin biopsy, in a patient with the mildest clinical features. RESULTS: We identified seven different heterozygous mutations in seven of the eight investigated patients, including three new single nucleotide deletion/duplication mutations: c.520delC; c.681dupA; c.956delC, three new donor splice site mutations: c.360+1G>C; c.899+1G>T; c.1570+2T>C, as well as a previously described nonsense mutation: p.Arg153X. RT-PCR analysis in the mildest affected patient with a heterozygous c.360+1G>C mutation, demonstrated expression of a short in-frame mutant transcript with exon 5 skipping, which may account for the mild phenotype. CONCLUSIONS: The results expand the known mutation spectrum in HHD and show the importance of RNA analysis for understanding the genotype-phenotype correlations more precisely.
18372165	1247	1256	c.520delC	DNAMutation	c|DEL|520|C
18372165	1258	1267	c.681dupA	DNAMutation	c|DUP|681|A
18372165	1269	1278	c.956delC	DNAMutation	c|DEL|956|C
18372165	1319	1329	c.360+1G>C	DNAMutation	c|G|360+1|C
18372165	1331	1341	c.899+1G>T	DNAMutation	c|G|899+1|T
18372165	1343	1354	c.1570+2T>C	DNAMutation	c|T|1570+2|C
18372165	1409	1418	p.Arg153X	ProteinMutation	p|R|153|X
18372165	1488	1498	c.360+1G>C	DNAMutation	c|G|360+1|C

18246537|t|Molecular allelokaryotyping of early-stage, untreated chronic lymphocytic leukemia.
18246537|a|BACKGROUND: To the authors' knowledge, genetic abnormalities in early-stage chronic lymphocytic leukemia (CLL) have not been examined fully. Single nucleotide polymorphism (SNP) genomic array (SNP-chip) is a new tool that can detect copy number changes and uniparental disomy (UPD) over the entire genome with very high resolution. METHODS: The authors performed SNP-chip analysis on 56 samples from patients with early-stage, untreated CLL. To validate the SNP-chip data, fluorescence in situ hybridization (FISH) analysis was performed at selected sites. Expression levels of ZAP-70 and the mutational status of immunoglobulin heavy-chain gene also were examined. RESULTS: SNP-chip analysis easily detected nearly all changes that were identified by FISH, including trisomy 12, deletion of TP53 (17p13), deletion of ATM (11q22), and deletion of 13q14. Only 10 of 56 CLL samples (18%) had no genomic abnormalities. Excluding the 4 common abnormalities mentioned above, 25 CLL samples (45%) had a total of 45 copy number changes detected by SNP-chip analysis. Four samples had 6q deletion at 6q21 that involved the AIM1 gene. UPD was detected in 4 samples; 2 samples involved whole chromosome 13 resulting in homozygous deletion of micro-RNA-15a (miR-15a)/miR-16-1. CLL samples with deletion of 13q14 and trisomy 12 were mutually exclusive. CONCLUSIONS: Genetic abnormalities, including whole chromosome 13 UPD, are very common events in early-stage CLL. SNP-chip analysis can detect small genetic abnormalities in CLL and may be able to support or even supplant FISH and cytogenetics.

18210757|t|No association with risk for colorectal cancer of the insertion/deletion polymorphism which affects levels of angiotensin-converting enzyme.
18210757|a|BACKGROUND: In the light of the established association of angiotensin-converting enzyme (ACE) with several types of cancer, the possible contribution of the insertion/deletion (I/D) polymorphism that affects ACE gene expression, in the development of colorectal cancer was investigated. MATERIALS AND METHODS: DNA samples of 92 patients with colorectal cancer (adenocarcinomas) and 102 healthy controls were examined by allele-specific polymerase chain reaction followed by electrophoretic analysis. The resulting allele and genotype frequencies of the patients were compared to those of the controls by Fischer's exact test and odds ratios. RESULTS: No statistical differences were observed between healthy controls and patients with colorectal cancer regarding either genotype distribution or low expression I allele frequency. CONCLUSION: The ACE I/D polymorphism is not a genetic predisposing factor concerning the risk for colorectal cancer.

18189233|t|RNASEL and RNASEL-inhibitor variation and prostate cancer risk in Afro-Caribbeans.
18189233|a|BACKGROUND: Afro-Caribbeans from Tobago are at high risk of developing prostate cancer. This elevated risk of prostate cancer is shared by populations of African ancestry living in diverse environments in the Western hemisphere. Variation in the ribonuclease L (RNASEL) gene has recently been reported to be associated with an increased risk of prostate cancer. However, whether RNASEL variation contributes to the increased risk of prostate cancer observed in populations of African ancestry remains unclear. METHODS: We resequenced the positional candidate gene RNASEL in 48 prostate cancer cases and genotyped the previously reported R462Q and D541E polymorphisms in 230 prostate cancer cases and 458 controls. We also examined the inhibitor of RNASEL (ABCE1) for variation associated with prostate cancer risk. RESULTS: We found no evidence of association between R462Q and D541E polymorphisms and prostate cancer risk in our case/control analysis. A novel variant (K294E) was identified in a single heterozygous individual with prostate cancer. We also observed a 20 bp insertion/deletion polymorphism 1,109 bp upstream of the initiation codon, but this variant was not associated with prostate cancer. We identified 16 single nucleotide polymorphisms in the ABCE1 gene, only 3 of which had a minor allele frequency >5%. A common A/G transition -1,071 bp from the transcriptional start site was genotyped and showed no evidence of association with prostate cancer. CONCLUSIONS: Our results suggest that common variation in the putative prostate cancer susceptibility gene, RNASEL, or its inhibitor does not contribute significantly to prostate cancer risk in this Afro-Caribbean population.
18189233	720	725	R462Q	ProteinMutation	p|R|462|Q
18189233	730	735	D541E	ProteinMutation	p|D|541|E
18189233	951	956	R462Q	ProteinMutation	p|R|462|Q
18189233	961	966	D541E	ProteinMutation	p|D|541|E
18189233	1053	1058	K294E	ProteinMutation	p|K|294|E
18189233	1418	1442	A/G transition -1,071 bp	DNAMutation	c|A|-1071|G

18166824|t|Genetic investigation of four meiotic genes in women with premature ovarian failure.
18166824|a|OBJECTIVE: The goal of this study was to determine whether mutations of meiotic genes, such as disrupted meiotic cDNA (DMC1), MutS homolog (MSH4), MSH5, and S. cerevisiae homolog (SPO11), were associated with premature ovarian failure (POF). DESIGN: Case-control study. METHODS: Blood sampling, karyotype, hormonal dosage, ultrasound, and ovarian biopsy were carried out on most patients. However, the main outcome measure was the sequencing of genomic DNA from peripheral blood samples of 41 women with POF and 36 fertile women (controls). RESULTS: A single heterozygous missense mutation, substitution of a cytosine residue with thymidine in exon 2 of MSH5, was found in two Caucasian women in whom POF developed at 18 and 36 years of age. This mutation resulted in replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29 (P29S). Neither 36 control women nor 39 other patients with POF possessed this genetic perturbation. Another POF patient of African origin showed a homozygous nucleotide change in the tenth of DMC1 gene that led to an alteration of the amino acid composition of the protein (M200V). CONCLUSIONS: The symptoms of infertility observed in the DMC1 homozygote mutation carrier and in both patients with a heterozygous substitution in exon 2 of the MSH5 gene provide indirect evidence of the role of genes involved in meiotic recombination in the regulation of ovarian function. MSH5 and DMC1 mutations may be one explanation for POF, albeit uncommon.
18166824	950	954	P29S	ProteinMutation	p|P|29|S
18166824	1224	1229	M200V	ProteinMutation	p|M|200|V

19276632|t|Mutation analysis of FOXF2 in patients with disorders of sex development (DSD) in combination with cleft palate.
19276632|a|In contrast to disorders of sexual differentiation caused by lack of androgen production or inhibited androgen action, defects affecting development of the bipotent genital anlagen have rarely been investigated in humans. We have previously documented that the transcription factor FOXF2 is highly expressed in human foreskin. Moreover, Foxf2 knockout mice present with cleft palate in combination with hypoplasia of the genital tubercle. We hypothesized that humans with disorders of sex development (DSD) in combination with cleft palate could have mutations in the FOXF2 gene. Eighteen children with DSD and cleft palate were identified in the L  beck DSD database (about 1,500 entries). Genomic DNA sequence analysis of the FOXF2 gene was performed and compared with 10 normal female and 10 normal male controls, respectively. Two heterozygous DNA sequence variations were solely present in one single patient each but in none of the 20 normal controls: a duplication of GCC (c.97GCC[9]+[10]) resulting in an extra alanine within exon 1 and a 25*G>A substitution in the 3'-untranslated region. Two patients carried a c.262G>A sequence variation predicting for an Ala88Thr exchange which was also detected in 2 normal controls. Two silent mutations, c.1272C>T (Ser424Ser) and c.1284T>C (Tyr428Tyr), respectively, occurred in the coding region of exon 2, again in both patients and normal controls. In conclusion, the majority of the detected sequence alterations were polymorphisms without obvious functional relevance. However, it cannot be excluded that the 2 unique DNA sequence alterations could have affected FOXF2 on the mRNA or protein level thus contributing to the observed disturbances in genital and palate development.
19276632	1093	1108	c.97GCC[9]+[10]	DNAMutation	c|DUP|97|GCC|9-10
19276632	1160	1166	25*G>A	DNAMutation	c|G|*25|A
19276632	1234	1242	c.262G>A	DNAMutation	c|G|262|A
19276632	1280	1288	Ala88Thr	ProteinMutation	p|A|88|T
19276632	1366	1375	c.1272C>T	DNAMutation	c|C|1272|T
19276632	1377	1386	Ser424Ser	ProteinMutation	p|S|424|S
19276632	1392	1401	c.1284T>C	DNAMutation	c|T|1284|C
19276632	1403	1412	Tyr428Tyr	ProteinMutation	p|Y|428|Y

17968299|t|Analysis of -1082 IL-10 gene polymorphism in Iranian patients with generalized aggressive periodontitis.
17968299|a|BACKGROUND: Periodontitis is a multifactorial disease and its severe forms, such as aggressive periodontitis, are suggested to have a genetic basis. Among the genetic factors, polymorphisms in cytokine genes have recently been described in susceptibility to periodontitis. IL-10 is a multi-functional cytokine thought to play a role in the pathogenesis of periodontitis. A substitution G/A polymorphism in the promoter region of the IL-10 gene at position -1082 has been associated with different amounts of IL-10 production. The aim of the present study was to investigate the possible links between -1082(G/A) polymorphism of the IL-10 gene and the generalized form of aggressive periodontitis. MATERIAL/METHODS: This study included 52 Iranian Khorasanian (north-east province of Iran) subjects suffering from generalized aggressive periodontitis referred to the Periodontology Department of Mashhad Dental School. They were compared to 61 age and sex-matched healthy controls of the same race. DNA was isolated from peripheral blood cells and genotyping was performed by means of the amplification refractory mutation system polymerase chain reaction (ARMS-PCR) method. Data were analyzed using the chi-squared test. RESULTS: There was no marked difference in genotype frequencies between the controls and generalized aggressive periodontitis patients (p=0.585). Moreover, no association between patients and normal subjects was found in their allele frequency (p=0.329). CONCLUSIONS: We conclude that the polymorphic nucleotide A at position -1082 of the IL-10 gene is not associated with generalized aggressive periodontitis in the Iranian population.
17968299	491	494	G/A	DNAMutation	|G||A
17968299	706	716	-1082(G/A)	DNAMutation	c|G|-1082|A

17961316|t|In vitro expression of beta-thalassaemia gene (IVS1-1G>C) reveals complete inactivation of the normal 5' splice site and alternative aberrant RNA splicing.
17961316|a|We previously reported a case of heterozygous beta-thalassaemia with IVS1-1G > C substitution in the beta-globin gene and a non-detectable level of mutant mRNA in the patient's reticulocytes. The purpose of this study was to determine whether the transcription and RNA splicing and processing of the mutant gene occurred. We analysed the expression of the mRNA encoded by the cloned mutant gene in COS-1 cells by reverse transcription-polymerase chain reaction followed by agarose gel electrophoresis and nucleotide sequencing. The G > C mutation completely inactivated the normal 5' splice site and resulted in the activation of two cryptic 5' splice sites, located 16 and 38 nt upstream of the normal site. The usage of these two cryptic sites accords with the findings of reports on IVS1-1G > A or IVS1-1G > C substitution of exon 1 of the beta-globin gene. Additional experiments that involved transfection of equal amounts of both normal and mutant vectors into COS-1 cells indicated the presence of mutant mRNAs. In conclusion, the beta-thalassaemia gene (IVS1-1G > C) was expressed in transfected cells, but showed aberrant RNA splicing. Further studies will be required to clarify the molecular mechanism that results in severe reduction in the mutant mRNA level in vivo.
17961316	47	56	IVS1-1G>C	DNAMutation	c|G|IVS1-1|C
17961316	225	236	IVS1-1G > C	DNAMutation	c|G|IVS1-1|C
17961316	688	693	G > C	DNAMutation	|G||C
17961316	942	953	IVS1-1G > A	DNAMutation	c|G|IVS1-1|A
17961316	957	968	IVS1-1G > C	DNAMutation	c|G|IVS1-1|C
17961316	1218	1229	IVS1-1G > C	DNAMutation	c|G|IVS1-1|C

17935240|t|Somatic and gonadal mosaicism in X-linked retinitis pigmentosa.
17935240|a|The g.ORF15 + 652-653delAG mutation in the RPGR gene is the most frequent mutation in X-linked retinitis pigmentosa (XLRP). The objective of this study was to investigate the possibility of mosaicism in an XLRP family. Eight subjects in the RP family were recruited. Blood samples were collected for DNA extraction. Haplotype analysis and mutational screening on the RPGR gene were performed. Additionally, samples of hair follicles and buccal cells from the mother of the proband were acquired for DNA extraction and molecular analysis. Phenotype was characterized with routine ophthalmic examination, Goldmann perimetry, electroretinography, and color fundus photography. A g.ORF15 + 652-653delAG mutation was identified in second- and third-generation patients/carriers. A first-generation female, who was considered to be an obligate carrier, demonstrated a normal phenotype as well as a normal genotype in lymphocytic DNA, indicating the gonadal mosaicism; however, a heterozygous AG-deletion at nucleotide 652 and 653 was identified in the genomic DNA of hair follicles, hair shaft, and buccal cells, indicating that the mutation is somatic. In conclusion, we reported on a family in which an asymptomatic woman with somatic-gonadal mosaicism for a RPGR gene mutation transmitted the mutation to an asymptomatic daughter and to a son with XLRP. Gonadal mosaicism may be responsible for a proportion of multiplex or simplex RP families, in which more than 50% of all cases of RP are found. (c) 2007 Wiley-Liss, Inc.
17935240	68	90	g.ORF15 + 652-653delAG	DNAMutation	g|DEL|ORF15+652_653|AG
17935240	740	762	g.ORF15 + 652-653delAG	DNAMutation	g|DEL|ORF15+652_653|AG

17909797|t|Impact of the CCR5 gene polymorphism on the survival of metastatic melanoma patients receiving immunotherapy.
17909797|a|PURPOSE: Chemokines influence both tumor progression and anti-tumor immune response. A 32-bp-deletion polymorphism in the chemokine receptor 5 gene (CCR5Delta32) has been shown to result in a non-functional protein. This study was aimed at evaluating the potential impact of this gene polymorphism on disease progression and treatment outcome in patients with melanoma. PATIENTS AND METHODS: CCR5 genotyping was performed by PCR on DNA extracted from serum samples of 782 cutaneous melanoma patients with known disease history and long-term clinical follow-up. Genotypes were correlated with patient survival and types of treatment. RESULTS: Of 782 melanoma patients, 90 (11.5%) were heterozygous and 12 (1.5%) were homozygous for CCR5Delta32. Analyzing the complete cohort, the disease-specific survival from date of primary diagnosis was not influenced by CCR5 status. Similarly, no significant impact could be detected on the treatment outcome of stage III patients. In 139 stage IV patients receiving immunotherapy, CCR5Delta32 was associated with a decreased survival compared to patients not carrying the deletion (median 12.5 vs. 20.3 months, P = 0.029). Multivariate analysis revealed the CCR5 genotype as an independent factor impacting disease-specific survival in this patient population (P = 0.002), followed by gender (P = 0.019) and pathological classification of the primary (pT; P = 0.022). CONCLUSION: The presence of the CCR5Delta32 polymorphism in patients with stage IV melanoma results in a decreased survival following immunotherapy and may help to select patients less likely to benefit from this type of treatment.
17909797	263	270	Delta32	DNAMutation	|DEL||32
17909797	845	852	Delta32	DNAMutation	|DEL||32
17909797	1134	1141	Delta32	DNAMutation	|DEL||32
17909797	1553	1560	Delta32	DNAMutation	|DEL||32

17641158|t|Characterization of the BMPR2 5'-untranslated region and a novel mutation in pulmonary hypertension.
17641158|a|RATIONALE: Familial pulmonary arterial hypertension results from heterozygous inactivating mutations of the BMPR2 gene. Traditional mutation analysis identifies pathogenic mutations in some 70% of linked families. We hypothesized that the apparent shortfall is due to mutations located in the promoter region of the gene, resulting in abnormal gene regulation. OBJECTIVES: To identify mutations in untranslated sequence regulating BMPR2 transcription. METHODS: DNA upstream of the coding region was analyzed by direct sequencing in 16 families. Reverse transcription-polymerase chain reaction analysis and rapid amplification of cDNA ends of normal human lung RNA were used to investigate transcription of this region. Transcript levels were assessed by allele-specific expression analysis and inhibition of nonsense-mediated decay in lymphoblastoid cell lines. MEASUREMENTS AND MAIN RESULTS: The wild-type transcriptional start site of BMPR2 was defined, 1,148 bp upstream of the ATG. Within this region, we identified a double-substitution mutation, predicted to form a cryptic translational start site, in one family. The mutant transcript contains a premature stop codon predicted to trigger nonsense-mediated decay. Expression analysis in the patient's cell line indeed showed reduced expression of the mutant transcript that could be restored to normal by inhibiting nonsense-mediated decay. CONCLUSIONS: Activation of a cryptic translation initiation site is a novel mutational mechanism in this disorder. These results demonstrate that the 5'-untranslated region of BMPR2 is considerably longer than previously thought, emphasizing the need to fully characterize the BMPR2 promoter and the importance of analyzing noncoding regions in patients with pulmonary arterial hypertension who are negative for mutations within the coding region and intron-exon junctions.

17395743|t|Identification of PVT1 as a candidate gene for end-stage renal disease in type 2 diabetes using a pooling-based genome-wide single nucleotide polymorphism association study.
17395743|a|To identify genetic variants contributing to end-stage renal disease (ESRD) in type 2 diabetes, we performed a genome-wide analysis of 115,352 single nucleotide polymorphisms (SNPs) in pools of 105 unrelated case subjects with ESRD and 102 unrelated control subjects who have had type 2 diabetes for > or =10 years without macroalbuminuria. Using a sliding window statistic of ranked SNPs, we identified a 200-kb region on 8q24 harboring three SNPs showing substantial differences in allelic frequency between case and control pools. These SNPs were genotyped in individuals comprising each pool, and strong evidence for association was found with rs2720709 (P = 0.000021; odds ratio 2.57 [95% CI 1.66-3.96]), which is located in the plasmacytoma variant translocation gene PVT1. We sequenced all exons, exon-intron boundaries, and the promoter of PVT1 and identified 47 variants, 11 of which represented nonredundant markers with minor allele frequency > or =0.05. We subsequently genotyped these 11 variants and an additional 87 SNPs identified through public databases in 319-kb flanking rs2720709 ( approximately 1 SNP/3.5 kb); 23 markers were associated with ESRD at P < 0.01. The strongest evidence for association was found for rs2648875 (P = 0.0000018; 2.97 [1.90-4.65]), which maps to intron 8 of PVT1. Together, these results suggest that PVT1 may contribute to ESRD susceptibility in diabetes.
17395743	822	831	rs2720709	SNP	rs2720709
17395743	1265	1274	rs2720709	SNP	rs2720709
17395743	1409	1418	rs2648875	SNP	rs2648875

17391797|t|The phosphatidylethanolamine N-methyltransferase gene V175M single nucleotide polymorphism confers the susceptibility to NASH in Japanese population.
17391797|a|BACKGROUND/AIMS: The genetic predisposition on the development of nonalcoholic steatohepatitis (NASH) has been poorly understood. A functional polymorphism Val175Met was reported in phosphatidylethanolamine N-methyltransferase (PEMT) that catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine. The aim of this study was to investigate whether the carriers of Val175Met variant impaired in PEMT activity are more susceptible to NASH. METHODS: Blood samples of 107 patients with biopsy-proven NASH and of 150 healthy volunteers were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism. RESULTS: Val175Met variant allele of the PEMT gene was significantly more frequent in NASH patients than in healthy volunteers (p<0.001), and carriers of Val175Met variant were significantly more frequent in NASH patients than in healthy volunteers (p<0.01). Among NASH patients, body mass index was significantly lower (p<0.05), and non-obese patients were significantly more frequent (p<0.001) in carriers of Val175Met variant than in homozygotes of wild type PEMT. CONCLUSIONS: Val175Met variant of PEMT could be a candidate molecule that determines the susceptibility to NASH, because it is more frequently observed in NASH patients and non-obese persons with Val175Met variant of PEMT are facilitated to develop NASH.
17391797	54	59	V175M	ProteinMutation	p|V|175|M
17391797	306	315	Val175Met	ProteinMutation	p|V|175|M
17391797	531	540	Val175Met	ProteinMutation	p|V|175|M
17391797	806	815	Val175Met	ProteinMutation	p|V|175|M
17391797	951	960	Val175Met	ProteinMutation	p|V|175|M
17391797	1208	1217	Val175Met	ProteinMutation	p|V|175|M
17391797	1278	1287	Val175Met	ProteinMutation	p|V|175|M
17391797	1461	1470	Val175Met	ProteinMutation	p|V|175|M

17292585|t|Semi-automated, reverse-hybridization detection of multiple mutations causing hereditary fructose intolerance.
17292585|a|Hereditary fructose intolerance (HFI) is a potentially fatal nutritional disease that is caused by mutations in the liver isoenzyme of fructoaldolase (aldolase B). Our aim was to evaluate a diagnostic assay capable of simultaneously analyzing three-point mutations and a small deletion in the aldolase B (ALDOB) gene. The test under investigation is based on multiplex DNA amplification and hybridization to membrane strips presenting a parallel array of allele-specific oligonucleotide probes. We used the novel reverse-hybridization (RH) protocol to analyze 54 individuals previously genotyped by direct sequencing. RH genotyping for ALDOB mutations Delta4E4, A149P, A174D, and N334K was in complete concordance with results obtained by DNA sequencing. The procedure is rapid (<6h) and may be automated to a large extent. The RH assay tested in this study represents an accurate and robust screening tool to identify common ALDOB mutations.
17292585	773	778	A149P	ProteinMutation	p|A|149|P
17292585	780	785	A174D	ProteinMutation	p|A|174|D
17292585	791	796	N334K	ProteinMutation	p|N|334|K

17199794|t|Angiotensin converting enzyme gene polymorphisms do not predict the course of idiopathic nephrotic syndrome in Swiss children.
17199794|a|AIM: Contradictory reports exist about a correlation of angiotensin I converting enzyme (ACE) gene polymorphisms to the outcome of idiopathic nephrotic syndrome (INS) in children. We investigated the frequency of ACE polymorphisms and their impact on the clinical course of INS in children in a Swiss hospital. METHODS: The ACE gene polymorphism (I, insertion; D, deletion) was assessed in 32 children - 22 with steroid-sensitive INS and 10 with steroid-resistant INS - with a median age at onset of INS of 2.9 years (range 1.1-15.0). Polymerase chain reaction amplification was performed on genomic DNA isolated from blood leucocytes. Results were correlated to clinical course and renal morphology. RESULTS: The ACE genotype was I/I, I/D and D/D in two, 12 and eight patients, respectively, with steroid-sensitive INS, and in one, eight and one patient, respectively, with steroid resistance. Renal morphology, available in 25 patients showed minimal change glomerulopathy in 17 patients (14 steroid-sensitive; three steroid-resistant) and focal segmental glomerulosclerosis in eight (one steroid-sensitive; seven steroid-resistant). There was no significant correlation between ACE genotype and steroid responsiveness, histology or outcome. ACE genotype was I/I, I/D and D/D in none, 12 and five patients, respectively, with minimal change glomerulopathy, and in one, five and two patients, respectively, with focal segmental glomerulosclerosis. Six patients with steroid-resistant nephrotic syndrome went into end stage renal disease; ACE genotype was I/I in one and I/D in five, but none were D/D. CONCLUSION: In contrast to previous reports, ACE gene polymorphism is irrelevant for clinical outcome, steroid responsiveness or morphology in Swiss children with INS.

17166870|t|Association between an endoglin gene polymorphism and systemic sclerosis-related pulmonary arterial hypertension.
17166870|a|Systemic sclerosis (SSc) is a connective tissue disorder characterized by early generalized microangiopathy with disturbed angiogenesis. Endoglin gene (ENG) encodes a transmembrane glycoprotein which acts as an accessory receptor for the transforming growth factor-beta (TGF-beta) superfamily, and is crucial for maintaining vascular integrity. A 6-base insertion in intron 7 (6bINS) of ENG has been reported to be associated with microvascular disturbance. OBJECTIVES: Our objective was to investigate the relationship between 6bINS and the vascular complication pulmonary arterial hypertension (PAH) in SSc in a French Caucasian population. METHODS: Two hundred eighty SSc cases containing 29/280 having PAH diagnosed by catheterism were compared with 140 patients with osteoarthritis. Genotyping was performed by polymerase-chain-reaction-based fluorescence and direct sequencing of genomic DNA. RESULTS: The polymorphism was in Hardy-Weinberg equilibrium. We observed a significant lower frequency of 6bINS allele in SSc patients with associated PAH compared with controls [10.3 vs 23.9%, P = 0.01; odds ratio (OR) 0.37, 95% confidence interval (CI) 0.15-0.89], and a trend in comparison with SSc patients without PAH (10.3 vs 20.3%, P = 0.05; OR: 0.45, 95% CI: 0.19-1.08). Genotypes carrying allele 6bINS were also less frequent in SSc patients with PAH than in controls (20.7 vs 42.9%, P = 0.02). CONCLUSIONS: Thus the frequency of 6bINS differs between SSc patients with or without PAH, suggesting the implication of ENG in this devastating vascular complication of SSc.
17166870	491	496	6bINS	DNAMutation	|INS||6
17166870	642	647	6bINS	DNAMutation	|INS||6
17166870	1119	1124	6bINS	DNAMutation	|INS||6
17166870	1418	1423	6bINS	DNAMutation	|INS||6
17166870	1552	1557	6bINS	DNAMutation	|INS||6

17160997|t|Severe beta(0) thalassemia/hemoglobin E disease caused by de novo 22-base pair duplication in the paternal allele of beta globin gene.
17160997|a|beta Thalassemia is a major public health concern in Southeast Asia. A prevention program has been implemented in Thailand comprising mass carrier screening and genetic testing. In this study, a Thai girl with severe beta thalassemia/hemoglobin (Hb) E disease was born from the mother with Hb E trait and the genotypically normal father. DNA sequencing revealed novel 22-bp tandem duplication in the paternal allele of beta globin gene, producing a severely truncated product. A short recurring nucleotide at the insertion site suggested a predisposition to this mutation. Therefore, spontaneous beta globin mutations occasionally occur in normal population. Its clinical significance is noteworthy in countries with high prevalence of beta thalassemia.

17157502|t|Quantitative analysis of CAPN3 transcripts in LGMD2A patients: involvement of nonsense-mediated mRNA decay.
17157502|a|Limb girdle muscular dystrophy type 2A (LGMD2A) is caused by single or small nucleotide changes widespread along the CAPN3 gene, which encodes the muscle-specific proteolytic enzyme calpain-3. About 356 unique allelic variants of CAPN3 have been identified to date. We performed analysis of the CAPN3 gene in LGMD2A patients at both the mRNA level using reverse transcription-PCR, and at the DNA level using PCR and denaturing high performance liquid chromatography. In four patients, we detected homozygous occurrence of a missense mutation or an in-frame deletion at the mRNA level although the DNA was heterozygous for this mutation in conjunction with a frame-shift mutation. The relationship observed in 12 patients between the quantity of CAPN3 mRNA, determined using real-time PCR, and the genotype leads us to propose that CAPN3 mRNAs which contain frame-shift mutations are degraded by nonsense-mediated mRNA decay. Our results illustrate the importance of DNA analysis for reliable establishment of mutation status, and provide a new insight into the process of mRNA decay in cells of LGMD2A patients.

17079875|t|Putative association of RUNX1 polymorphisms with IgE levels in a Korean population.
17079875|a|RUNX1, a member of the runt domain gene family of transcription factors, encodes a heterodimeric transcription factor and regulates the expression of various genes related to hematopoiesis and myeloid differentiation. RUNX1 has been one of the target genes for research into various autoimmune diseases due to its properties as a transcription factor and functional distribution for chromosomal translocation. In an effort to identify additional gene polymorphisms in which variants have been implicated in asthma, we investigated the genetic polymorphisms in RUNX1 to evaluate it as a potential candidate gene for a host genetic study of asthma and IgE production. We identified 19 sequence variants by direct DNA sequencing in 24 individuals of which four common variants were selected for genotyping in our asthma cohort (1,055 asthmatic patients, 384 normal controls). Using logistic regression analysis for association with the risk of asthma, while controlling for age, gender, and smoking status as covariates, no significant associations with the risk of asthma were detected. However, two polymorphisms in the promoter region (-2084G>C and -1282G>A) showed a marginal association with total IgE levels (0.03 and 0.03 in recessive models, respectively). Our findings suggest that polymorphisms in RUNX1 might be one of the genetic factors for the regulation of IgE production.
17079875	1220	1228	-2084G>C	DNAMutation	c|G|-2084|C
17079875	1233	1241	-1282G>A	DNAMutation	c|G|-1282|A

17065198|t|Analysis of skin cancer risk factors in immunosuppressed renal transplant patients shows high levels of UV-specific tandem CC to TT mutations of the p53 gene.
17065198|a|Immunosuppressed renal transplant recipients (RTRs) are predisposed to non-melanoma skin cancers (NMSCs), predominantly squamous cell carcinomas (SCCs). We have analyzed skin lesions from RTRs with aggressive tumors for p53 gene modifications, the presence of Human Papillomas Virus (HPV) DNA in relation to the p53 codon 72 genotype and polymorphisms of the XPD repair gene. We detected 24 p53 mutations in 15/25 (60%) NMSCs, 1 deletion and 23 base substitutions, the majority (78%) being UV-specific C to T transitions at bipyrimidine sites. Importantly, 35% (6/17) are tandem mutations, including 4 UV signature CC to TT transitions possibly linked to modulated DNA repair caused by the immunosuppressive drug cyclosporin A (CsA). We found 8 p53 mutations in 7/17 (41%) precancerous actinic keratosis (AK), suggesting that p53 mutations are early events in RTR skin carcinogenesis. Immunohistochemical analysis shows a good correlation between p53 accumulation and mutations. HPV DNA was detected in 78% of skin lesions (60% Basal Cell Carcinomas, 82%AK and 79% SCCs). Thus, immunosuppression has increased the risk of infections by HPVs, predominantly epidermodysplasia verruciformis, speculated to play a role in skin cancer development. No association is found between HPV status and p53 mutation. Moreover, p53 codon 72 or frequencies of three XPD genotypes of RTRs are comparable with control populations. The p53 mutation spectrum, presenting a high level of CC to TT mutations, shows that the UV component of sunlight is the major risk factor and modulated DNA repair by immunosuppressive drug treatment may be significant in the skin carcinogenesis of RTRs.

17059986|t|A novel splicing mutation in SLC12A3 associated with Gitelman syndrome and idiopathic intracranial hypertension.
17059986|a|We report a case of Gitelman syndrome (GS) in a dizygotic twin who presented at 12 years of age with growth delay, metabolic alkalosis, hypomagnesemia and hypokalemia with inappropriate kaliuresis, and idiopathic intracranial hypertension with bilateral papilledema (pseudotumor cerebri). The patient, her twin sister, and her mother also presented with cerebral cavernous malformations. Based on the early onset and normocalciuria, Bartter syndrome was diagnosed first. However, mutation analysis showed that the proband is a compound heterozygote for 2 mutations in SLC12A3: a substitution of serine by leucine at amino acid position 555 (p.Ser555Leu) and a novel guanine to cytosine transition at the 5' splice site of intron 22 (c.2633+1G>C), providing the molecular diagnosis of GS. These mutations were not detected in 200 normal chromosomes and cosegregated within the family. Analysis of complementary DNA showed that the heterozygous nucleotide change c.2633+1G>C caused the appearance of 2 RNA molecules, 1 normal transcript and 1 skipping the entire exon 22 (r.2521_2634del). Supplementation with potassium and magnesium improved clinical symptoms and resulted in catch-up growth, but vision remained impaired. Three similar associations of Bartter syndrome/GS with pseudotumor cerebri were found in the literature, suggesting that electrolyte abnormalities and secondary aldosteronism may have a role in idiopathic intracranial hypertension. This study provides further evidence for the phenotypical heterogeneity of GS and its association with severe manifestations in children. It also shows the independent segregation of familial cavernomatosis and GS.
17059986	754	765	p.Ser555Leu	ProteinMutation	p|S|555|L
17059986	846	857	c.2633+1G>C	DNAMutation	c|G|2633+1|C
17059986	1074	1085	c.2633+1G>C	DNAMutation	c|G|2633+1|C
17059986	1183	1197	r.2521_2634del	DNAMutation	r|DEL|2521_2634|

17033974|t|Mutation in the auxiliary calcium-channel subunit CACNA2D4 causes autosomal recessive cone dystrophy.
17033974|a|Retinal signal transmission depends on the activity of high voltage-gated l-type calcium channels in photoreceptor ribbon synapses. We recently identified a truncating frameshift mutation in the Cacna2d4 gene in a spontaneous mouse mutant with profound loss of retinal signaling and an abnormal morphology of ribbon synapses in rods and cones. The Cacna2d4 gene encodes an l-type calcium-channel auxiliary subunit of the alpha (2) delta type. Mutations in its human orthologue, CACNA2D4, were not yet known to be associated with a disease. We performed mutation analyses of 34 patients who received an initial diagnosis of night blindness, and, in two affected siblings, we detected a homozygous nucleotide substitution (c.2406C-->A) in CACNA2D4. The mutation introduces a premature stop codon that truncates one-third of the corresponding open reading frame. Both patients share symptoms of slowly progressing cone dystrophy. These findings represent the first report of a mutation in the human CACNA2D4 gene and define a novel gene defect that causes autosomal recessive cone dystrophy.
17033974	823	834	c.2406C-->A	DNAMutation	c|C|2406|A

17003357|t|A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.
17003357|a|A recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P < 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk.
17003357	359	366	1858C/T	DNAMutation	|C|1858|T
17003357	907	914	2250G/C	DNAMutation	|G|2250|C
17003357	1216	1223	1858C/T	DNAMutation	|C|1858|T

16780885|t|16q-linked autosomal dominant cerebellar ataxia: a clinical and genetic study.
16780885|a|The autosomal dominant cerebellar ataxias (ADCAs) comprise a genetically and clinically heterogenous group of neurodegenerative disorders. Very recently, a C-to-T single nucleotide substitution in the puratrophin-1 gene was found to be strongly associated with a form of ADCA linked to chromosome 16q22.1 (16q-linked ADCA; OMIM 600223). We found the C-to-T substitution in the puratrophin-1 gene in 20 patients with ataxia (16 heterozygotes and four homozygotes) and four asymptomatic carriers in 9 of 24 families with an unknown type of ADCA. We also found two cases with 16q-linked ADCA among 43 sporadic patients with late-onset cortical cerebellar atrophy (LCCA). The mean age at onset in the 22 patients was 61.8 years, and that of homozygous patients was lower than that of heterozygous ones in one family. Neurological examination revealed that the majority of our patients showed exaggerated deep tendon reflexes in addition to the cardinal symptom of cerebellar ataxia (100%), and 37.5% of them had sensorineural hearing impairment, whereas sensory axonal neuropathy was absent. The frequency of 16q-linked ADCA was about 1/10 of our series of 110 ADCA families, making it the third most frequent ADCA in Japan.

16728705|t|Association of TNF haplotypes with asthma, serum IgE levels, and correlation with serum TNF-alpha levels.
16728705|a|Both biochemical and genetic evidence have implicated the genes for TNF-alpha (TNFA) and lymphotoxin-alpha (LTA) in atopic asthma. Here, we report for the first time the association of their genotypes and haplotypes with atopic asthma in Indian populations. We genotyped seven single nucleotide polymorphisms, encompassing the two genes, in patients and control subjects in two independent cohorts. Serum TNF-alpha levels of selected individuals were measured and correlated with genotypes and haplotypes. The A allele of the TNFA-863C > A polymorphism was associated with reduced risk of asthma (P = 0.002 and 0.007 in Cohorts A and B, respectively), reduced TsIgE levels (P = 0.0024 and P = 0.0029 in Cohorts A and B, respectively), and reduced serum TNF-alpha levels (P < 0.05). A marginal association was also observed for LTA_NcoI polymorphism with asthma and TsIgE levels. Furthermore, analysis using HAPLO. STATS showed significant differences in the major haplotype frequencies (> 3%) between patients and control subjects (P = 0.002 and P = 0.006 for Cohorts A and B, respectively). Individually, the haplotype GATCCG was the most frequent in patients (P = 0.0029 and P = 0.0025 for Cohorts A and B, respectively), and was associated with high TsIgE and serum TNF-alpha levels, whereas AACACG was the most frequent in the control subjects (P = 0.0032 and P = 0.022 for Cohorts A and B, respectively), and was associated with low TsIgE and serum TNF-alpha levels. We also report here that the C > A substitution at position -863 of the TNFA influences the binding of nuclear proteins in electrophoretic mobility shift assay experiments. Thus, the TNFA-863C > A polymorphism in the promoter region of TNFA may influence TNF-alpha expression and affect TsIgE levels and susceptibility to asthma.
16728705	636	645	-863C > A	DNAMutation	c|C|-863|A
16728705	1607	1642	C > A substitution at position -863	DNAMutation	c|C|-863|A
16728705	1765	1774	-863C > A	DNAMutation	c|C|-863|A

16644711|t|A functional Tyr1306Cys variant in LARG is associated with increased insulin action in vivo.
16644711|a|Diminished insulin sensitivity is a characteristic feature of type 2 diabetes. Inhibition of insulin action, resulting in reduced skeletal muscle glucose uptake, is mediated in part through stimulation of RhoA activity. One regulator of RhoA activity is leukemia-associated Rho guanine nucleotide exchange factor (LARG). The LARG gene maps to a region on chromosome 11q23-24 that shows genetic linkage to BMI and type 2 diabetes in Pima Indians. Because of its role in RhoA activation, the LARG gene was analyzed as a positional candidate gene for this linkage. Sequencing of the LARG gene and genotyping of variants identified several polymorphisms that were associated with in vivo rates of insulin-mediated glucose uptake, at both physiological and maximally stimulating insulin concentrations, among 322 nondiabetic Pima Indians who had undergone a hyperinsulinemic-euglycemic clamp. The strongest association with rate of glucose uptake was found with a Tyr1306Cys polymorphism (P < 0.0001, adjusted for age, sex, percent body fat, and nuclear family membership). In transient transfection studies in NIH3T3 cells, the LARG(Cys1306) protein had reduced activity compared with LARG(Tyr1306) protein (P < 0.05). We propose that the Tyr1306Cys substitution in LARG, through its differential activation of RhoA, increases insulin sensitivity in nondiabetic Pima Indians.
16644711	13	23	Tyr1306Cys	ProteinMutation	p|Y|1306|C
16644711	1052	1062	Tyr1306Cys	ProteinMutation	p|Y|1306|C
16644711	1328	1338	Tyr1306Cys	ProteinMutation	p|Y|1306|C

16543197|t|A G1103R mutation in CRB1 is co-inherited with high hyperopia and Leber congenital amaurosis.
16543197|a|PURPOSE: To identify the genetic basis of recessive inheritance of high hyperopia and Leber congenital amaurosis (LCA) in a family of Middle Eastern origin. MATERIALS AND METHODS: The patients were examined using standard ophthalmic techniques. DNA samples were obtained and genetic linkage was carried out using polymorphic markers flanking the known genes and loci for LCA. Exons were amplified and sequenced. RESULTS: All four members of this family affected by LCA showed high to extreme hyperopia, with average spherical refractive errors ranging from +5.00 to +10.00. Linkage was obtained to 1q31.3 with a maximal LOD score of 5.20 and a mutation found in exon 9 of the CRB1 gene, causing a G1103R substitution at a highly conserved site in the protein. CRB1 is a vertebrate homolog of the Drosophila crumbs gene, which is required for photoreceptor morphogenesis, and has been associated with either retinitis pigmentosa (RP) or LCA. This sequence variant has previously been reported as a compound heterozygote in one sporadic LCA patient. CONCLUSION: Although hyperopia has been associated with LCA, it is typically moderate and variable between patients with the same mutation. In addition, some CRB1 mutations can be associated with either RP or LCA. We have shown that hyperopia and LCA are linked to the mutant CRB1 gene itself and are not dependent on unlinked modifiers.
16543197	2	8	G1103R	ProteinMutation	p|G|1103|R
16543197	791	797	G1103R	ProteinMutation	p|G|1103|R

16540739|t|Loss of p16 (INK4A) expression is associated with allelic imbalance/loss of heterozygosity of chromosome 9p21 in microdissected malignant peripheral nerve sheath tumors.
16540739|a|The p16 is a tumor suppressor gene on the short arm of chromosome 9p21. The product of the p16 acts as a negative cell cycle regulator by inhibiting G1 cyclin-dependent kinases that phosphorylate the retinoblastoma protein. This study was designed to assess the frequency of genetic loss of 9p21 and to determine the role of p16 the pathogenesis of sporadic and neurofibromatosis 1 (NF1)-associated malignant peripheral nerve sheath tumors (MPNSTs). The authors examined 15 cases for p16 protein expression and 10 cases for allelic imbalance (AI)/loss of heterozygosity (LOH) of chromosome 9p. DNA was microdissected from normal and neoplastic tissues. AI/LOH analysis was performed using six microsatellite markers on the 9p region. On immunohistochemical analysis 80% of cases showed abnormal expression of p16. Similarly, 8 of 10 cases revealed genetic loss with at least one microsatellite marker. The most frequent deletion was that within the coding sequence. Of p16 at me D9S974 locus. These findings emphasize the role of loss of p16 in the development of both sporadic and NF1-associated MPNSTs.

16525586|t|Mutations in coagulation factor XIII A gene in eight unrelated Indians. Five novel mutations identified by a novel PCR-CSGE approach.
16525586|a|Factor XIII deficiency is a rare autosomal (1:2,000,000) recessive disorder of blood coagulation usually attributed to mutations in the coagulation factor XIII (FXIII) A gene. We have studied the molecular basis of FXIII deficiency in eight unrelated South Indian patients. Their diagnosis was based on clinical history, normal plasma clotting times and increased solubility of fibrin clot in 5 mol/l urea. Genomic DNA was screened for FXIII A gene defects by a novel PCR and CSGE strategy. Mutations were identified in all these patients. Five of these were novel mutations occurring in four patients. These included a novel c.210T > G transversion in homozygosity in exon 3 predicting a Tyr69X in the beta-sandwich domain in one patient. Another patient was compound heterozygote for a novel c.791C > T transition predicting a Ser263Phe in the core domain and a novel c.2045-1G > A transition at the acceptor splice junction of intron 14. Two novel frame shifts were also identified in two patients in a homozygous condition. One of them resulted from a single base 'G' duplication (c.892_895dupG) at codons Ser290/Ala291fs affecting the core domain and the other was due to a single base 'A' duplication (c.1642_1644dupA) and at codonTyr547fs affecting barrel-1 domain. The remaining four patients had the previously reported Arg260His, Ser413Leu, and Val414Phe (n = 2) missense mutations in the core domain. The novel mutations identified were considered to be disease causative by studying the nature of mutation, the degree of conservation of the mutated aminoacid among transglutaminases of different species and by molecular modeling. Apart from describing a significant number of novel mutations, this report is the first study from Southern India to describe FXIII A gene mutations.
16525586	760	770	c.210T > G	DNAMutation	c|T|210|G
16525586	823	829	Tyr69X	ProteinMutation	p|Y|69|X
16525586	928	938	c.791C > T	DNAMutation	c|C|791|T
16525586	963	972	Ser263Phe	ProteinMutation	p|S|263|F
16525586	1004	1017	c.2045-1G > A	DNAMutation	c|G|2045-1|A
16525586	1219	1232	c.892_895dupG	DNAMutation	c|DUP|892_895|G
16525586	1244	1259	Ser290/Ala291fs	ProteinMutation	p|S,A|290,291||FS
16525586	1342	1357	c.1642_1644dupA	DNAMutation	c|DUP|1642_1644|A
16525586	1371	1379	Tyr547fs	ProteinMutation	p|Y|547||FS
16525586	1463	1472	Arg260His	ProteinMutation	p|R|260|H
16525586	1474	1483	Ser413Leu	ProteinMutation	p|S|413|L
16525586	1489	1498	Val414Phe	ProteinMutation	p|V|414|F

16480574|t|Epstein-Barr virus infection in precursor lesions of nasopharyngeal carcinoma.
16480574|a|BACKGROUND _#38; OBJECTIVE: The infiltrating neoplastic cells within early-stage nasopharyngeal carcinoma (NPC) are consistently infected with Epstein-Barr virus (EBV). The precursor lesions could often be found in paracancerous epithelium of early-stage NPC. This study was to investigate the role of EBV infection and the intrahost evolution of EBV genotype developed in nasopharyngeal carcinogenesis through detection of EBV harboring in precursor lesions. METHODS: EBV-encoded RNA (EBER) in 15 cases of early-stage NPC biopsy tissue was detected by nucleic acid in situ hybridization. EBV type and latent membrane protein 1 (LMP1) EBV strain in precursor lesions and carcinoma nests were detected by nested polymerase chain reaction (PCR). DNA sequencing of the representative PCR products of carboxyl-terminus of LMP1 gene was analyzed by using four-colored fluorescence terminator sequencing technique. RESULTS: Most infiltrating carcinoma cells of all 15 cases of NPC showed EBER-positive. EBER-positive abnormal epithelial cells and/or infiltrating lymphocytes were found in 14 of 15 cases of precursor lesion. Single A-type EBV was detected in 9 of 11 available DNA samples of carcinoma nest and 9 of 10 available DNA samples of precursor lesion. The carboxyl-terminus of EBV LMP1 gene was detected in all 15 DNA samples of carcinoma nest, among which 14 were single 30-bp deleted LMP1 (del-LMP1) EBV infection and 1 was coinfection of wild-type LMP1 (wt-LMP1) EBV strain and del-LMP1 EBV strain. Among the 11 available DNA samples of precursor lesion suitable for carboxyl-terminus amplification, 5 were coinfection of wt-LMP1 and del-LMP1 EBV, 4 were single del-LMP1 EBV infection, 1 was single wt-LMP1 EBV infection, and 1 showed negative reaction. The DNA sequence of the carboxyl-terminus of wt-LMP1 gene was identical with that of B95-8 cells, while that of del-LMP1 gene had a 30-bp deletion (codon: 346-355) and 4 missense point mutations (codon: 334, 335, 338, and 366). CONCLUSION: EBV infection in nasopharyngeal epithelial cells is a preinvasive event of carcinogenesis of NPC, and the intrahost evolution of EBV genotype would take place during nasopharyngeal carcinogenesis.

16424663|t|A juvenile hemochromatosis patient homozygous for a novel deletion of cDNA nucleotide 81 of hemojuvelin.
16424663|a|BACKGROUND: A 25-year-old woman of English/Irish background was diagnosed with hemochromatosis. She manifested hypogonadotrophic hypogonadism and congestive heart failure. Although there were abnormal liver function tests, no cirrhosis was present. The patient has been treated intermittently by phlebotomy for 24 years. The aim of this study was to investigate the genetic basis of the patient's iron overload disease. METHODS: Genetic analysis was performed by direct sequencing of the genes for hemojuvelin, HFE, hepcidin, ferroportin and transferrin receptor 2. RESULTS AND CONCLUSIONS: Molecular analysis showed that the patient was homozygous for a previously undescribed mutation of HJV, the gene encoding hemojuvelin. This mutation, nt 81G deletion, causes a frameshift encoding 23 additional irrelevant amino acids and premature termination. No mutations were found in the other hemochromatosis genes, hepcidin, HFE, ferroportin or transferrin receptor 2, which might have contributed to her iron overload.

16391785|t|Homozygous deletion and reduced expression of the DOCK8 gene in human lung cancer.
16391785|a|A homozygous deletion of the DOCK8 (dedicator of cytokinesis 8) locus at chromosome 9p24 was found in a lung cancer cell line by array-CGH analysis. Cloning of the full-length DOCK8 cDNA led us to define that the DOCK8 gene encodes a protein consisting of 2,099 amino acids. DOCK8 was expressed in a variety of human organs, including the lungs, and was also expressed in type II alveolar, bronchiolar epithelial and bronchial epithelial cells, which are considered as being progenitors for lung cancer cells. DOCK8 expression was reduced in 62/71 (87%) primary lung cancers compared with normal lung tissue, and the reduction occurred irrespective of the histological type of lung cancer. 5-Aza-2'-deoxy-cytidine and/or Trichostatin A treatments induced DOCK8 expression in lung cancer cell lines with reduced DOCK8 expression. Therefore, epigenetic mechanisms, including DNA methylation and histone deacetylation, were indicated to be involved in DOCK8 down-regulation in lung cancer cells. Further screening revealed homozygous deletions of the DOCK8 gene in a gastric and a breast cancer cell line. DOCK family proteins have been shown to play roles in regulation of migration, morphology, adhesion and growth of cells. Thus, the present results suggest that genetic and epigenetic inactivation of DOCK8 is involved in the development and/or progression of lung and other cancers by disturbing such regulations.

16380922|t|Inactivating mutations in ESCO2 cause SC phocomelia and Roberts syndrome: no phenotype-genotype correlation.
16380922|a|The rare, autosomal recessive Roberts syndrome (RBS) is characterized by tetraphocomelia, profound growth deficiency of prenatal onset, craniofacial anomalies, microcephaly, and mental deficiency. SC phocomelia (SC) has a milder phenotype, with a lesser degree of limb reduction and with survival to adulthood. Since heterochromatin repulsion (HR) is characteristic for both disorders and is not complemented in somatic-cell hybrids, it has been hypothesized that the disorders are allelic. Recently, mutations in ESCO2 (establishment of cohesion 1 homolog 2) on 8p21.1 have been reported in RBS. To determine whether ESCO2 mutations are also responsible for SC, we studied three families with SC and two families in which variable degrees of limb and craniofacial abnormalities, detected by fetal ultrasound, led to pregnancy terminations. All cases were positive for HR. We identified seven novel mutations in exons 3-8 of ESCO2. In two families, affected individuals were homozygous--for a 5-nucleotide deletion in one family and a splice-site mutation in the other. In three nonconsanguineous families, probands were compound heterozygous for a single-nucleotide insertion or deletion, a nonsense mutation, or a splice-site mutation. Abnormal splice products were characterized at the RNA level. Since only protein-truncating mutations were identified, regardless of clinical severity, we conclude that genotype does not predict phenotype. Having established that RBS and SC are caused by mutations in the same gene, we delineated the clinical phenotype of the tetraphocomelia spectrum that is associated with HR and ESCO2 mutations and differentiated it from other types of phocomelia that are negative for HR.

16379547|t|Polymerase chain reaction-based analysis using deaminated DNA of dodecamer expansions in CSTB, associated with Unverricht-Lundborg myoclonus epilepsy.
16379547|a|Progressive myoclonus epilepsy of the Unverricht-Lundborg type is an autosomal recessive disorder that is characterized clinically by myoclonic seizures and ataxia. The majority of affected individuals carry repeat expansions of a dodecamer in the promoter region of the cystatin B gene. The unusually high GC content of this tract is refractory to conventional polymerase chain reaction (PCR), and, as a result, a circumventive procedure involving the deamination of DNA with sodium bisulfite has been proposed. This study evaluates the effectiveness of this deamination modification for the detection of dodecamer repeat variants. An analysis of 258 healthy Japanese individuals revealed an allele with four copies of the dodecamer repeat with a frequency of 0.01, in addition to the more commonly observed two and three copy repeat alleles. Homozygous repeat expansions 600 and 680 base pairs in length were detected in the analyses of two affected individuals. For these cases, sequencing, along with an alternative PCR-stutter formation, revealed 41 and 48 copies, respectively, of the dodecamer repeat. The complete conversion of C to T was observed in the expanded tracts, indicating that no methylation occurred at the CpG sites. Based on these results, it was concluded that the use of deaminated DNA allows for a precise analysis of consecutive GC tracts.

16333097|t|Distribution of insertion- and deletion-associated genetic polymorphisms among four Mycobacterium tuberculosis phospholipase C genes and associations with extrathoracic tuberculosis: a population-based study.
16333097|a|The Mycobacterium tuberculosis genome contains four phospholipase C (PLC)-encoding genes, designated plcA, plcB, plcC, and plcD, respectively. Each of the four genes contributes to the overall PLC activity of M. tuberculosis. PLC is hypothesized to contribute to M. tuberculosis virulence. Infection of M. tuberculosis strains carrying a truncated plcD gene is associated with the occurrence of extrathoracic tuberculosis. However, whether the other three plc genes are also associated with extrathoracic tuberculosis remains to be assessed. We investigated the insertion- and deletion-associated genetic diversity in all four plc genes among 682 epidemiologically and clinically well-characterized M. tuberculosis clinical isolates using PCR, DNA sequencing, and Southern hybridization. Two hundred sixty-six (39%) of the 682 isolates had an interruption in at least one of the four plc genes, most often associated with an IS6110 insertion. The plcD gene interruption was the most common: it was observed in 233 (34%) of the isolates, compared to 4.7%, 4.1%, and 5.9% for plcA, plcB, and plcC gene interruption, respectively. The association between the plc gene genotypes and disease presentation was adjusted for clustering using generalized estimating equations for both bivariate and multivariate analyses. After controlling for the genotypes of the plcABC genes and the host-related risk factors, interruption in the plcD gene remained significantly associated with extrathoracic tuberculosis (odds ratio, 3.27; 95% confidence interval, 1.32 to 8.14). The data suggest that the plcD gene might play a more important role in the pathogenesis of thoracic TB than it does in the pathogenesis of extrathoracic TB.

16330669|t|Array-based comparative genomic hybridization analysis reveals recurrent chromosomal alterations and prognostic parameters in primary cutaneous large B-cell lymphoma.
16330669|a|PURPOSE: To evaluate the clinical relevance of genomic aberrations in primary cutaneous large B-cell lymphoma (PCLBCL). PATIENTS AND METHODS: Skin biopsy samples of 31 patients with a PCLBCL classified as either primary cutaneous follicle center lymphoma (PCFCL; n = 19) or PCLBCL, leg type (n = 12), according to the WHO-European Organisation for Research and Treatment of Cancer (EORTC) classification, were investigated using array-based comparative genomic hybridization, fluorescence in situ hybridization (FISH), and examination of promoter hypermethylation. RESULTS: The most recurrent alterations in PCFCL were high-level DNA amplifications at 2p16.1 (63%) and deletion of chromosome 14q32.33 (68%). FISH analysis confirmed c-REL amplification in patients with gains at 2p16.1. In PCLBCL, leg type, most prominent aberrations were a high-level DNA amplification of 18q21.31-q21.33 (67%), including the BCL-2 and MALT1 genes as confirmed by FISH, and deletions of a small region within 9p21.3 containing the CDKN2A, CDKN2B, and NSG-x genes. Homozygous deletion of 9p21.3 was detected in five of 12 patients with PCLBCL, leg type, but in zero of 19 patients with PCFCL. Complete methylation of the promoter region of the CDKN2A gene was demonstrated in one PCLBCL, leg type, patient with hemizygous deletion, in one patient without deletion, but in zero of 19 patients with PCFCL. Seven of seven PCLBCL, leg type, patients with deletion of 9p21.3 and/or complete methylation of CDKN2A died as a result of their lymphoma. CONCLUSION: Our results demonstrate prominent differences in chromosomal alterations between PCFCL and PCLBCL, leg type, that support their classification as separate entities within the WHO-EORTC scheme. Inactivation of CDKN2A by either deletion or methylation of its promoter could be an important prognostic parameter for the group of PCLBCL, leg type.

16256386|t|Phenylketonuria mutations in Northern China.
16256386|a|Mutation spectrum of phenylalanine hydroxylase (PAH) gene in patients with phenylketonuria (PKU) in Northern China is described with a discussion on genotype-phenotype correlation. By using PCR/SSCP and DNA sequencing, all exons of PAH gene in the 185 unrelated patients with PKU from Northern China were studied. A total of 70 different mutations, including 42 missense, 12 splice, 7 nonsense, 5 deletion, 3 insertion, and 1 silence/splice mutations, were detected in 349/370 mutant alleles (94.3%). Deletion, insertion, and frameshift mutations were found for the first time in China PKU patients. The mutations R243Q, EX6-96A>G, R111X, Y356X, and R413P were the prevalent mutations with relative frequencies of 22.2, 11.1, 8.7, 6.5, and 6.5%, respectively. Fifteen novel mutations were identified in this study: I38fsX19, IVS4+3G>C, Y154H, R157K, R157I, T200fsX6, Q267H, Q267E, F302fsX39, G346R, S349A, L367L, R400K, IVS12+4A>G, and IVS12+6T>A. Each of them occurs at very low frequency (0.3-1.1%). The mutation spectrum of PKU in Chinese is similar to other Asian populations but significantly different from European populations. Altogether, 70 different mutations are found in 109 genotypes distributed among 185 PKU patients. As shown by the analysis, the predicted residual activity found in the majority of PKU individuals match their in vivo phenotypes, though evidence is also found for both phenotypic inconsistencies among subjects with similar genotypes and discordance between the in vitro and in vivo effects of some mutant alleles. The study enables us to construct a national database in China serving as a valuable tool for genetic counseling and prognostic evaluation of future cases of PKU.
16256386	659	664	R243Q	ProteinMutation	p|R|243|Q
16256386	666	675	EX6-96A>G	DNAMutation	c|A|EX6-96|G
16256386	677	682	R111X	ProteinMutation	p|R|111|X
16256386	684	689	Y356X	ProteinMutation	p|Y|356|X
16256386	695	700	R413P	ProteinMutation	p|R|413|P
16256386	860	868	I38fsX19	ProteinMutation	p|I|38||FSX|19
16256386	870	879	IVS4+3G>C	DNAMutation	c|G|IVS4+3|C
16256386	881	886	Y154H	ProteinMutation	p|Y|154|H
16256386	888	893	R157K	ProteinMutation	p|R|157|K
16256386	895	900	R157I	ProteinMutation	p|R|157|I
16256386	902	910	T200fsX6	ProteinMutation	p|T|200||FSX|6
16256386	912	917	Q267H	ProteinMutation	p|Q|267|H
16256386	919	924	Q267E	ProteinMutation	p|Q|267|E
16256386	926	935	F302fsX39	ProteinMutation	p|F|302||FSX|39
16256386	937	942	G346R	ProteinMutation	p|G|346|R
16256386	944	949	S349A	ProteinMutation	p|S|349|A
16256386	951	956	L367L	ProteinMutation	p|L|367|L
16256386	958	963	R400K	ProteinMutation	p|R|400|K
16256386	965	975	IVS12+4A>G	DNAMutation	c|A|IVS12+4|G
16256386	981	991	IVS12+6T>A	DNAMutation	c|T|IVS12+6|A

16252083|t|Polymorphisms of the DNA mismatch repair gene HMSH2 in breast cancer occurence and progression.
16252083|a|The response of the cell to DNA damage and its ability to maintain genomic stability by DNA repair are crucial in preventing cancer initiation and progression. Therefore, polymorphism of DNA repair genes may affect the process of carcinogenesis. The importance of genetic variability of the components of mismatch repair (MMR) genes is well documented in colorectal cancer, but little is known about its role in breast cancer. hMSH2 is one of the crucial proteins of MMR. We performed a case-control study to test the association between two polymorphisms in the hMSH2 gene: an A --> G transition at 127 position producing an Asn --> Ser substitution at codon 127 (the Asn127Ser polymorphism) and a G --> A transition at 1032 position resulting in a Gly --> Asp change at codon 322 (the Gly322Asp polymorphism) and breast cancer risk and cancer progression. Genotypes were determined in DNA from peripheral blood lymphocytes of 150 breast cancer patients and 150 age-matched women (controls) by restriction fragment length polymorphism and allele-specific PCR. We did not observe any correlation between studied polymorphisms and breast cancer progression evaluated by node-metastasis, tumor size and Bloom-Richardson grading. A strong association between breast cancer occurrence and the Gly/Gly phenotype of the Gly322Asp polymorphism (odds ratio 8.39; 95% confidence interval 1.44-48.8) was found. Therefore, MMR may play a role in the breast carcinogenesis and the Gly322Asp polymorphism of the hMSH2 gene may be considered as a potential marker in breast cancer.
16252083	674	708	A --> G transition at 127 position	DNAMutation	|A|CODON127|G
16252083	722	759	Asn --> Ser substitution at codon 127	ProteinMutation	p|N|127|S
16252083	765	774	Asn127Ser	ProteinMutation	p|N|127|S
16252083	795	830	G --> A transition at 1032 position	DNAMutation	g|G|1032|A
16252083	846	877	Gly --> Asp change at codon 322	ProteinMutation	p|G|322|D
16252083	883	892	Gly322Asp	ProteinMutation	p|G|322|D
16252083	1410	1419	Gly322Asp	ProteinMutation	p|G|322|D
16252083	1565	1574	Gly322Asp	ProteinMutation	p|G|322|D

16186368|t|Characterization of Bietti crystalline dystrophy patients with CYP4V2 mutations.
16186368|a|PURPOSE: Mutations of the CYP4V2 gene, a novel family member of the cytochrome P450 genes on chromosome 4q35, have recently been identified in patients with Bietti crystalline dystrophy (BCD). The aim of this study was to investigate the spectrum of mutations in this gene in BCD patients from Singapore, and to characterize their phenotype. METHODS: Nine patients with BCD from six families were recruited into the study. The 11 exons of the CYP4V2 gene were amplified from genomic DNA of patients by polymerase chain reaction and then sequenced. Detailed characterization of the patients' phenotype was performed with fundal photography, visual field testing, fundal fluorescein angiography, and electroretinography (ERG). RESULTS: Three pathogenic mutations were identified; two mutations, S482X and K386T, were novel and found in three patients. The third mutation, a previously identified 15-bp deletion that included the 3' splice site for exon 7, was found in all nine patients, with six patients carrying the deletion in the homozygous state. Haplotype analysis in patients and controls indicated a founder effect for this deletion mutation in exon 7. Clinical heterogeneity was present in the patients. Compound heterozygotes for the deletion in exon 7 seemed to have more severe disease compared to patients homozygous for the deletion. There was good correlation between clinical stage of disease and ERG changes, but age did not correlate with disease severity. CONCLUSIONS: This study identified novel mutations in the CYP4V2 gene as a cause of BCD. A high carrier frequency for the 15-bp deletion in exon 7 may exist in the Singapore population. Phenotype characterization showed clinical heterogeneity, and age did not correlate with disease severity.
16186368	874	879	S482X	ProteinMutation	p|S|482|X
16186368	884	889	K386T	ProteinMutation	p|K|386|T

16181814|t|Mono-allelic POLG expression resulting from nonsense-mediated decay and alternative splicing in a patient with Alpers syndrome.
16181814|a|Alpers syndrome is an autosomal recessive mitochondrial DNA depletion disorder that affects children and young adults. It is characterized by a progressive, fatal brain and liver disease. This syndrome has been associated with mutations in POLG, the gene encoding the mitochondrial DNA polymerase (pol gamma). Most patients with Alpers syndrome have been found to be compound heterozygotes, carrying two pathogenic mutations in trans at the POLG locus. POLG is a nuclear-encoded gene whose protein product is imported into mitochondria, where it is essential for mtDNA replication and repair. We studied the skin fibroblasts of a patient with Alpers syndrome having the genotype E873stop/A467T. The E873stop mutation produces a premature termination codon (TAG) in exon 17. The A467T mutation produces a threonine to alanine substitution at a highly conserved site in exon 7. The allele bearing the stop codon (E873-TAG) is predicted to produce a truncated, catalytically inactive polymerase. However, only full-length pol gamma protein was detected by Western blot analysis. Here, we show that transcripts containing this stop codon undergo nonsense-associated alternative splicing and nonsense-mediated decay. More than 95% of the functional POLG mRNA was derived from the allele bearing the A467T mutation and less than 5% contained the E873stop mutation. These events ensured that virtually all POLG protein in the cell was expressed from the A467T allele. Therefore, the Alpers phenotype in this patient was a consequence of a single-copy gene dose of the A467T allele, and selective elimination of transcripts bearing the E873stop mutation.
16181814	807	815	E873stop	ProteinMutation	p|E|873|X
16181814	816	821	A467T	ProteinMutation	p|A|467|T
16181814	827	835	E873stop	ProteinMutation	p|E|873|X
16181814	906	911	A467T	ProteinMutation	p|A|467|T
16181814	1039	1047	E873-TAG	ProteinMutation	p|E|873|X
16181814	1422	1427	A467T	ProteinMutation	p|A|467|T
16181814	1468	1476	E873stop	ProteinMutation	p|E|873|X
16181814	1575	1580	A467T	ProteinMutation	p|A|467|T
16181814	1689	1694	A467T	ProteinMutation	p|A|467|T
16181814	1756	1764	E873stop	ProteinMutation	p|E|873|X

16143638|t|Combinations of genetic changes in the human cAMP-responsive element modulator gene: a clue towards understanding some forms of male infertility?
16143638|a|The cAMP-responsive element modulator (CREM) gene plays a pivotal role in the mouse spermatogenesis, but its role in the human infertility has not been fully established. We performed a mutation screening in 13 Slovenian men with round spermatid arrest and in six controls. Eleven genetic changes have been identified in the human CREM gene, three novel single-nucleotide polymorphisms [within the promoters P1, P3 and intervening sequence 1 (IVS1)], one insertion (IVS2) and one non-sense mutation (exon gamma). Some infertile patients seem to accumulate potentially harmful genetic changes. We identified a patient with no CREM immunoreactive protein that was homozygous for the nucleotide changes in all promoters, IVS 1, 2, 6, and was heterozygous for the mutation in exon gamma. Interestingly, insertion in IVS2 (IVS2-58_55insT) results in a four-fold decrease in binding of nuclear proteins. Computer predictions suggested the presence of a potential novel CREM promoter, however, random amplification of cDNA ends from the human testis cDNA library was not successful in confirming a novel transcription start site of the CREM gene. Screening of a larger number of patients and controls is required to elucidate whether the observed combinations of genetic changes in the CREM gene can explain some forms of male infertility.
16143638	964	978	IVS2-58_55insT	DNAMutation	c|INS|IVS2-58_55|T

16088915|t|Novel amino acid substitution in the Y-position of collagen type II causes spondyloepimetaphyseal dysplasia congenita.
16088915|a|We report on monozygotic twins with short stature and severe spondyloepimetaphyseal dysplasia congenita (SEMDC) from the Polish population. Phenotype of the twin girls resembles spondyloepiphyseal dysplasia congenita Spranger-Wiedemann (SEDC-SW), but shortening of the stature is more severe and the cranioface is normal. The distinctive radiographic features, in spite of similarity to SEDC-SW, indicate different spinal and, notably, severe metaphyseal involvement. Molecular analysis of the COL2A1 gene revealed an A to G transition at nucleotide +79 of exon 41 that converted the codon for arginine at amino acid 792 to a codon for glycine (Arg792Gly). The twins were heterozygous for the mutation and neither parent had this change. The Arg792Gly substitution is located at the Y-position of Gly-X-Y triplet, and it is likely that this substitution decreased the thermal stability of the triple helix and may affect fibril growth by replacement of an arginine residue, which is important for a conformation of the triple helix.
16088915	764	773	Arg792Gly	ProteinMutation	p|R|792|G
16088915	861	870	Arg792Gly	ProteinMutation	p|R|792|G

16051693|t|Polymorphism of the PEMT gene and susceptibility to nonalcoholic fatty liver disease (NAFLD).
16051693|a|Phosphatidylethanolamine N-methyltransferase (PEMT) catalyzes phosphatidylcholine synthesis. PEMT knockout mice have fatty livers, and it is possible that, in humans, nonalcoholic fatty liver disease (NAFLD) might be associated with PEMT gene polymorphisms. DNA samples from 59 humans without fatty liver and from 28 humans with NAFLD were genotyped for a single nucleotide polymorphism in exon 8 of PEMT, which leads to a V175M substitution. V175M is a loss of function mutation, as determined by transiently transfecting McArdle-RH7777 cells with constructs of wild-type PEMT open reading frame or the V175M mutant. Met/Met at residue 175 (loss of function SNP) occurred in 67.9% of the NAFLD subjects and in only 40.7% of control subjects (P<0.03). For the first time we report that a polymorphism of the human PEMT gene (V175M) is associated with diminished activity and may confer susceptibility to NAFLD.
16051693	517	522	V175M	ProteinMutation	p|V|175|M
16051693	537	542	V175M	ProteinMutation	p|V|175|M
16051693	698	703	V175M	ProteinMutation	p|V|175|M
16051693	919	924	V175M	ProteinMutation	p|V|175|M

16001362|t|An autosomal dominant cerebellar ataxia linked to chromosome 16q22.1 is associated with a single-nucleotide substitution in the 5' untranslated region of the gene encoding a protein with spectrin repeat and Rho guanine-nucleotide exchange-factor domains.
16001362|a|Autosomal dominant cerebellar ataxia (ADCA) is a group of heterogeneous neurodegenerative disorders. By positional cloning, we have identified the gene strongly associated with a form of degenerative ataxia (chromosome 16q22.1-linked ADCA) that clinically shows progressive pure cerebellar ataxia. Detailed examination by use of audiogram suggested that sensorineural hearing impairment may be associated with ataxia in our families. After restricting the candidate region in chromosome 16q22.1 by haplotype analysis, we found that all patients from 52 unrelated Japanese families harbor a heterozygous C-->T single-nucleotide substitution, 16 nt upstream of the putative translation initiation site of the gene for a hypothetical protein DKFZP434I216, which we have called "puratrophin-1" (Purkinje cell atrophy associated protein-1). The full-length puratrophin-1 mRNA had an open reading frame of 3,576 nt, predicted to contain important domains, including the spectrin repeat and the guanine-nucleotide exchange factor (GEF) for Rho GTPases, followed by the Dbl-homologous domain, which indicates the role of puratrophin-1 in intracellular signaling and actin dynamics at the Golgi apparatus. Puratrophin-1--normally expressed in a wide range of cells, including epithelial hair cells in the cochlea--was aggregated in Purkinje cells of the chromosome 16q22.1-linked ADCA brains. Consistent with the protein prediction data of puratrophin-1, the Golgi-apparatus membrane protein and spectrin also formed aggregates in Purkinje cells. The present study highlights the importance of the 5' untranslated region (UTR) in identification of genes of human disease, suggests that a single-nucleotide substitution in the 5' UTR could be associated with protein aggregation, and indicates that the GEF protein is associated with cerebellar degeneration in humans.
16001362	858	863	C-->T	DNAMutation	|C||T

15983230|t|Polymorphisms in the SLC2A2 (GLUT2) gene are associated with the conversion from impaired glucose tolerance to type 2 diabetes: the Finnish Diabetes Prevention Study.
15983230|a|Impaired insulin secretion is a fundamental defect in type 2 diabetes. The aim of this study was to investigate whether single nucleotide polymorphisms (SNPs) in the genes regulating insulin secretion (SLC2A2 [encoding GLUT2], GCK, TCF1 [encoding HNF-1alpha], HNF4A, GIP, and GLP1R) are associated with the conversion from impaired glucose tolerance (IGT) to type 2 diabetes in participants of the Finnish Diabetes Prevention Study. With the exception of SLC2A2, other genes were not associated with the risk of type 2 diabetes. All four SNPs of SLC2A2 predicted the conversion to diabetes, and rs5393 (AA genotype) increased the risk of type 2 diabetes in the entire study population by threefold (odds ratio 3.04, 95% CI 1.34-6.88, P = 0.008). The risk for type 2 diabetes in the AA genotype carriers was increased in the control group (5.56 [1.78-17.39], P = 0.003) but not in the intervention group. We conclude that the SNPs of SLC2A2 predict the conversion to diabetes in obese subjects with IGT.
15983230	762	768	rs5393	SNP	rs5393

15951966|t|Screening for exonic copy number mutations at MSH2 and MLH1 by MAPH.
15951966|a|BACKGROUND: Exonic deletions in MSH2 and MLH1 are significant contributors to the mutation spectrum in HNPCC, and heterozygous changes in exon copy number are not detected by conventional mutation screening methods. AIMS: We aimed to develop methods for screening copy number changes in all the exons of the MLH1 and MSH2 genes using a single multiplex amplifiable probe hybridisation (MAPH) assay. METHODS: We developed a probe set consisting of probes from the 19 exons of MLH1 and 16 exons of MSH2, and 3 control probes, and applied it to screening for deletions and duplications using fluorescent detection of amplified fragments. RESULTS: We tested 73 DNA samples from controls and 50 from HNPCC patients in whom no point mutations had been found, and detected 10 copy number changes among the patient samples. A deletion of about 1.4 kb including exon 3 of MSH2 was confirmed by amplification of a junction fragment, and was shown to be the result of an unequal recombination between intronic Alu elements. CONCLUSIONS: MAPH can detect exonic copy number changes in MLH1 and MSH2 in DNA from HNPCC patients. Since finding an exonic deletion or duplication makes full sequence analysis unnecessary, it may be most cost-effective to pre-screen samples by MAPH or MLPA before screening for point mutations.

15929706|t|Detection of a new 3-base pair insertion mutation in the protease gene of human immunodeficiency virus type 1 during highly active antiretroviral therapy (HAART).
15929706|a|To investigate a new insertion mutation in the protease (PR) gene of human immunodeficiency virus type 1 (HIV-1) in a patient extensively pretreated with antiretroviral drugs, genotypic analyses of plasma-derived viruses were performed by sequencing segments of 1302 nucleotides in the pol gene of HIV-1. Despite optimal compliance to highly active antiretroviral therapy (HAART) the patient showed poor virological success. Nucleotide sequences of retrospective available plasma samples exhibited a previously unknown 3-bp insertion mutation, corresponding to a leucine, between codons 31 and 32 of the PR gene. This kind of mutation appears to be very rare and it does not seem to be associated with any phenotypic resistance profile known so far. It should be noted that the insert mutation, once it appeared, did not revert to the wild-type variant, suggesting that it seems to correspond to a better fitness of the variant viruses.

15880727|t|The spectrum of aldolase B (ALDOB) mutations and the prevalence of hereditary fructose intolerance in Central Europe.
15880727|a|We investigated the molecular basis of hereditary fructose intolerance (HFI) in 80 patients from 72 families by means of a PCR-based mutation screening strategy, consisting of heteroduplex analysis, restriction enzyme digest, DNA single strand electrophoresis, and direct sequencing. For a subset of patients mutation screening with DHPLC was established which turned out to be as fast and as sensitive as the more conventional methods. Fifteen different mutations of the aldolase B (ALDOB) gene were identified in HFI patients. As in smaller previous studies, p.A150P (65%), p.A175D (11%) and p.N335K (8%) were the most common mutated alleles, followed by c.360_363delCAAA, p.R60X, p.Y204X, and c.865delC. Eight novel mutations were identified in eight families with HFI: a small indel mutation (c.1044_1049delTTCTGGinsACACT), two small deletions (c.345_372del28; c.841_842delAC), two splice site mutations (c.113-1G>A, c.799+2T>A), one nonsense mutation (c.612T>G (p.Y204X)), and two missense mutations (c.532T>C (p.C178R), c.851T>C (p.L284P)). By mutation screening for the three most common ALDOB mutations by DHPLC in 2,000 randomly selected newborns we detected 21 heterozygotes. Based on these data and after correction for less common and private ALDOB mutations, HFI prevalence in central Europe is estimated to be 1:26,100 (95% confidence interval 1: 12,600-79,000).
15880727	679	686	p.A150P	ProteinMutation	p|A|150|P
15880727	694	701	p.A175D	ProteinMutation	p|A|175|D
15880727	712	719	p.N335K	ProteinMutation	p|N|335|K
15880727	775	791	c.360_363delCAAA	DNAMutation	c|DEL|360_363|CAAA
15880727	793	799	p.R60X	ProteinMutation	p|R|60|X
15880727	801	808	p.Y204X	ProteinMutation	p|Y|204|X
15880727	814	823	c.865delC	DNAMutation	c|DEL|865|C
15880727	915	943	c.1044_1049delTTCTGGinsACACT	DNAMutation	c|INDEL|1044_1049|ACACT
15880727	967	981	c.345_372del28	DNAMutation	c|DEL|345_372|28
15880727	983	997	c.841_842delAC	DNAMutation	c|DEL|841_842|AC
15880727	1027	1037	c.113-1G>A	DNAMutation	c|G|113-1|A
15880727	1039	1049	c.799+2T>A	DNAMutation	c|T|799+2|A
15880727	1075	1083	c.612T>G	DNAMutation	c|T|612|G
15880727	1085	1092	p.Y204X	ProteinMutation	p|Y|204|X
15880727	1124	1132	c.532T>C	DNAMutation	c|T|532|C
15880727	1134	1141	p.C178R	ProteinMutation	p|C|178|R
15880727	1144	1152	c.851T>C	DNAMutation	c|T|851|C
15880727	1154	1161	p.L284P	ProteinMutation	p|L|284|P

15867855|t|Genetic variants of the T-cell immunoglobulin mucin 1 but not the T-cell immunoglobulin mucin 3 gene are associated with asthma in an African American population.
15867855|a|BACKGROUND: The T-cell immunoglobulin mucin ( TIM ) proteins and their genetic variants have been suggested to play a role in regulating allergic diseases. OBJECTIVE: Genetic association of the sequence variants for TIM-1 and TIM-3 genes with asthma in an African American population was investigated. METHODS: Both case-control and family-based association analyses were performed for a total of 7 polymorphisms, including 3 single nucleotide polymorphism (SNPs) and 1 insertion/deletion polymorphism in the TIM-1 and 3 SNPs in the TIM-3 genes. The exposure to hepatitis A virus as judged by seropositivity was also examined. RESULTS: In the case-control design, the frequencies of the TT genotype for SNP rs2277025 and the homozygous deletion variant (157delMTTTVP) in the fourth exon of the TIM-1 gene were higher among patients with patients with asthma compared with the controls (odds ratio [OR], 2.779, P = .016; and OR, 3.09, P = .022, respectively). This association was substantiated by haplotype analysis of these and 2 additional SNPs (OR, 2.48; P = .004), and also by family-based tests for the allele and haplotype carrying 157delMTTTVP (P = .009 and P = .048, respectively). Furthermore, this association seems to exist even in the hepatitis A virus-seronegative subjects in our data. None of the 3 variants in TIM-3 genes yielded significant association with either asthma or asthma-related phenotypes. CONCLUSION: Our findings suggest that the genetic variants of the TIM-1 but not the TIM-3 gene contribute to asthma susceptibility in this African-American population.
15867855	870	879	rs2277025	SNP	rs2277025
15867855	917	929	157delMTTTVP	ProteinMutation	p|DEL|157|MTTTVP
15867855	1301	1313	157delMTTTVP	ProteinMutation	p|DEL|157|MTTTVP

15834874|t|Nucleotide mutations associated with hepatitis B e antigen negativity.
15834874|a|One hundred and forty four patients with chronic hepatitis B were tested to identify new mutations associated with hepatitis B e antigen (HBeAg) negativity, using a full genome sequence analysis. All the patients were Chinese and had hepatitis B virus infection of genotype C. Patients with none of the pre-core or core promoter mutations were significantly (P < 0.001) less common in the group with anti-HBe (13%) than in the group with HBeAg (56%). The complete nucleotide sequence was determined in four anti-HBe-positive patients who had neither pre-core nor core promoter mutations and in five HBeAg-positive patients who also had neither of these mutations (the groups were matched for age and sex). Six mutations were found to be significantly more common in the former group than in the latter: G529A (3/4 vs. 0/5), C934A (4/4 vs. 1/5), A1053G (4/4 vs. 1/5), G1915T/A (4/4 vs. 0/5), T2005C/A (4/4 vs. 0/5), and C3026T (3/4 vs. 0/5). Three of the six mutations were significantly more common in the four anti-HBe-positive patients who had neither pre-core nor core promoter mutations, compared to 11 HBeAg-positive patients who had pre-core and core promoter mutations, and also compared to 15 anti-HBe-positive patients who had pre-core and core promoter mutations, suggesting further the specificity of these mutations. Of the six mutations, two resulted in amino acid substitution in the polymerase protein, and one is located near the enhancer I region. The results suggest that the six newly discovered mutations are associated with HBeAg negativity.
15834874	874	879	G529A	DNAMutation	|G|529|A
15834874	895	900	C934A	DNAMutation	|C|934|A
15834874	916	922	A1053G	DNAMutation	|A|1053|G
15834874	938	946	G1915T/A	DNAMutation	|G|1915|T,A
15834874	962	970	T2005C/A	DNAMutation	|T|2005|C,A
15834874	990	996	C3026T	DNAMutation	|C|3026|T

15824163|t|No Evidence for BRAF as a melanoma/nevus susceptibility gene.
15824163|a|Somatic mutations of BRAF have been identified in both melanoma tumors and benign nevi. Germ line mutations in BRAF have not been identified as causal in families predisposed to melanoma. However, a recent study suggested that a BRAF haplotype was associated with risk of sporadic melanoma in men. Polymorphisms or other variants in the BRAF gene may therefore act as candidate low-penetrance genes for nevus/melanoma susceptibility. We hypothesized that promoter variants would be the most likely candidates for determinants of risk. Using denaturing high-pressure liquid chromatography and sequencing, we screened peripheral blood DNA from 184 familial melanoma cases for BRAF promoter variants. We identified a promoter insertion/deletion in linkage disequilibrium with the previously described BRAF polymorphism in intron 11 (rs1639679) reported to be associated with melanoma susceptibility in males. We therefore investigated the contribution of this BRAF polymorphism to melanoma susceptibility in 581 consecutively recruited incident cases, 258 incident cases in a study of late relapse, 673 female general practitioner controls, and the 184 familial cases. We found no statistically significant difference in either genotype or allele frequencies between cases and controls overall or between male and female cases for the BRAF polymorphism in the two incident case series. Our results therefore suggest that the BRAF polymorphism is not significantly associated with melanoma and the promoter insertion/deletion linked with the polymorphism is not a causal variant. In addition, we found that there was no association between the BRAF genotype and mean total number of banal or atypical nevi in either the cases or controls.
15824163	892	901	rs1639679	SNP	rs1639679

15820770|t|Vitamin D-binding protein gene polymorphism association with IA-2 autoantibodies in type 1 diabetes.
15820770|a|BACKGROUND: Vitamin D-binding protein (DBP) is the main systemic transporter of 1.25(OH)2D3 and is essential for its cellular endocytosis. There are two known polymorphisms in exon 11 of the DBP gene resulting in amino acid variants: GAT-->GAG substitution replaces aspartic acid by glutamic acid in codon 416; and ACG-->AAG substitution in codon 420 leads to an exchange of threonine for lysine. These DBP variants lead to differences in the affinity for 1.25(OH)2D3. Correlations between DBP alleles and type 1 diabetes have been described in different populations. Therefore, we investigated the polymorphism in codon 416 of the DBP gene for an association with autoimmune markers of type 1 diabetes. DESIGN AND METHODS: The present analysis was a case control study. 110 patients, 68 controls, and 115 first-degree relatives were genotyped for the DBP polymorphism in codon 416. DNA typing of DBP locus was performed by the PCR-restriction fragment length polymorphism method (RFLP). RESULTS: The frequencies of the Asp/Glu and Glu/Glu were significantly increased in diabetic subjects with detectable IA-2 antibodies (P < 0.01). On the contrary, the DBP Glu-containing genotype was not accompanied by differences in the prevalence of GAD65 antibodies. These finding supports a role of the vitamin D endocrine system in the autoimmune process of type 1 diabetes.
15820770	335	344	GAT-->GAG	DNAMutation	|GAT||GAG
15820770	416	451	ACG-->AAG substitution in codon 420	DNAMutation	|ACG|CODON420|AAG

15784611|t|Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.
15784611|a|We assessed the disease-causing potential of single nucleotide polymorphisms (SNPs) based on a simple set of sequence-based features. We focused on SNPs from the dbSNP database in G-protein-coupled receptors (GPCRs), a large class of important transmembrane (TM) proteins. Apart from the location of the SNP in the protein, we evaluated the predictive power of three major classes of features to differentiate between disease-causing mutations and neutral changes: (i) properties derived from amino-acid scales, such as volume and hydrophobicity; (ii) position-specific phylogenetic features reflecting evolutionary conservation, such as normalized site entropy, residue frequency and SIFT score; and (iii) substitution-matrix scores, such as those derived from the BLOSUM62, GRANTHAM and PHAT matrices. We validated our approach using a control dataset consisting of known disease-causing mutations and neutral variations. Logistic regression analyses indicated that position-specific phylogenetic features that describe the conservation of an amino acid at a specific site are the best discriminators of disease mutations versus neutral variations, and integration of all our features improves discrimination power. Overall, we identify 115 SNPs in GPCRs from dbSNP that are likely to be associated with disease and thus are good candidates for genotyping in association studies.

15770495|t|New mutations, hotspots, and founder effects in Brazilian patients with steroid 5alpha-reductase deficiency type 2.
15770495|a|Mutations of the steroid 5alpha-reductase type 2 (SRD5A2) gene in 46,XY subjects cause masculinization defects of varying degrees, due to reduced or impaired enzymatic activity. In this study, sequence abnormalities of the SRD5A2 gene were assessed by polymerase chain reaction with specific primers and automated sequencing analysis in DNA samples from 20 patients with suspected steroid 5alpha-reductase type 2 deficiency from 18 Brazilian families. Eleven subjects presented SRD5A2 homozygous single-base mutations (two first cousins and four unrelated patients with G183S, two with R246W, one with del642T, one with G196S, and one with 217_218insC plus the A49T variant in heterozygosis), whereas four were compound heterozygotes (one with Q126R/IVS3+1G>A, one with Q126R/del418T, and two brothers with Q126R/G158R). Three patients were heterozygous for A207D, G196S, and R266W substitutions. The V89L polymorphism was found in heterozygosis in one of them (with A207D) and in one case with an otherwise normal gene sequence. The A49T variant was also detected in heterozygosis in the second case without other sequencing abnormalities. Four patients harbor yet non-described SRD5A2 gene mutations: a single nucleotide deletion (del642T), a G158R amino acid substitution, a splice junction mutation (IVS3+1G>A), and the insertion of a cytosine (217_218insC) occurring at a CCCC motif. This is the first report of a single-nucleotide insertion in the coding sequence of the SRD5A2 gene. In addition to these new mutations, this investigation reveals the prevalence of G183S substitution among a subset of African-Brazilian patients and presents evidences of the recurrence of already known mutations.
15770495	686	691	G183S	ProteinMutation	p|G|183|S
15770495	702	707	R246W	ProteinMutation	p|R|246|W
15770495	718	725	del642T	DNAMutation	c|DEL|642|T
15770495	736	741	G196S	ProteinMutation	p|G|196|S
15770495	756	767	217_218insC	DNAMutation	c|INS|217_218|C
15770495	777	781	A49T	ProteinMutation	p|A|49|T
15770495	860	865	Q126R	ProteinMutation	p|Q|126|R
15770495	866	875	IVS3+1G>A	DNAMutation	c|G|IVS3+1|A
15770495	886	891	Q126R	ProteinMutation	p|Q|126|R
15770495	892	899	del418T	DNAMutation	c|DEL|418|T
15770495	923	928	Q126R	ProteinMutation	p|Q|126|R
15770495	929	934	G158R	ProteinMutation	p|G|158|R
15770495	974	979	A207D	ProteinMutation	p|A|207|D
15770495	981	986	G196S	ProteinMutation	p|G|196|S
15770495	992	997	R266W	ProteinMutation	p|R|266|W
15770495	1017	1021	V89L	ProteinMutation	p|V|89|L
15770495	1083	1088	A207D	ProteinMutation	p|A|207|D
15770495	1150	1154	A49T	ProteinMutation	p|A|49|T
15770495	1349	1356	del642T	DNAMutation	c|DEL|642|T
15770495	1361	1366	G158R	ProteinMutation	p|G|158|R
15770495	1420	1429	IVS3+1G>A	DNAMutation	c|G|IVS3+1|A
15770495	1465	1476	217_218insC	DNAMutation	c|INS|217_218|C
15770495	1687	1692	G183S	ProteinMutation	p|G|183|S

15755837|t|Common dihydrofolate reductase 19-base pair deletion allele: a novel risk factor for preterm delivery.
15755837|a|BACKGROUND: Folate is critical for cell division, a major feature of in utero development. Dihydrofolate reductase (DHFR) is required to convert the folic acid used in supplements and for food fortification and the dihydrofolate produced by thymidylate synthase during DNA synthesis to the reduced folate forms used by the cell. OBJECTIVE: We aimed to determine whether a common, recently discovered deletion polymorphism in the DHFR gene is a risk factor for preterm delivery or low birth weight. DESIGN: We studied 324 pregnant women from Camden, NJ. Folate intake was computed from folate supplement intake plus the mean of two 24-h recalls completed during the course of pregnancy. Genomic DNA was extracted from the women's leukocytes and genotyped. RESULTS: Women with a deletion allele had a significantly greater risk of preterm delivery [adjusted odds ratio (AOR): 3.0; 95% CI: 1.0, 8.8; P < 0.05] than did those without a deletion allele. Women with both a DHFR deletion allele and low folate intake (<400 microg/d from diet plus supplements) had a significantly greater risk of preterm delivery (AOR: 5.5; 95% CI: 1.5, 20.4; P = 0.01) and a significantly greater risk of having an infant with a low birth weight (AOR: 8.3; 95% CI: 1.8, 38.6; P = 0.01) than did women without a deletion allele and with a folate intake >/=400 microg/d. CONCLUSIONS: The DHFR 19-base pair deletion allele may be a risk factor for preterm delivery. In the presence of low dietary folate, the allele may also be a risk factor for low birth weight. This may be a gene-environment interaction.

15754732|t|Novel somatic MEN1 gene alterations in sporadic primary hyperparathyroidism and correlation with clinical characteristics.
15754732|a|Primary hyperparathyroidism (pHPT) is a common endocrine disease that in more than 95% of cases is sporadic and only in some cases is caused by inherited disorders, isolated or as part of multiple endocrine neoplasia (MEN1 and 2). Somatic mutations of MEN1 gene have also been described in sporadic parathyroid tumors. In our study, we examined the presence of alterations in MEN1 gene in a series of 39 patients who had undergone surgery for sporadic pHPT (35 with parathyroid adenoma or hyperplasia, 4 with a carcinoma). A genotype-phenotype correlation was also analysed. After DNA extraction from paraffin-embedded tissues, we amplified by PCR and sequenced the exons 2-10 of the MEN1 gene. Somatic MEN1 mutations were detected in 6 of the 35 patients with a benign parathyroid lesion examined (17.1%), whereas no alterations were found in the carcinomas. Four novel MEN1 gene mutations were identified as follows: one frameshift mutation (222insT, exon 2), one frameshift deletion (912delTA, exon 5), one in-frame deletion (835del18, exon 4) and one missense mutation (P291A, exon 6). In addition, one missense mutation (L89R, exon 2) and one nonsense mutation (Q536X, exon 10) were previously reported. Moreover, two polymorphisms were also found: one allele carried a R171Q polymorphism (1/39 tumors), while a D418D polymorphism (GAC/GAT) was found in 15 and 8 tumors in hetero (CT) and homozygosity (TT), respectively. In no case (mutations and/or polymorphisms) did we find a genotype-phenotype correlation. In conclusion, our data demonstrate the presence of somatic alterations of the MEN1 tumor suppressor gene in about one fifth of benign sporadic parathyroid tumors. The absence of a genotype-phenotype correlation, however, suggests the involvement of other genetic/epigenetic factors for the full expression of the disease.
15754732	1067	1074	222insT	DNAMutation	|INS|222|T
15754732	1110	1118	912delTA	DNAMutation	|DEL|912|TA
15754732	1152	1160	835del18	DNAMutation	|DEL|835|18
15754732	1197	1202	P291A	ProteinMutation	p|P|291|A
15754732	1249	1253	L89R	ProteinMutation	p|L|89|R
15754732	1290	1295	Q536X	ProteinMutation	p|Q|536|X
15754732	1398	1403	R171Q	ProteinMutation	p|R|171|Q
15754732	1440	1445	D418D	ProteinMutation	p|D|418|D
15754732	1460	1467	GAC/GAT	DNAMutation	|GAC||GAT

15749661|t|Two novel mutations, L490R and V561X, of the transferrin receptor 2 gene in Japanese patients with hemochromatosis.
15749661|a|BACKGROUND AND OBJECTIVES: The low prevalence of the C282Y mutation of the HFE gene in Japan means that the genetic background of hemochromatosis in Japanese patients remains unclear. In a previous report, we showed that 3 patients from one family had an AVAQ 594-597 deletion of the transferrin receptor (TfR2) gene. This suggests that the TfR2 gene is involved in hemochromatosis in Japanese patients. DESIGN AND METHODS: Nine patients clinically diagnosed with hemochromatosis were included in the study. DNA was extracted from whole blood samples collected with informed consent. The HFE and TfR2 genes were analyzed by sequencing the coding region and splicing sites. RESULTS: There were no mutations in the HFE gene. In the TfR2 gene, 2 novel mutations, 1469T->G (L490R) and 1665delC (V561X), were found in 2 patients. A known variation, 714C-> (I238M), was also found in the patient with L490R. The patient homozygous for both L490R and I238M presented with a mild manifestation of hemochromatosis at the age of 41 years. His liver was cirrhotic with parenchymal iron deposits and the result of a glucose tolerance test was compatible with diabetes mellitus. The patient homozygous for V561X had severe iron overload with the triad of cirrhosis, diabetes mellitus and skin pigmentation at the age of 58 years. INTERPRETATION AND CONCLUSIONS: Taken together with the previous report, 5 of our 12 patients with hemochromatosis manifesting in middle age had mutations in the TfR2 gene. Thus, TfR2 plays a role in the pathogenesis of hemochromatosis in Japan.
15749661	21	26	L490R	ProteinMutation	p|L|490|R
15749661	31	36	V561X	ProteinMutation	p|V|561|X
15749661	169	174	C282Y	ProteinMutation	p|C|282|Y
15749661	876	884	1469T->G	DNAMutation	c|T|1469|G
15749661	886	891	L490R	ProteinMutation	p|L|490|R
15749661	897	905	1665delC	DNAMutation	c|DEL|1665|C
15749661	907	912	V561X	ProteinMutation	p|V|561|X
15749661	968	973	I238M	ProteinMutation	p|I|238|M
15749661	1011	1016	L490R	ProteinMutation	p|L|490|R
15749661	1050	1055	L490R	ProteinMutation	p|L|490|R
15749661	1060	1065	I238M	ProteinMutation	p|I|238|M
15749661	1309	1314	V561X	ProteinMutation	p|V|561|X

15702130|t|Association between SLC11A1 (formerly NRAMP1) and the risk of sarcoidosis in Poland.
15702130|a|Sarcoidosis (SA) is a systemic granulomatous disorder of unknown etiology characterized by T helper 1-type inflammatory responses at sites of disease with signs of B cell hyperactivity. Like rheumatoid arthritis and diabetes, an infectious etiology has frequently been postulated but no single infectious trigger definitively identified. Polymorphic alleles at SLC11A1 have previously been associated with susceptibility to both the putative infectious agents and to these autoimmune disorders. We therefore investigated its candidacy as a genetic determinant of SA in Poland in an association-based study comparing 86 SA patients with 85 tuberculosis (TB) patients and 93 control subjects. The functional promoter (GT)(n) polymorphism and four of 10 other single nucleotide or insertion/deletion polymorphisms genotyped across SLC11A1 were informative in our sample. Consistent with previous autoimmune disease studies, allele 3 at the functional (GT)(n) promoter region repeat polymorphism was significantly associated with SA when compared with healthy controls (odds ratio 1.68; 95% CI: 1.01-2.81; P=0.04) or with TB patients (odds ratio 1.69; 95% CI: 1.042-0.78; P=0.03).

15684865|t|Mutation scanning of the NF2 gene: an improved service based on meta-PCR/sequencing, dosage analysis, and loss of heterozygosity analysis.
15684865|a|We describe the development and implementation of a neurofibromatosis type 2 (NF2) mutation scanning service based on novel techniques. All 17 exons of the NF2 gene are amplified in four polymerase chain reaction (PCR) reactions, using the meta-PCR technique to link the NF2 exons into chimeric concatamers. The meta-PCR products are then scanned for point mutations by direct sequencing. A four-exon dosage assay is used to test for large deletion/duplication mutations. In certain cases when tumour studies are necessary, these techniques are also combined with loss of heterozygosity analysis with three highly polymorphic microsatellite markers located within or close to the NF2 gene. Over a period of 2 years, we have applied these techniques in a service setting to the analysis of 271 patient samples (245 lymphocyte DNA; 26 schwannoma DNA). Meta-PCR and sequencing identified 90 point mutations in the 271 blood and tumor samples, 48 of which have not been reported previously. Dosage analysis identified large deletions in 12 of the lymphocyte DNA samples. In addition, over 84% of mutations were identified in 23 schwannoma DNA samples in which complete analysis was possible. Adoption of this novel strategy has increased the overall mutation detection rate in familial NF2 cases to 88% and sporadic NF2 cases to 59%. It has also allowed us to decrease our reporting turnaround times, and because of a low overall failure rate, permitted the running of an efficient and cost-effective service.

15672026|t|A single nucleotide A>G polymorphism at position -670 in the Fas gene promoter: relationship to preterm premature rupture of fetal membranes in multifetal pregnancies.
15672026|a|OBJECTIVE: The relationship between a polymorphism at position -670 in the Fas gene (TNFRSF6) and preterm premature rupture of membranes (PPROM) in multifetal pregnancies was examined. METHODS: Buccal swabs from 119 mother-infant sets were analyzed for an adenine (A) to guanine (G) substitution at position -670 in the TNFRSF6 promoter. Pregnancy outcome data were subsequently obtained. Analysis was by Fisher exact test. RESULTS: Maternal allele G homozygosity (TNFRSF6*G) was observed in 42.4% of 33 PPROM pregnancies as opposed to 19.5% of 77 with no spontaneous preterm birth (P = .01). Similarly, TNFRSF6*G homozygosity was present in 37.5% of 32 first-born neonates from PPROM pregnancies as opposed to 18.7% of 75 uncomplicated pregnancies (P = .04). PPROM occurred in 8 of 14 (57.1%) pregnancies in which mother and all neonates were TNFRSF6*G homozygotes as opposed to 25 of 105 (23.8%) cases in which uniform TNFRSF6*G homozygosity was not observed (P = .02). CONCLUSIONS: A genetic variant in the Fas gene is associated with an increased rate of PPROM in multifetal pregnancies.
15672026	20	53	A>G polymorphism at position -670	DNAMutation	c|A|-670|G

15668505|t|Common BRCA2 variants and modification of breast and ovarian cancer risk in BRCA1 mutation carriers.
15668505|a|The HH genotype of the nonconservative amino acid substitution polymorphism N372H in the BRCA2 gene was reported to be associated with a 1.3- to 1.5-fold increase in risk of both breast and ovarian cancer. As these studies concerned sporadic cancer cases, we investigated whether N372H and another common variant located in the 5'-untranslated region (203G > A) of the BRCA2 gene modify breast or ovarian cancer risk in BRCA1 mutation carriers. The study includes 778 women carrying a BRCA1 germ-line mutation belonging to 403 families. The two BRCA2 variants were analyzed by the TaqMan allelic discrimination technique. Genotypes were analyzed by disease-free survival analysis using a Cox proportional hazards model. We found no evidence of a significant modification of breast cancer penetrance in BRCA1 mutation carriers by either polymorphism. In respect of ovarian cancer risk, we also saw no effect with the N372H variant but we did observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no departure from Hardy-Weinberg equilibrium in the distribution of N372H alleles for our female BRCA1 carriers. We conclude that if these single-nucleotide polymorphisms do modify the risk of cancer in BRCA1 mutation carriers, their effects are not significantly larger than that of N372H previously observed in the general population.
15668505	177	182	N372H	ProteinMutation	p|N|372|H
15668505	381	386	N372H	ProteinMutation	p|N|372|H
15668505	453	461	203G > A	DNAMutation	g|G|203|A
15668505	1017	1022	N372H	ProteinMutation	p|N|372|H
15668505	1322	1327	N372H	ProteinMutation	p|N|372|H
15668505	1538	1543	N372H	ProteinMutation	p|N|372|H

15667541|t|Severe FVII deficiency caused by a new point mutation combined with a previously undetected gene deletion.
15667541|a|A 3-week-old Caucasian female presented with severe unprovoked parenchymal cerebral haemorrhage. Her plasma factor VII (FVII) activity was <0.01 units/ml. FVII activities for her mother and sister were 0.65 units/ml and 0.51 units/ml, respectively, while her father's level was normal. These results indicated that the mother was heterozygous for a non-functional F7 gene that had also been inherited by the proband's sister. The proband's severe FVII deficiency was caused by a new mutation in her paternal F7 gene coupled with the inheritance of the non-functional maternal F7 gene. DNA sequence analysis revealed that the proband had apparent homozygosity for a novel single point mutation (g.3907G >A) changing the codon for Glu29 to Lys (E29K); neither parent had the E29K mutation. Because of the unlikelihood that the proband was homozygous for two identical new point mutations, the DNA sequence abnormality was more likely to have arisen from a single mutated gene on one allele and a F7 gene deletion on the other allele. Real time polymerase chain reaction (PCR) analysis confirmed that the proband had inherited a gene deletion that was present in the maternal side of the family. Subsequent clotting assays and real time PCR revealed that the maternal deletion also included the closely linked F10 gene.
15667541	801	811	g.3907G >A	DNAMutation	g|G|3907|A
15667541	836	848	Glu29 to Lys	ProteinMutation	p|E|29|K
15667541	850	854	E29K	ProteinMutation	p|E|29|K
15667541	880	884	E29K	ProteinMutation	p|E|29|K

15661214|t|Matrix metalloproteinase 1 gene polymorphism as a prognostic predictor of invasive cervical cancer.
15661214|a|OBJECTIVES: Whereas human papillomavirus (HPV) infection is the major determinant of cervical carcinogenesis, host genetic factors may confer individual susceptibility and prognosis. Matrix metalloproteinase 1 (MMP-1) is an important modulator of carcinogenesis. A guanine insertion (2G) polymorphism at nucleotide -1607 of the MMP-1 gene promoter creates an Ets-1-binding site, which increases transcription activity. The present study investigates the association between MMP-1 polymorphism and cervical neoplasia, and their prognostic significance. METHODS: In this study, the MMP-1 polymorphism was assessed in 135 high-grade squamous intraepithelial lesions (HSILs) and 197 invasive squamous cell carcinomas (SCCs), and in age-matched controls, by capillary electrophoresis. The association of clinicopathological factors and HPV status with MMP-1 genotypes was tested. RESULTS: Frequencies of the 2G allele in HSIL and SCC were 64% and 65%, respectively, which did not differ significantly from control values (66% and 64%, respectively). The 2G allele was associated with advanced stages of disease (P = 0.03), whereas the G allele was more common in patients with regional lymph node metastases (P = 0.02). The survival time in patients with the heterozygous genotype G/2G (median, 55.3 months) was significantly longer than those with either the G/G (50.3 months) or 2G/2G genotype (43.9 months) (P = 0.02). No significant correlation between HPV status and MMP-1 genotype was identified. CONCLUSIONS: The genetic polymorphisms of MMP-1 are not associated with the risk of HSIL and SCC, but with the invasiveness and prognosis of SCC. The heterozygous genotype of MMP-1 can be used as a prognostic marker in patients with invasive cervical cancer.

15636431|t|Polymorphic changes in the KAL1 gene: not all of them should be classified as polymorphisms.
15636431|a|The KAL1 gene has a closely related nonfunctional pseudogene on the Y chromosome; a high degree of X-Y sequence similarity is observed. Some individuals present a T to C substitution at position 1833 (exon 12). Because this nucleotide differs in the X (thymine) and in the Y (cytosine) chromosome, we investigated if this was truly a polymorphism, or if in some cases the Y sequence had been amplified. The complete sequence of exon 12 of KAL1 was analyzed in 11 Kallmann Syndrome (KS) males, in 50 normal males, in 50 normal females, and in 16 patients with Ullrich-Turner Syndrome (UTS). Nucleotide 1833 was found in a heterozygous or a homozygous state in KS, normal males and normal females; UTS patients were always homozygous. Of the 61 males, 17 were heterozygous, while 11 were TT and 33 were CC. With these observations we can not assure whether these patients present a "real" polymorphism. Besides, all males were heterozygous in nucleotides 1678, 1694, 1699, 1708 and 1825, whilst females were homozygous; and in these positions, KAL1 also differs from its pseudogene. These results indicate that we are identifying the X and the Y nucleotide and these variants are not polymorphisms. Sequence variations may be pseudogene products rather than true polymorphisms, so we should always determine if the position where the variation is located differs between KAL1 and its pseudogene, because it has been suggested that the presence of various polymorphisms in affected individuals could be the cause of KS.

15595630|t|Treatment of MDS patients with recombinant human erythropoietin and the role of GSTs.
15595630|a|Glutathione S-transferases (GSTs) are a group of enzymes involved in the detoxification process of carcinogens and other substances. The genes encoding isoenzymes M1 and T1 have "null" alleles, which are polymorphic in humans. Our purpose was to examine whether the GSTM1 and GSTT1 homozygous null genotypes have an impact on the response to recombinant human erythropoietin (rhuEpo) treatment in MDS patients. We analyzed lymphocyte DNA samples from 27 patients with all types of myelodysplastic syndromes (MDS) at the time of diagnosis. All patients were scheduled to receive rHuEpo in doses of 150 u/Kg/day for a period of 12 weeks in order to obtain and maintain stable responses. A multiplex polymerase chain reaction (PCR) was used to genotype both GSTM1 and GSTT1 simultaneously, in responders and non-responders to rhuEpo with respect to various pretreatment parameters: haemoglobin, white blood cell count, platelets, serum erythropoietin, transfusion requirements and bone marrow blasts. The data obtained were evaluated by chi2 test and odds ratio were extracted. Twelve out of 27 evaluated patients demonstrated an erythroid response (44%). Nine out of the 12 patients (75%) responding after 12 weeks of treatment had GSTM1 null genotype (OR=3.4). In contrast, only 1 responder (8.3%) was homozygotes of GSTT1 null genotype. Furthermore, no statistically significant difference in the response rate of the different MDS subgroups was observed. Our results suggest that a treatment with rHuEpo may be effective in achieving a stable erythroid response in MDS patients who carry an homozygous deletion of the GSTM1 gene.

15579915|t|Sequence variant in the intron 10 of the RET oncogene in a patient with microfollicular thyroid carcinoma with medullar differentiation: implications for newly generated chi-like sequence.
15579915|a|Sequence alterations in the RET proto-oncogene are becoming increasingly important to clinical assessment of the malignant disease of the thyroid. A spectrum of mutations is necessary to establish comprehensive phenotype to genotype relationship relevant to diagnosis and therapy of thyroid malignancies. We aimed to append to the increasing database of these oncogenic lesions and, therefore, analyzed DNA from tumor tissue and constitutive DNA from a patient with thyroid carcinoma. Mutational screening and sequence characterization of the RET proto-oncogene was performed to include part of the intronic sequences. We report a germline sequence variant in DNA from the patient diagnosed with microfollicular thyroid carcinoma. The carcinoma presented not as fully developed medullar carcinoma (MTC) but as microfollicular carcinoma with tendency to evolve into MTC. We characterized the sequence variant located in the intron 10 of the RET oncogene as an A to G substitution denoted IVS10 + 4G. The described sequence alteration generates a chi-like sequence surrounded by several chi-like sequences with recombinational potential. Such alteration may be involved in the pathogenesis of the microfollicular carcinoma via genome destabilization through homologous recombination in the process of tumor progression. This result further substantiates the importance of the database correlating specific sequence variations in the RET gene with distinct disease phenotypes.
15579915	1176	1186	IVS10 + 4G	DNAMutation	c||IVS10+4|G

15578687|t|High-resolution gene copy number and expression profiling of human chromosome 22 in ovarian carcinomas.
15578687|a|Previous low-resolution studies of chromosome 22 in ovarian carcinoma have suggested its involvement in the development of the disease. We report a high-resolution analysis of DNA copy number and gene expression of 22q in 18 ovarian carcinomas using a 22q-specific genomic microarray. We identified aberrations in 67% of the studied tumors, which displayed 3 distinct gene copy number profiles. The majority of the cases (11 of 18) demonstrated heterozygous terminal deletions of various sizes, the smallest of which was 3.5 Mb. The second profile, detected in 3 tumors, revealed the coexistence of heterozygous deletions and different patterns of low-copy-number gain that involved the proximal half of 22q. The latter finding has not been reported previously in ovarian carcinoma. One case displayed a continuous deletion encompassing the entire 22q, consistent with monosomy 22. Furthermore, we compared the results with the available data on these tumors by using cDNA microarrays to define the degree of correlation between abnormalities at the DNA level and variation in mRNA expression. By a comparison with the expression data, we were able to identify 21 deleted genes showing low mRNA levels and 12 amplified genes displaying elevated gene expression, several of which play roles in cell cycle control and the induction of apoptosis. Our results indicated significant correlation between DNA copy number aberrations and variation in mRNA expression. We also identified several regions and candidate genes on 22q that should be studied further to determine their role in the development of ovarian cancer.

15485686|t|A novel SCN5A mutation manifests as a malignant form of long QT syndrome with perinatal onset of tachycardia/bradycardia.
15485686|a|OBJECTIVE: Congenital long QT syndrome (LQTS) with in utero onset of the rhythm disturbances is associated with a poor prognosis. In this study we investigated a newborn patient with fetal bradycardia, 2:1 atrioventricular block and ventricular tachycardia soon after birth. METHODS: Mutational analysis and DNA sequencing were conducted in a newborn. The 2:1 atrioventricular block improved to 1:1 conduction only after intravenous lidocaine infusion or a high dose of mexiletine, which also controlled the ventricular tachycardia. RESULTS: A novel, spontaneous LQTS-3 mutation was identified in the transmembrane segment 6 of domain IV of the Na(v)1.5 cardiac sodium channel, with a G-->A substitution at codon 1763, which changed a valine (GTG) to a methionine (ATG). The proband was heterozygous but the mutation was absent in the parents and the sister. Expression of this mutant channel in tsA201 mammalian cells by site-directed mutagenesis revealed a persistent tetrodotoxin-sensitive but lidocaine-resistant current that was associated with a positive shift of the steady-state inactivation curve, steeper activation curve and faster recovery from inactivation. We also found a similar electrophysiological profile for the neighboring V1764M mutant. But, the other neighboring I1762A mutant had no persistent current and was still associated with a positive shift of inactivation. CONCLUSIONS: These findings suggest that the Na(v)1.5/V1763M channel dysfunction and possible neighboring mutants contribute to a persistent inward current due to altered inactivation kinetics and clinically congenital LQTS with perinatal onset of arrhythmias that responded to lidocaine and mexiletine.
15485686	807	839	G-->A substitution at codon 1763	DNAMutation	|G|CODON1763|A
15485686	1366	1372	V1764M	ProteinMutation	p|V|1764|M
15485686	1408	1414	I1762A	ProteinMutation	p|I|1762|A
15485686	1566	1572	V1763M	ProteinMutation	p|V|1763|M

15464247|t|Influence of interleukin 12B (IL12B) polymorphisms on spontaneous and treatment-induced recovery from hepatitis C virus infection.
15464247|a|BACKGROUND/AIMS: Interleukin-12 (IL-12) governs the Th1-type immune response, affecting the spontaneous and treatment-induced recovery from HCV-infection. We investigated whether the IL12B polymorphisms within the promoter region (4 bp insertion/deletion) and the 3'-UTR (1188-A/C), which have been reported to influence IL-12 synthesis, are associated with the outcome of HCV infection. METHODS: We analyzed 186 individuals with spontaneous HCV clearance, 501 chronically HCV infected patients, and 217 healthy controls. IL12B 3'-UTR and promoter genotyping was performed by Taqman-based assays with allele-specific oligonucleotide probes and PCR-based allele-specific DNA-amplification, respectively. RESULTS: The proportion of IL12B promoter and 3'-UTR genotypes did not differ significantly between the different cohorts. However, HCV genotype 1-infected patients with high baseline viremia carrying the IL12B 3'-UTR 1188-C-allele showed significantly higher sustained virologic response (SVR) rates (25.3% vs. 46% vs. 54.5% for A/A, A/C and C/C) due to reduced relapse rates (24.2% vs. 12% vs. zero % for A/A, A/C and C/C). CONCLUSIONS: IL12B 3'-UTR 1188-C-allele carriers appear to be capable of responding more efficiently to antiviral combination therapy as a consequence of a reduced relapse rate. No association of IL12B polymorphisms and self-limited HCV infection could be demonstrated.
15464247	403	411	1188-A/C	DNAMutation	g|A|1188|C

15461822|t|Vaccine candidates derived from a novel infectious cDNA clone of an American genotype dengue virus type 2.
15461822|a|BACKGROUND: A dengue virus type 2 (DEN-2 Tonga/74) isolated from a 1974 epidemic was characterized by mild illness and belongs to the American genotype of DEN-2 viruses. To prepare a vaccine candidate, a previously described 30 nucleotide deletion (Delta30) in the 3' untranslated region of DEN-4 has been engineered into the DEN-2 isolate. METHODS: A full-length cDNA clone was generated from the DEN-2 virus and used to produce recombinant DEN-2 (rDEN-2) and rDEN2Delta30. Viruses were evaluated for replication in SCID mice transplanted with human hepatoma cells (SCID-HuH-7 mice), in mosquitoes, and in rhesus monkeys. Neutralizing antibody induction and protective efficacy were also assessed in rhesus monkeys. RESULTS: The rDEN2Delta30 virus was ten-fold reduced in replication in SCID-HuH-7 mice when compared to the parent virus. The rDEN-2 viruses were not infectious for Aedes mosquitoes, but both readily infected Toxorynchites mosquitoes. In rhesus monkeys, rDEN2Delta30 appeared to be slightly attenuated when compared to the parent virus as measured by duration and peak of viremia and neutralizing antibody induction. A derivative of rDEN2Delta30, designated rDEN2Delta30-4995, was generated by incorporation of a point mutation previously identified in the NS3 gene of DEN-4 and was found to be more attenuated than rDEN2Delta30 in SCID-HuH-7 mice. CONCLUSIONS: The rDEN2Delta30 and rDEN2Delta30-4995 viruses can be considered for evaluation in humans and for inclusion in a tetravalent dengue vaccine.
15461822	356	363	Delta30	DNAMutation	|DEL||30
15461822	573	580	Delta30	DNAMutation	|DEL||30
15461822	842	849	Delta30	DNAMutation	|DEL||30
15461822	1083	1090	Delta30	DNAMutation	|DEL||30
15461822	1262	1269	Delta30	DNAMutation	|DEL||30
15461822	1287	1294	Delta30	DNAMutation	|DEL||30
15461822	1445	1452	Delta30	DNAMutation	|DEL||30
15461822	1495	1502	Delta30	DNAMutation	|DEL||30
15461822	1512	1519	Delta30	DNAMutation	|DEL||30

15455371|t|Breast cancer risk associated with genotype polymorphism of the catechol estrogen-metabolizing genes: a multigenic study on cancer susceptibility.
15455371|a|Estrogen has been suggested to trigger breast cancer development via an initiating mechanism involving its metabolite, catechol estrogen (CE). To examine this hypothesis, we carried out a multigenic case-control study of 469 incident breast cancer patients and 740 healthy controls to define the role of important genes involved in the different metabolic steps that protect against the potentially harmful effects of CE metabolism. We studied the 3 genes involved in CE detoxification by conjugation reactions involving methylation (catechol-O-methyltransferase, COMT), sulfation (sulfotransferase 1A1, SULT1A1), or glucuronidation (UDP-glucuronosyltransferase 1A1, UGT1A1), one (manganese superoxide dismutase, MnSOD) involved in protection against reactive oxidative species-mediated oxidation during the conversion of CE-semiquinone (CE-SQ) to CE-quinone (CE-Q), and 2 of the glutathione S-transferase superfamily, GSTM1 and GSTT1, involved in CE-Q metabolism. Support for this hypothesis came from the observations that (i) there was a trend toward an increased risk of breast cancer in women harboring a greater number of putative high-risk genotypes of these genes (p < 0.05); (ii) this association was stronger and more significant in those women who were more susceptible to estrogen [no history of pregnancy or older (> or =26 years) at first full-term pregnancy (FFTP)]; and (iii) the risks associated with having one or more high-risk genotypes were not the same in women having experienced different menarche-to-FFTP intervals, being more significant in women having been exposed to estrogen for a longer period (> or =12 years) before FFTP. Furthermore, because CE-Q can attack DNA, leading to the formation of double-strand breaks (DSB), we examined whether the relationship between cancer risk and the genotypic polymorphism of CE-metabolizing genes was modified by the genotypes of DSB repair genes, and found that a joint effect of CE-metabolizing genes and one of the two DSB repair pathways, the homologous recombination pathway, was significantly associated with breast cancer development. Based on comprehensive CE metabolizing gene profiles, our study provides support to the hypotheses that breast cancer can be initiated by estrogen exposure and that increased estrogen exposure confers a higher risk of breast cancer by causing DSB to DNA.

15304120|t|Genetic polymorphisms of bilirubin uridine diphosphate-glucuronosyltransferase gene in Japanese patients with Crigler-Najjar syndrome or Gilbert's syndrome as well as in healthy Japanese subjects.
15304120|a|BACKGROUND AND AIM: Numerous mutations of bilirubin uridine diphosphate-glucuronosyltransferase gene (UGT1A1) have been reported in patients with familial unconjugated hyperbilirubinemia. The UGT1A1 mutation appears to be considerably different among ethnic groups. To clarify the incidence of this gene mutation in the Japanese population, the presence of UGT1A1 mutation was investigated in a group of Japanese patients with Crigler-Najjar syndrome type 2 (CNS2) and Gilbert's syndrome (GS), as well as in healthy anicteric subjects. METHODS: Four patients with CNS2, 63 patients with GS, and 71 healthy subjects were enrolled in the study. The promoter and coding regions of UGT1A1 were amplified by polymerase chain reaction (PCR) from genomic DNA isolated from leukocytes. The PCR products were directly sequenced by a dye terminating method. The UGT1A1 enzyme activity was determined in COS7 cells transfected with wild or P364L (1091 C > T) mutant DNA. RESULTS: Homozygous Y486D was observed in all four patients with CNS2. The GS patients had UGT1A1 mutations with 13 different genotypes in the promoter and coding region. Homozygous TA insertion in the TATA box (TA7) of the promoter region (TA7/7; 33%), homozygous G71R (9%), and combination of TA7/6 and heterozygous G71R (17%) were the most frequent findings in GS patients. Homozygous or heterozygous Y486D (8%) and P229Q (8%) were also observed in GS. A novel mutation, heterozygous P364L, was also identified in a GS patient. In addition to GS patients, homozygous or heterozygous TA7, G71R, and heterozygous Y486D were also observed in healthy subjects. The allele frequency of G71R and TA7 was 0.183 and 0.113 in healthy subjects, respectively. The P364L UGT1A1 enzyme activity was 64.4% lower than the wild-type enzyme activity. CONCLUSIONS: Polymorphisms in the coding region of UGT1A1 were commonly observed in Japanese patients with GS and in healthy subjects. The genetic basis of hyperbilirubinemia appears to be different between the Japanese and Caucasian populations.
15304120	1126	1131	P364L	ProteinMutation	p|P|364|L
15304120	1133	1143	1091 C > T	DNAMutation	c|C|1091|T
15304120	1177	1182	Y486D	ProteinMutation	p|Y|486|D
15304120	1422	1426	G71R	ProteinMutation	p|G|71|R
15304120	1475	1479	G71R	ProteinMutation	p|G|71|R
15304120	1561	1566	Y486D	ProteinMutation	p|Y|486|D
15304120	1576	1581	P229Q	ProteinMutation	p|P|229|Q
15304120	1644	1649	P364L	ProteinMutation	p|P|364|L
15304120	1748	1752	G71R	ProteinMutation	p|G|71|R
15304120	1771	1776	Y486D	ProteinMutation	p|Y|486|D
15304120	1841	1845	G71R	ProteinMutation	p|G|71|R
15304120	1913	1918	P364L	ProteinMutation	p|P|364|L

15200509|t|De novo germline mutation in the serine-threonine kinase STK11/LKB1 gene associated with Peutz-Jeghers syndrome.
15200509|a|Peutz-Jeghers syndrome (PJS) is an autosomal dominant disease, characterized phenotypically by mucocutaneous pigmentation and hamartomatous polyposis. Affected patients are at an increased risk of developing gastrointestinal and other malignancies. Mutations in the STK11/LKB1 (LKB1) gene, which encodes for a serine-threonine kinase, have been identified as a genetic cause of PJS. Molecular analysis of the LKB1 gene in a simplex case of PJS revealed a substitution of cytosine (C) for guanine (G) at codon 246 in exon 6, resulting in the Tyr246X mutation. The nucleotide substitution leads to a premature stop codon at the 246 residue, predicting a truncated protein and presumed loss of kinase activity. Analysis of DNA from both parents of the PJS patient did not show this mutation, which is therefore a de novo mutation. We isolated DNA from microdissected gastrointestinal hamartomatous polyps in the PJS patient and investigated the loss of heterozygosity (LOH) at the LKB1 locus by real-time fluorescence polymerase chain reaction genotyping using a fluorescent resonance energy transfer technique. The results suggest a different mechanism from LOH in the formation of hamartomatous polyps.
15200509	654	661	Tyr246X	ProteinMutation	p|Y|246|X

15162062|t|Quantitative PCR analysis reveals a high incidence of large intragenic deletions in the FANCA gene in Spanish Fanconi anemia patients.
15162062|a|Fanconi anaemia is an autosomal recessive disease characterized by chromosome fragility, multiple congenital abnormalities, progressive bone marrow failure and a high predisposition to develop malignancies. Most of the Fanconi anaemia patients belong to complementation group FA-A due to mutations in the FANCA gene. This gene contains 43 exons along a 4.3-kb coding sequence with a very heterogeneous mutational spectrum that makes the mutation screening of FANCA a difficult task. In addition, as the FANCA gene is rich in Alu sequences, it was reported that Alu-mediated recombination led to large intragenic deletions that cannot be detected in heterozygous state by conventional PCR, SSCP analysis, or DNA sequencing. To overcome this problem, a method based on quantitative fluorescent multiplex PCR was proposed to detect intragenic deletions in FANCA involving the most frequently deleted exons (exons 5, 11, 17, 21 and 31). Here we apply the proposed method to detect intragenic deletions in 25 Spanish FA-A patients previously assigned to complementation group FA-A by FANCA cDNA retroviral transduction. A total of eight heterozygous deletions involving from one to more than 26 exons were detected. Thus, one third of the patients carried a large intragenic deletion that would have not been detected by conventional methods. These results are in agreement with previously published data and indicate that large intragenic deletions are one of the most frequent mutations leading to Fanconi anaemia. Consequently, this technology should be applied in future studies on FANCA to improve the mutation detection rate.

15147378|t|Genetic variants of the extra-large stimulatory Gs protein alpha-subunit and risk of thrombotic and haemorrhagic disorders.
15147378|a|A polymorphism of the gene encoding the extra-large stimulatory G-protein alpha-subunit (XLalphas), originally identified in three patients with a bleeding tendency, involved a 36-bp insertion and two missense changes. A paternally-inherited insertion displayed a moderate platelet Gsalpha over-expression, which lead to platelet hypo-reactivity. These data prompted us to investigate the genetic, functional and clinical relevance of this polymorphism in the Mediterranean population. We included 414 healthy subjects and three case/control studies: 263 consecutive patients with a first episode of primary intracerebral haemorrhage, 195 patients with deep venous thrombosis, and 104 patients with cerebrovascular disease. Controls were selected by approximating criteria to match selected risk factors to patients. Moreover, we performed studies of platelet function. We developed a simple method to determine the methylated allele, by digestion of genomic DNA with Sma I before polymerase chain reaction amplification. We identified two new rare variants, resulting from the loss of repeat units 7 and 5. The AB genotype was present in 3.6% of healthy population and the prevalence of the B allele was similar among cases and controls. Accordingly, the non-methylated B allele did not modify either the expression of platelet Gsalpha or the platelet response to Gs-agonists. Thus, our study suggests a minor functional role of XLalphas polymorphism in thrombotic or in haemorrhagic disorders.

15086338|t|Does the position of the premature termination codon in COL7A1 correlate with the clinical severity in recessive dystrophic epidermolysis bullosa?
15086338|a|Recessive dystrophic epidermolysis bullosa (RDEB) is an inherited skin disease caused by mutations in the gene encoding type VII collagen (COL7A1). The mutations are highly variable and this greatly complicates the study of the genotype-phenotype relationships. To date, three recurrent mutations, specific to Japanese RDEB patients have been reported. By comparing the phenotypes of RDEB patients with different recurrent mutations, the upstream positions of the premature termination codons (PTCs) showed strong correlation with the RDEB clinical disease severity. However, such correlations have not been supported by patients with mutations that were different from these recurrent Japanese patients mutations. In this study, we report a case of RDEB with a very mild clinical phenotype, who was a compound heterozygote harbouring both a recurrent Japanese mutation and a novel deletion mutation resulting in a more upstream PTC. The patient and his mother were shown to have a recurrent donor splice site mutation within intron 81 (6573 + 1G > C), a recurrent Japanese mutation that activates a cryptic donor splicing site and results in a downstream PTC. The patient and his father shared a single-nucleotide deletion within exon 64 (5504delA), which causes a downstream frame shift in five amino acids before creating a PTC. Occurrence of the PTCs in mRNA was confirmed by reverse transcription-polymerase chain reaction (RT)-PCR. The patient's skin showed reduced immunofluorescence staining for COL7A1 and reduced number of abnormal or short anchoring fibrils by electron microscopy. Although the position of the mutation 5504delA PTC was located upstream of the previous mutations reported in combination with the 6573 + 1G > C mutation, the two mutations together give an apparently milder clinical phenotype. Therefore, genotype-phenotype relationships in RDEB cannot be explained purely by the position of PTC.
15086338	1184	1197	6573 + 1G > C	DNAMutation	c|G|6573+1|C
15086338	1387	1395	5504delA	DNAMutation	|DEL|5504|A
15086338	1778	1786	5504delA	DNAMutation	|DEL|5504|A
15086338	1871	1884	6573 + 1G > C	DNAMutation	c|G|6573+1|C

15033202|t|Nijmegen breakage syndrome in 13% of age-matched Czech children with primary microcephaly.
15033202|a|The Nijmegen breakage syndrome is a rare autosomal recessive chromosomal instability disorder characterized by early growth retardation, congenital microcephaly, immunodeficiency, borderline mental development, and a high tendency to lymphoreticular malignancies. Most Nijmegen breakage syndrome patients are of Slavonic origin, and all of them known so far carry a founder homozygous 5 nucleotide deletion in the NBS1 gene. Microcephaly was present in 100% of Nijmegen breakage syndrome patients in a recent large international cooperative study. The frequency of Nijmegen breakage syndrome among children with primary microcephaly was not known. Early correct diagnosis of the syndrome is crucial for appropriate preventive care and therapy. We tested 67 Czech patients of different ages with simple microcephaly for the presence of the most common mutation in the NBS1 gene. Three new Nijmegen breakage syndrome cases were detected in this cohort, representing 4.5% of the cohort. All these newly diagnosed Nijmegen breakage syndrome patients were younger than 10 months at the time of diagnosis. They were all born within a 2.5-year period. Twenty-three of the 67 children in the cohort were born within this 2.5-year period, representing a 13% incidence of Nijmegen breakage syndrome. Frequency of Nijmegen breakage syndrome heterozygotes among infants in the Czech Republic is 1: 130-158 and the birth rate is 90,000 per year, therefore in the time span of 2.5 years, three new Nijmegen breakage syndrome homozygotes are expected to be born. Therefore we assume that by DNA testing of Czech primary microcephalic children it is possible to detect all Nijmegen breakage syndrome patients to be expected. The age at correct diagnosis was lowered from 7.1 years at the time before DNA testing, to well under 1 year of age. All new Nijmegen breakage syndrome patients could receive appropriate preventive care, which should significantly improve their life expectancy and prognosis.

15009222|t|Autosomal dominant lateral temporal epilepsy: two families with novel mutations in the LGI1 gene.
15009222|a|PURPOSE: Mutations in the leucine rich, glioma inactivated gene (LGI1) were recently described in a small number of families with autosomal dominant lateral temporal epilepsy (ADLTE). ADLTE is characterized by partial seizures with symptoms suggestive of a lateral temporal onset, including frequent auditory aura. Here we report the results of clinical and genetic analyses of two newly identified families with ADTLE. METHODS: We identified two families whose seizure semiology was suggestive of ADLTE. Evaluation included a detailed history and neurologic examination, as well as collection of DNA. The coding sequence of the LGI1 gene from affected subjects from both families was analyzed for evidence of mutation. RESULTS: Each patient had a history of partial seizures, often with secondary generalization earlier in the course. Auditory aura was reported by approximately two thirds of affected patients in each pedigree. Novel mutations in LGI1 were detected in both families. A heterozygous single-nucleotide deletion at position 329 (del 329C) was detected in affected individuals from one family, whereas patients from the second family had a nonsynonymous variation, corresponding to C435G. CONCLUSIONS: We identified two novel mutations in the LGI1 gene. The phenotype of these two families was similar to that of other kindreds with ADLTE, as auditory aura was absent in one third of affected individuals. Our results further support that LGI1 mutations should be considered in patients with a history of partial seizures if the semiology of seizures is consistent with the onset in the lateral temporal lobe.
15009222	1143	1151	del 329C	DNAMutation	|DEL|329|C
15009222	1295	1300	C435G	DNAMutation	|C|435|G

14751036|t|Thyroperoxidase gene mutations in congenital goitrous hypothyroidism with total and partial iodide organification defect.
14751036|a|Mutations of the thyroperoxidase (TPO) gene have been reported as being the most severe and frequent abnormality in thyroid iodide organification defect (IOD) causing goitrous congenital hypothyroidism. The objective of this study was to screen and subsequently identify TPO gene mutations in patients with congenital hypothyroidism with evidence of total iodine organification defects (TIOD) or partial iodine organification defect (PIOD) as defined by the perchlorate discharge test. Seven goitrous patients with TIOD and seven patients with PIOD, from three and five unrelated families, respectively, were studied. We were able to detect different TPO genes mutations in patients with TIOD and PIOD. In TIOD families the results were as follows: (1) a homozygous GGCC insertion at exon 8, position 1277 (family 1); (2) compound heterozygosity with a GGCC insertion at exon 8 (1277) and a nucleotide substitution in exon 11 (2068G>C) (family 2); (3) compound heterozygosity with the mutation 2068G>C in exon 11 and a C insertion in exon 14 between positions 2505-2511 (family 3). In patients with PIOD we have detected: (1) only one heterozygous mutation in two families (4 and 5), in exons 11 and 10 (2084G>A and 1780C>A); (2) a compound heterozygous condition in one family (family 6), with mutations, respectively in exons 8 and 10 (1242G>T and 1780C>A); (3) only polymorphisms (family VII) and (4) a heterozygous mutation in the first base of the border exon/intron 9 +1G>T (family VIII). We did not detect inactivating mutations in exons 11, 16, and 21 of the THOX2 gene where mutations have been previously described. We concluded that homozygous and compound heterozygous mutations found in TIOD characterized the autosomal recessive mode of inheritance and will translate a nonfunctional protein or a protein that may not reach the apical membrane. As for PIOD, the majority of the studied kindreds had only heterozygous mutations and/or polymorphisms. It is conceivable that these TPO gene sequence alterations may partially affect the functional state of the translated protein or affect its transport to the apical membrane.
14751036	1049	1056	2068G>C	DNAMutation	c|G|2068|C
14751036	1116	1123	2068G>C	DNAMutation	c|G|2068|C
14751036	1326	1333	2084G>A	DNAMutation	c|G|2084|A
14751036	1338	1345	1780C>A	DNAMutation	c|C|1780|A
14751036	1460	1467	1242G>T	DNAMutation	c|G|1242|T
14751036	1472	1479	1780C>A	DNAMutation	c|C|1780|A
14751036	1594	1601	9 +1G>T	DNAMutation	c|G|9+1|T

14749703|t|Deletion and reduced expression of the Fanconi anemia FANCA gene in sporadic acute myeloid leukemia.
14749703|a|Fanconi anemia (FA) is an autosomal recessive chromosomal instability disorder caused by mutations in one of seven known genes (FANCA,C,D2,E,F,G and BRCA2). Mutations in the FANCA gene are the most prevalent, accounting for two-thirds of FA cases. Affected individuals have greatly increased risks of acute myeloid leukemia (AML). This raises the question as to whether inherited or acquired mutations in FA genes might be involved in the development of sporadic AML. Quantitative fluorescent PCR was used to screen archival DNA from sporadic AML cases for FANCA deletions, which account for 40% of FANCA mutations in FA homozygotes. Four heterozygous deletions were found in 101 samples screened, which is 35-fold higher than the expected population frequency for germline FANCA deletions (P<0.0001). Sequencing FANCA in the AML samples with FANCA deletions did not detect mutations in the second allele and there was no evidence of epigenetic silencing by hypermethylation. However, real-time quantitative PCR analysis in these samples showed reduced expression of FANCA compared to nondeleted AML samples and to controls. These findings suggest that gene deletions and reduced expression of FANCA may be involved in the promotion of genetic instability in a subset of cases of sporadic AML.

14734447|t|Loss of heterozygosity and internal tandem duplication mutations of the CBP gene are frequent events in human esophageal squamous cell carcinoma.
14734447|a|PURPOSE: Cyclic AMP response element binding protein binding protein (CBP), a nuclear transcriptional coactivator protein, is an important component of the cAMP signal transduction pathway. In this study, we systematically analyzed the pattern and frequency of CBP gene alterations in esophageal squamous cell carcinoma (ESCC) samples from Linzhou (Linxian), China. Experimental Design: Using microsatellite markers D16S475, D16S2622, and D16S523 within the chromosome 16p13.3 locus flanking the CBP gene, we observed loss of heterozygosity (LOH), microsatellite instability (MSI), or homozygous deletion in 16 of 26 ESCC samples. Additional ESCC samples were analyzed using different sets of microsatellite markers (CS1-CS5) within the introns or in close proximity to the 3' end of the CBP gene. RESULTS: The data showed that CBP gene LOH or MSI occurred in 9 of 19 ESCC samples. A detailed genetic alteration map of the CBP gene showed that an LOH or MSI hot spot occurred within intron 2 of the CBP gene. Furthermore, ESCC samples were investigated for CBP gene mutation by conformation sensitive gel electrophoresis and DNA sequencing. These results revealed that most of the shifted fragments contained internal tandem duplication (ITD), frequently in the regions encoding the histone acetyltransferase domain and COOH-terminal transactivating domain one of the CBP gene. The presence of ITD within the CBP gene was additionally confirmed by Southern blot analysis and sequencing. CONCLUSIONS: These studies show that LOH and ITD of the CBP gene are frequent genetic events in human ESCC. These alterations may have functional importance in the development of human ESCC.

14639526|t|Reciprocal crossovers and a positional preference for strand exchange in recombination events resulting in deletion or duplication of chromosome 17p11.2.
14639526|a|Smith-Magenis syndrome (SMS) is caused by an approximately 4-Mb heterozygous interstitial deletion on chromosome 17p11.2 in approximately 80%-90% of affected patients. Three large ( approximately 200 kb), complex, and highly homologous ( approximately 98%) low-copy repeats (LCRs) are located inside or flanking the SMS common deletion. These repeats, also known as "SMS-REPs," are termed "distal," "middle," and "proximal." The directly oriented distal and proximal copies act as substrates for nonallelic homologous recombination resulting in both the deletion associated with SMS and the reciprocal duplication: dup(17)(p11.2p11.2). Using restriction enzyme cis-morphism analyses and direct sequencing, we mapped the regions of strand exchange in 16 somatic-cell hybrids that harbor only the recombinant SMS-REP. Our studies showed that the sites of crossovers were distributed throughout the region of homology between the distal and proximal SMS-REPs. However, despite approximately 170 kb of high homology, 50% of the recombinant junctions occurred in a 12.0-kb region within the KER gene clusters. DNA sequencing of this hotspot (positional preference for strand exchange) in seven recombinant SMS-REPs narrowed the crossovers to an approximately 8-kb interval. Four of them occurred in a 1,655-bp region rich in polymorphic nucleotides that could potentially reflect frequent gene conversion. For further evaluation of the strand exchange frequency in patients with SMS, novel junction fragments from the recombinant SMS-REPs were identified. As predicted by the reciprocal-recombination model, junction fragments were also identified from this hotspot region in patients with dup(17)(p11.2p11.2), documenting reciprocity of the positional preference for strand exchange. Several potential cis-acting recombination-promoting sequences were identified within the hotspot. It is interesting that we found 2.1-kb AT-rich inverted repeats flanking the proximal and middle KER gene clusters but not the distal one. The role of any or all of these in stimulating double-strand breaks around this positional recombination hotspot remains to be explored.

14630830|t|Mutations of the PML tumor suppressor gene in acute promyelocytic leukemia.
14630830|a|The promyelocytic leukemia (PML) tumor suppressor of acute promyelocytic leukemia (APL) is essential for a number of proapoptotic and growth-suppressive pathways as well as for the activity of differentiating agents such as retinoic acid (RA). In human APL, the dose of PML is reduced to heterozygosity given that one allele is involved in the chromosomal translocation while the status of the remaining PML allele is unknown. We have therefore used single-strand conformational polymorphism (SSCP) and sequencing analysis to screen DNA from APL patients for mutations at the PML locus. We identified DNA sequence variations resulting in a truncated PML protein in APL cases that displayed RA resistance and a very poor prognosis. Mutation analysis also led to the identification of aberrant PML sequence variations in other hematopoietic malignancies. Complete functional loss of PML is therefore selected by the APL phenotype and associates with poor prognosis and RA unresponsiveness.

14623369|t|The C270T polymorphism of the brain-derived neurotrophic factor gene is associated with schizophrenia.
14623369|a|We investigated a novel polymorphism of single nucleotide substitution (C270T) of the brain-derived neurotrophic factor (BDNF) gene in schizophrenia patients (n=101) and in controls (n=68). The frequency of the C/T genotype and the T allele were significantly higher in the schizophrenia patients (25.7% and 13.9%, respectively) compared with the controls (5.9% and 2.9%). There were no significant differences in Positive and Negative Symptom Scale (PANSS) items and Global Assessment of Functioning (GAF) scores between the patients with C/C and C/T genotypes. Further studies are warranted to elucidate the significance of this finding in the pathophysiology of schizophrenia.
14623369	4	9	C270T	DNAMutation	|C|270|T
14623369	175	180	C270T	DNAMutation	|C|270|T

14562027|t|Polymorphisms in the CYP1B1 gene are associated with increased risk of prostate cancer.
14562027|a|CYP1B1 has been evaluated as a candidate gene for various cancers because of its function in activating environmental procarcinogens and catalysing the conversion of oestrogens to genotoxic catechol oestrogens. To test the hypothesis that genetic polymorphisms in the CYP1B1 gene may associate with the risk for prostate cancer (CaP), we compared the allele, genotype, and haplotype frequencies of 13 single nucleotide polymorphisms (SNPs) of CYP1B1 among 159 hereditary prostate cancer (HPC) probands, 245 sporadic CaP cases, and 222 unaffected men. When each of the SNPs was analysed separately, marginally significant differences were observed for allele frequencies between sporadic cases and controls for three consecutive SNPs (-1001C/T, -263G/A, and -13C/T, P=0.04-0.07). Similarly, marginally significant differences between sporadic cases and controls in the frequency of variant allele carriers were observed for five consecutive SNPs (-1001C/T, -263G/A, -13C/T, +142C/G, and +355G/T, P=0.02-0.08). Interestingly, when the combination of these five SNPs was analysed using a haplotype approach, a larger difference was found (P=0.009). One frequent haplotype (C-G-C-C-G of -1001C/T, -263G/A, -13C/T, +142C/G, and +355G/T) was associated with an increased risk for CaP, while the other frequent haplotype (T-A-T-G-T) was associated with a decreased risk for CaP. These findings suggest that genetic polymorphisms in CYP1B1 may modify the risk for CaP.
14562027	822	830	-1001C/T	DNAMutation	c|C|-1001|T
14562027	832	839	-263G/A	DNAMutation	c|G|-263|A
14562027	845	851	-13C/T	DNAMutation	c|C|-13|T
14562027	1034	1042	-1001C/T	DNAMutation	c|C|-1001|T
14562027	1044	1051	-263G/A	DNAMutation	c|G|-263|A
14562027	1053	1059	-13C/T	DNAMutation	c|C|-13|T
14562027	1061	1068	+142C/G	DNAMutation	c|C|+142|G
14562027	1074	1081	+355G/T	DNAMutation	c|G|+355|T
14562027	1271	1279	-1001C/T	DNAMutation	c|C|-1001|T
14562027	1281	1288	-263G/A	DNAMutation	c|G|-263|A
14562027	1290	1296	-13C/T	DNAMutation	c|C|-13|T
14562027	1298	1305	+142C/G	DNAMutation	c|C|+142|G
14562027	1311	1318	+355G/T	DNAMutation	c|G|+355|T

14517957|t|Identification of twelve novel mutations in patients with classic and variant forms of maple syrup urine disease.
14517957|a|Maple syrup urine disease (MSUD) is an autosomal recessive metabolic disorder of panethnic distribution caused by a deficiency of the activity of branched-chain alpha-ketoacid dehydrogenase (BCKD) complex. Mutations in the human BCKD genes E1alpha (BCKDHA), E1beta (BCKDHB) and E2 (DBT) are known to result in MSUD, referred to as type Ia, Ib and II mutations respectively. In this study 16 patients with the classic severe form of MSUD and three patients with milder variant forms of the disease were investigated for mutations in the E1alpha-, E1beta- and E2-gene by single-strand conformation polymorphism (SSCP) analysis and DNA sequencing. The patients' clinical and biochemical phenotypes were well characterized. One novel type Ia missense mutation, eight novel type Ib (three missense, two nonsense, two small deletions, one small duplication) and three novel type II (two missense, one splice site) mutations were identified in patients. Moreover, eleven previously described mutations were detected: five type Ia (four missense, one nonsense), three type Ib mutations (two missense, one nonsense) and three type II mutations (two missense, one small deletion). Fourteen patients are homozygous for one single mutation, five patients are compound-heterozygous for two different mutations affecting one of the three genes. Thus, in all 19 patients the identified mutations can most probably be considered the molecular basis of the disease.

14508191|t|Genetic polymorphism of the renin-angiotensin-aldosterone system and arterial hypertension in the Italian population: the GENIPER Project.
14508191|a|OBJECTIVE: To detect the association of single polymorphisms of the renin-angiotensin-aldosterone system (RAAS), or different combinations thereof, with hypertension. DESIGN AND METHODS: The GENIPER database is the result of a collaborative effort of 13 Italian research centres to collect genomic DNA in subjects well characterized in terms of blood pressure status. A total of 2461 subjects (normotensive = 611; hypertensive = 1850) were selected and genotyped for the angiotensin-converting enzyme insertion/deletion (ACE I/D), angiotensinogen (AGT) T/C704, angiotensin receptor type 1 (AT1) A/C1166 and aldosterone synthase (ALDO) T/C-344 genetic variants. RESULTS: Allele frequencies were homogeneous over the Italian territory, with the relevant exception of the ACE I/D, the D allele being significantly less frequent in the northern region (61%) than in the rest of the country (67%; P < 0.0001). When comparing allele and genotype distributions in normotensives and hypertensives, the latter presented a small but statistically significant increase of the C allele of AGT T/C704, the A allele of AT1 A/C1166 and the T allele of ALDO T/C-344 polymorphisms (P = 0.018, P = 0.037 and P = 0.015, respectively), with similar trends all over the country. A step-wise logistic regression analysis confirmed these findings, by entering in the model as independent predictors of blood pressure status of AGT T/C704 (P = 0.013), ALDO T/C-344 (P = 0.032) and AT1 A/C1166 polymorphisms (P = 0.075), but not ACE I/D (P = 0.996). We also found some evidence of an additive effect of individual genetic variants of the RAAS, modulating at different levels the same functional pathway, on the risk of developing hypertension, but no synergistic interaction was observed. CONCLUSIONS: Our results suggest that some allelic variants of RAAS genes carry a small but identifiable risk of developing arterial hypertension.
14508191	692	698	T/C704	DNAMutation	c|T|704|C
14508191	734	741	A/C1166	DNAMutation	c|A|1166|C
14508191	774	781	T/C-344	DNAMutation	c|T|-344|C
14508191	1220	1226	T/C704	DNAMutation	c|T|704|C
14508191	1248	1255	A/C1166	DNAMutation	c|A|1166|C
14508191	1281	1288	T/C-344	DNAMutation	c|T|-344|C
14508191	1547	1553	T/C704	DNAMutation	c|T|704|C
14508191	1572	1579	T/C-344	DNAMutation	c|T|-344|C
14508191	1600	1607	A/C1166	DNAMutation	c|A|1166|C

12927934|t|Progressive familial intrahepatic cholestasis type 1 and extrahepatic features: no catch-up of stature growth, exacerbation of diarrhea, and appearance of liver steatosis after liver transplantation.
12927934|a|BACKGROUND/AIMS: Progressive familial intrahepatic cholestasis characterized by normal serum gamma-glutamyltransferase activity can be due to mutations in familial intrahepatic cholestasis type 1 (FIC1) (ATP8B1), a gene expressed in several organs. In some cases, it is associated with extrahepatic features. We searched for FIC1 mutations and analyzed the outcome of extrahepatic features after liver transplantation in two children with this form of progressive familial intrahepatic cholestasis associated with chronic unexplained diarrhea and short stature. METHODS: FIC1 sequence was determined after polymerase chain reaction (PCR) of genomic lymphocyte DNA and/or reverse transcription-PCR of liver or lymphocyte RNA. RESULTS: A homozygous amino acid change deletion was found in one child. The second child harboured compound heterozygous missense and nonsense mutations. In both children, despite successful liver transplantation, evolution (follow-up: 9.5-11 years) was characterized by exacerbation of diarrhea and no catch-up of stature growth, and appearance of liver steatosis. CONCLUSIONS: Progressive familial intrahepatic cholestasis characterized by normal serum gamma-glutamyltransferase activity and extrahepatic features corresponds to progressive familial intrahepatic cholestasis type 1. Extrahepatic symptomatology is not corrected or may be aggravated by liver transplantation, impairing life quality.

12925671|t|Distinct mutations in IRAK-4 confer hyporesponsiveness to lipopolysaccharide and interleukin-1 in a patient with recurrent bacterial infections.
12925671|a|We identified previously a patient with recurrent bacterial infections who failed to respond to gram-negative LPS in vivo, and whose leukocytes were profoundly hyporesponsive to LPS and IL-1 in vitro. We now demonstrate that this patient also exhibits deficient responses in a skin blister model of aseptic inflammation. A lack of IL-18 responsiveness, coupled with diminished LPS and/or IL-1-induced nuclear factor-kappaB and activator protein-1 translocation, p38 phosphorylation, gene expression, and dysregulated IL-1R-associated kinase (IRAK)-1 activity in vitro support the hypothesis that the defect lies within the signaling pathway common to toll-like receptor 4, IL-1R, and IL-18R. This patient expresses a "compound heterozygous" genotype, with a point mutation (C877T in cDNA) and a two-nucleotide, AC deletion (620-621del in cDNA) encoded by distinct alleles of the IRAK-4 gene (GenBank/EMBL/DDBJ accession nos. AF445802 and AY186092). Both mutations encode proteins with an intact death domain, but a truncated kinase domain, thereby precluding expression of full-length IRAK-4 (i.e., a recessive phenotype). When overexpressed in HEK293T cells, neither truncated form augmented endogenous IRAK-1 kinase activity, and both inhibited endogenous IRAK-1 activity modestly. Thus, IRAK-4 is pivotal in the development of a normal inflammatory response initiated by bacterial or nonbacterial insults.
12925671	919	932	C877T in cDNA	DNAMutation	c|C|877|T
12925671	969	987	620-621del in cDNA	DNAMutation	c|DEL|620_621|

12918106|t|Refinement of heterozygosity loss on chromosome 5p15 in sporadic colorectal cancer.
12918106|a|AIM: To refine the loss of heterozygosity on chromosome 5p15 and to identify the new tumor suppressor gene (s) in colorectal tumorigenesis. METHODS: Sixteen polymorphic microsatellite markers were analyzed on chromosome 5 and another 6 markers were applied on chromosome 5p15 in 83 cases of colorectal and normal DNA by PCR. PCR products were electrophoresed on an ABI 377 DNA sequencer. Genescan 3.1 and Genotype 2.1 software were used for LOH scanning and analysis. RESULTS: We observed 2 distinct regions of frequent allelic deletions on Chromosome 5, at D5S416 on 5p15 and D5S428-D5S410 on 5q. Another 6 polymorphric microsatellite markers were applied to 5p15 and the minimal region of frequent loss of heterozygosity was established on 5p15 spanning the D5S416 locus. CONCLUSION: Through our detailed deletion mapping studies, we have found a critical and precise location of 5p deletions, 5p15.2-5p15.3, which must contain one or more unknown tumor suppressor gene (s) of colorectal cancer.

12915397|t|Uncoupling protein-2 polymorphisms in type 2 diabetes, obesity, and insulin secretion.
12915397|a|The onset of type 2 diabetes (T2DM) is preceded by obesity, insulin resistance, and impaired beta-cell function. Uncoupling protein-2 (UCP2) is a widely expressed inner mitochondrial membrane protein. Common polymorphisms of the UCP2 gene have been implicated in diabetes, in obesity, and with changes in UCP2 mRNA levels. We tested the hypothesis that common UCP2 variants influence T2DM susceptibility in four parallel studies of separate populations. We typed the -866 promoter (G/A) variant, a nonsynonymous (Ala55Val or A55V) single-nucleotide polymorphism in exon 4, and a 45-nt insertion in the 3'-untranslated (3'UTR) region. Study populations included a case-control population study, a family-based association study, and a metabolic study of individuals who had been characterized for insulin sensitivity and secretion. To evaluate UCP2 mRNA levels, we examined a fourth population of subjects, who had undergone subcutaneous fat biopsy. All three variants showed a trend to an association with T2DM (P = 0.05 to 0.07) in the population but not the family-based association study. The 3' insertion/deletion (3'UTR I/D) variant was associated with body mass index (BMI, P = 0.035) among nondiabetic family members. Haplotype combinations were significantly associated with BMI (P = 0.028), triglyceride levels (P = 0.026), and fasting insulin (P = 0.029); highest values for the three traits were observed in individuals with the heterozygous combination GVI/AVD. In the metabolic study, all three variants were associated with an index of beta-cell compensation for insulin sensitivity (disposition index), particularly in interaction with family membership (P < 0.000001). Individuals homozygous for the -866 A allele had decreased adipose mRNA levels relative to GG homozygous individuals (P = 0.009), but the 3'UTR I/D variant had no impact on mRNA levels. We confirm modest effects of UCP2 variants on BMI and T2DM and show significant effects on insulin secretion in interaction with family-specific factors. However, the associated allele and the effects on gene expression are opposite to those reported previously.
12915397	554	573	-866 promoter (G/A)	DNAMutation	c|G|-866|A
12915397	600	608	Ala55Val	ProteinMutation	p|A|55|V
12915397	612	616	A55V	ProteinMutation	p|A|55|V

12872254|t|A genetic and phenotypic analysis in Spanish spinal muscular atrophy patients with c.399_402del AGAG, the most frequently found subtle mutation in the SMN1 gene.
12872254|a|Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by mutations in the SMN1 (survival motor neuron) gene. It is classified by age of onset and maximal motor milestones achieved in type I, II, and III (severe, intermediate, and mild form, respectively). Of 369 unrelated SMA patients who were investigated for homozygous deletions in the SMN1 gene, 18 patients (4.8%) revealed at least one copy of exon 7. A 4-bp deletion in exon 3 (c.399_402delAGAG) was detected in 15 patients from 10 families. This mutation was associated with a large spectrum of phenotypes from type I to asymptomatic patients. Five patients from two consanguineous families were homozygous for the mutation with diverse mild phenotypes. Determination of the SMN2 copy number showed that the presence of two or three copies generally correlated with a better evolution. RT-PCR studies of SMN transcripts in control and patients with the same SMN2 copy number showed that the full-length/Delta7 ratio is influenced by the SMN1 genotype although it seems independent of the SMN2 copy number. Moreover, protein analysis in these patients showed a reduction in SMN protein in compound heterozygous patients (c.399_402delAGAG/deletion) when compared with homozygous c.399_402delAGAG/c.399_402delAGAG patients. Microsatellite DNA markers flanking the SMA locus revealed the occurrence of the 4-bp deletion in the background of the same haplotype, suggesting that a single mutational event was involved in the 10 families. The geographic origins of ancestors point to a founder effect from the south and east of Spain. The c.399_402delAGAG, which is to date unique to the Spanish population, constitutes the most frequently found subtle mutation in SMA. Hum Mutat 22:136-143, 2003.
12872254	83	100	c.399_402del AGAG	DNAMutation	c|DEL|399_402|AGAG
12872254	629	645	c.399_402delAGAG	DNAMutation	c|DEL|399_402|AGAG
12872254	1372	1388	c.399_402delAGAG	DNAMutation	c|DEL|399_402|AGAG
12872254	1429	1445	c.399_402delAGAG	DNAMutation	c|DEL|399_402|AGAG
12872254	1446	1462	c.399_402delAGAG	DNAMutation	c|DEL|399_402|AGAG
12872254	1784	1800	c.399_402delAGAG	DNAMutation	c|DEL|399_402|AGAG

12829659|t|Promoter polymorphisms of the TNF-alpha (G-308A) and IL-6 (C-174G) genes predict the conversion from impaired glucose tolerance to type 2 diabetes: the Finnish Diabetes Prevention Study.
12829659|a|High levels of cytokines are risk factors for type 2 diabetes. Therefore, we investigated whether the promoter polymorphisms of the tumor necrosis factor-alpha (TNF-alpha; G-308A) and interleukin 6 (IL-6; C-174G) genes predict the conversion from impaired glucose tolerance (IGT) to type 2 diabetes in the Finnish Diabetes Prevention Study. Altogether, 490 overweight subjects with IGT whose DNA was available were randomly divided into one of the two treatment assignments: the control group and the intensive, individualized diet and exercise intervention group. The -308A allele of the TNF-alpha gene was associated with an approximate twofold higher risk for type 2 diabetes compared with the G-308G genotype (odds ratio 1.80, 95% CI 1.05-3.09; P = 0.034). Subjects with both the A allele of the TNF-alpha gene and the C-174C genotype of the IL-6 gene had a 2.2-fold (CI 1.02-4.85, P = 0.045) higher risk of developing type 2 diabetes than subjects without the risk genotypes. We conclude that the -308A allele of the promoter polymorphism (G-308A) of the TNF-alpha gene is a predictor for the conversion from IGT to type 2 diabetes. Furthermore, this polymorphism seems to have a gene-gene interaction with the C-174C genotype of the IL-6 gene.
12829659	41	47	G-308A	DNAMutation	c|G|-308|A
12829659	59	65	C-174G	DNAMutation	c|C|-174|G
12829659	359	365	G-308A	DNAMutation	c|G|-308|A
12829659	392	398	C-174G	DNAMutation	c|C|-174|G
12829659	1232	1238	G-308A	DNAMutation	c|G|-308|A

12716337|t|Polymorphism at position -174 of IL-6 gene is associated with susceptibility to chronic periodontitis in a Caucasian Brazilian population.
12716337|a|BACKGROUND: Interleukin-6 (IL-6) is a multifunctional cytokine that mediates inflammatory tissue destruction. A G to C substitution at position -174 in the promoter of IL-6 gene reduces in vitro transcription of IL-6. This polymorphism has been associated with inflammatory diseases like chronic arthritis. OBJECTIVE: The aim of this study was to investigate the association between the IL-6-174 polymorphism and susceptibility to chronic periodontitis in Brazilians. MATERIAL AND METHODS: Eighty-four nonsmoking subjects over 25 years (mean age 42.4) were divided according to the severity level of periodontal disease: 36 healthy individuals (control group), 24 subjects with moderate and 24 with severe periodontitis. Genomic DNA was obtained from epithelial cells through a mouthwash with 3% glucose and scraping of oral mucosa. The samples were analyzed for IL-6-174 polymorphism using PCR-RFLP. The significance of the differences in the frequencies of the polymorphism in the control and groups with periodontitis was assessed by chi2 test (p<0.05). RESULTS: Differences were found between control and groups with periodontitis in the genotype (p=0.0036, OR=3.0) and in the allele (p=0.0838, OR=1.9) frequencies. CONCLUSION: We concluded that the IL-6-174 polymorphism is associated with susceptibility to chronic periodontitis in the population studied.

12661032|t|KLF5 is frequently deleted and down-regulated but rarely mutated in prostate cancer.
12661032|a|BACKGROUND: Previous studies mapped a region at the q21 band of chromosome 13 (13q21), which is frequently deleted in various human cancers including prostate cancer, suggesting the existence of a tumor suppressor gene at 13q21. The target gene of deletion in prostate cancer, however, has not been identified at present. METHODS: We examined four non-neoplastic and 18 neoplastic prostatic cell lines or xenografts. Homozygous/hemizygous deletion was detected by assays of duplex PCR and real-time PCR. Expression levels of genes were determined by the methods of RT-PCR, real time PCR, and northern blot analysis. Mutations of KLF5 were detected by the approaches of single strand conformational polymorphism (SSCP) and direct sequencing. For the detection of promoter methylation, Southern blotting of genomic DNA and restriction digestion or SSCP analysis of methylation specific PCR products were used. Finally, an expression plasmid of KLF5 was introduced into prostate cancer cell lines with reduced KLF5 expression to investigate colony formation for cell growth. RESULTS: A 2-Mb region of homozygous deletion at 13q21 was detected in the LUCaP70 xenograft of prostate cancer. This region of deletion was further narrowed to 142 Kb by a hemizygous deletion in the NCI-H660 cell line. KLF5 was identified as the only complete gene in the smallest region of deletion. Quantitative deletion of KLF5 genome occurred in six of the 18 (33%) prostate cancer xenografts/cell lines. Each of the six samples with deletion also showed loss of expression for KLF5, suggesting that hemizygous deletion is one mechanism for loss of KLF5 expression. In total, 16 of the 18 cases (89%) showed loss of KLF5 expression at different degrees. In contrast, mutations and promoter methylations were not detected in any of the samples. Functionally, restoration of KLF5 in DU 145 and 22Rv1 cell lines significantly inhibited their growth in vitro. CONCLUSIONS: Frequent genomic deletion and loss of expression as well as cell growth suppression indicate that KLF5 is a reasonable candidate for the tumor suppressor gene at 13q21 in prostate cancer. Mutation and promoter methylation are not common mechanisms for the inactivation of KLF5 in prostate cancer.

12650796|t|Card15 and Crohn's disease: healthy homozygous carriers of the 3020insC frameshift mutation.
12650796|a|OBJECTIVES: Single nucleotide variations in the CARD15 gene have recently been shown to be associated with Crohn's disease (CD). Of special interest is a cytosine insertion at position 3020 of exon 11 (3020insC), which leads to a stop codon, truncation of the CARD15 protein, and an altered function of CARD15. The aim of the study was to evaluate this frameshift mutation in Dutch, multiple-affected families with inflammatory bowel disease (IBD). METHODS: Ninety-three Caucasian, multiple-affected families with IBD were recruited by interviewing patients attending our department. Sixty-one probands had CD, and 32 probands ulcerative colitis (UC). The diagnosis of probands and affected family members was verified according to standard criteria. In addition, 81 healthy, unrelated controls were included. Genomic DNA was isolated from venous blood of all participants to determine the CARD15 3020insC mutation by using an allele-specific polymerase chain reaction, followed by agarose gel electrophoresis and DNA sequencing. RESULTS: Association with CARD15 3020insC was statistically significant for CD, but not for UC. In one of the multiple-affected families, middle-aged and elderly homozygous carriers were identified without CD. CONCLUSIONS: Although CARD15 3020insC appears to be etiologically important in CD, homozygous carriage does not always lead to IBD.
12650796	63	71	3020insC	DNAMutation	|INS|3020|C
12650796	295	303	3020insC	DNAMutation	|INS|3020|C
12650796	990	998	3020insC	DNAMutation	|INS|3020|C
12650796	1156	1164	3020insC	DNAMutation	|INS|3020|C
12650796	1362	1370	3020insC	DNAMutation	|INS|3020|C

12626442|t|Total C4B deficiency due to gene deletion and gene conversion in a patient with severe infections.
12626442|a|Deficiencies of the early components of the classical complement pathway impair the actions of innate and humoral immunity and may lead to increased susceptibility to infections. We have studied the genetic basis of total C4B deficiency in a Finnish patient with recurrent meningitis, chronic fistulas and abscesses. The maternal chromosome carried a four-gene deletion including the C4B gene, and a conversion from C4B to C4A gene was found on the paternal chromosome resulting in complete deficiency of C4B. In the converted C4A gene, mutation screening did not reveal any amino acid changes or prominent mutations, yet a large number of nucleotide variations were found. Further, the patient was heterozygous for structural deficiency of mannan binding lectin (MBL) associating with medium levels of serum MBL. Our data provides new information on the genetic instability of the C4 gene region, and on the association of homozygous C4B deficiency and variant MBL genotype with increased susceptibility to recurrent and chronic infections. Importantly, plasma therapy induced a prompt clinical cure with long-term effects.

