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Association and linkage analyses of RGS4 polymorphisms in schizophrenia.
Chowdari KV, Mirnics K, Semwal P, Wood J, Lawrence E, Bhatia T, Deshpande SN, B K T, Ferrell RE, Middleton FA, Devlin B, Levitt P, Lewis DA, Nimgaonkar VL
(2002) Hum Mol Genet 11: 1373-80
MeSH Terms: Bipolar Disorder, Cerebral Cortex, Chromosome Mapping, Gene Expression Profiling, Haplotypes, Humans, Linkage Disequilibrium, Molecular Sequence Data, Polymorphism, Single Nucleotide, RGS Proteins, Schizophrenia, Sequence Analysis, DNA
Show Abstract · Added February 12, 2015
Gene expression analyses of postmortem cerebral cortex suggest that transcription of the regulator of G-protein signaling 4 (RGS4) is decreased in a diagnosis-specific manner in subjects with schizophrenia. To evaluate the possible role of RGS4 in the pathogenesis of schizophrenia, we conducted genetic association and linkage studies using samples ascertained independently in Pittsburgh and New Delhi and by the NIMH Collaborative Genetics Initiative. Using the transmission disequilibrium test, significant transmission distortion was observed in the Pittsburgh and NIMH samples. Among single-nucleotide polymorphisms (SNPs) spanning approximately 300 kb, significant associations involved four SNPs localized to a 10 kb region at RGS4, but the associated haplotypes differed. A trend for transmission distortion was also present in the Indian sample for haplotypes incorporating the same SNPs. Consistent with the linkage/association observed from the family-based tests, samples with affected siblings (NIMH, India) showed higher levels of allele sharing, identical by descent, at RGS4. When the US patients were contrasted to two population-based control samples, however, no significant differences were observed. To check the specificity of the transmission bias, we therefore examined US families with bipolar I disorder (BD1) probands. This sample also showed a trend for transmission distortion, and differed significantly from the population-based controls for the four-SNP haplotypes tested in the other samples. The transmission distortion is unlikely to be due to chance, but its mechanism and specificity require further study. Our results illustrate the potential power of combining gene expression profiling and genomic analyses to identify susceptibility genes for genetically complex disorders.
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12 MeSH Terms
Variation in three single nucleotide polymorphisms in the calpain-10 gene not associated with type 2 diabetes in a large Finnish cohort.
Fingerlin TE, Erdos MR, Watanabe RM, Wiles KR, Stringham HM, Mohlke KL, Silander K, Valle TT, Buchanan TA, Tuomilehto J, Bergman RN, Boehnke M, Collins FS
(2002) Diabetes 51: 1644-8
MeSH Terms: Aged, Calpain, Cohort Studies, Diabetes Mellitus, Type 2, Female, Finland, Gene Frequency, Genetic Predisposition to Disease, Haplotypes, Humans, Male, Middle Aged, Phenotype, Polymorphism, Single Nucleotide, Risk Factors
Show Abstract · Added October 1, 2014
Variations in the calpain-10 gene have recently been reported to be associated with type 2 diabetes in a Mexican-American population. We typed three single nucleotide polymorphisms (SNPs) in the calpain-10 gene (SNPs 43, 56, and 63) to test for association between variation at these loci and type 2 diabetes and diabetes-related traits in 1,603 Finnish subjects: two samples of 526 (Finland-U.S. Investigation of NIDDM Genetics [FUSION] 1) and 255 (FUSION 2) index case subjects with type 2 diabetes, 185 and 414 unaffected spouses and offspring of FUSION 1 index case subjects or their affected siblings, and 223 elderly normal glucose-tolerant control subjects. We found no significant differences in allele, genotype, haplotype, or haplogenotype frequencies between index case subjects with diabetes and the elderly and spouse control populations (all P > 0.087). Although variation in these three SNPs was associated with variation in some type 2 diabetes-related traits within each of the case and control groups, no consistent pattern of the implicated variant or combination of variants was discerned. We conclude that variation in these three SNPs in the calpain-10 gene is unlikely to confer susceptibility to type 2 diabetes in this Finnish cohort.
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15 MeSH Terms
Geographic and haplotype structure of candidate type 2 diabetes susceptibility variants at the calpain-10 locus.
Fullerton SM, Bartoszewicz A, Ybazeta G, Horikawa Y, Bell GI, Kidd KK, Cox NJ, Hudson RR, Di Rienzo A
(2002) Am J Hum Genet 70: 1096-106
MeSH Terms: Africa, Alleles, Animals, Calpain, Chromosomes, Human, Pair 2, Continental Population Groups, Diabetes Mellitus, Type 2, Gene Frequency, Genetic Predisposition to Disease, Genetic Variation, Haplorhini, Haplotypes, Humans, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Selection, Genetic
Show Abstract · Added February 22, 2016
Recently, a positional cloning study proposed that haplotypes at the calpain-10 locus (CAPN10) are associated with increased risk of type 2 diabetes, or non-insulin-dependent diabetes mellitus, in Mexican Americans, Finns, and Germans. To inform the interpretation of the original mapping results and to look for evidence for the action of natural selection on CAPN10, we undertook a population-based genotyping survey of the candidate susceptibility variants. First, we genotyped sites 43, 19, and 63 (the haplotype-defining variants previously proposed) and four closely linked SNPs, in 561 individuals from 11 populations from five continents, and we examined the linkage disequilibrium among them. We then examined the ancestral state of these sites by sequencing orthologous portions of CAPN10 in chimpanzee and orangutan (the identity of sites 43 and 19 was further investigated in a limited sample of other great apes and Old World and New World monkeys). Our survey suggests larger-than-expected differences in the distribution of CAPN10 susceptibility variants between African and non-African populations, with common, derived haplotypes in European and Asian samples (including one of two proposed risk haplotypes) being rare or absent in African samples. These results suggest a history of positive natural selection at the locus, resulting in significant geographic differences in polymorphism frequencies. The relationship of these differences to disease risk is discussed.
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16 MeSH Terms
Molecular haplotyping of genomic DNA for multiple single-nucleotide polymorphisms located kilobases apart using long-range polymerase chain reaction and intramolecular ligation.
McDonald OG, Krynetski EY, Evans WE
(2002) Pharmacogenetics 12: 93-9
MeSH Terms: Alleles, Cloning, Molecular, Cytochrome P-450 CYP3A, Cytochrome P-450 Enzyme System, DNA, DNA Primers, Haplotypes, Humans, Ligation, Methyltransferases, Mixed Function Oxygenases, Pedigree, Pharmacogenetics, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Receptors, Interleukin-4, Sequence Analysis, DNA
Show Abstract · Added May 5, 2016
Genetic polymorphisms are well-recognized causes of interindividual differences in disease risk and treatment response in humans. For genes containing multiple single-nucleotide polymorphisms (SNPs), haplotype structure is often the principal determinant of phenotypic consequences, and haplotype distribution represents the best approach for assessing patterns of linkage disequilibrium. To permit more widespread molecular determination of haplotypes, we developed a simple yet robust method to determine haplotype structure for multiple SNPs located up to 30 kb apart in genomic DNA using long-range polymerase chain reaction (LR-PCR) and intramolecular ligation. Complete concordance was shown between the new method and conventional approaches, such as family pedigree analysis or cloning and sequencing. The availability of a simple method to directly determine haplotype structure using genomic DNA, without family pedigree analysis, cloning or complex instrumentation, provides an important new tool for elucidating the genetic determinants of drug disposition and effects, disease risk, and molecular evolution.
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17 MeSH Terms
A statistical method for identification of polymorphisms that explain a linkage result.
Sun L, Cox NJ, McPeek MS
(2002) Am J Hum Genet 70: 399-411
MeSH Terms: Alleles, Chromosome Mapping, Computer Simulation, Diabetes Mellitus, Type 2, Female, Gene Frequency, Genetic Linkage, Genetic Markers, Genetic Predisposition to Disease, Genotype, Humans, Linkage Disequilibrium, Male, Matched-Pair Analysis, Microsatellite Repeats, Models, Genetic, Nuclear Family, Pedigree, Polymorphism, Single Nucleotide, Quantitative Trait, Heritable
Show Abstract · Added February 22, 2016
Suppose that many polymorphic sites have been identified and genotyped in a region showing strong linkage with a trait. A key question of interest is which site (or combination of sites) in the region influences susceptibility to the trait. We have developed a novel statistical approach to this problem, in the context of qualitative-trait mapping, in which we use linkage data to identify the polymorphic sites whose genotypes could fully explain the observed linkage to the region. The information provided by this analysis is different from that provided by tests of either linkage or association. Our approach is based on the observation that if a particular site is the only site in the region that influences the trait, then-conditional on the genotypes at that site for the affected relatives-there should be no unexplained oversharing in the region among affected individuals. We focus on the affected sib-pair study design and develop test statistics that are variations on the usual allele-sharing methods used in linkage studies. We perform hypothesis tests and derive a confidence set for the true causal polymorphic site, under the assumption that there is only one site in the region influencing the trait. Our method is appropriate under a very general model for how the site influences the trait, including epistasis with unlinked loci, correlated environmental effects within families, and gene-environment interaction. We extend our method to larger sibships and apply it to an NIDDM1 data set.
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20 MeSH Terms
In-vivo effects of Glu298Asp endothelial nitric oxide synthase polymorphism.
Sofowora G, Dishy V, Xie HG, Imamura H, Nishimi Y, Morales CR, Morrow JD, Kim RB, Stein CM, Wood AJ
(2001) Pharmacogenetics 11: 809-14
MeSH Terms: Adult, Aspartic Acid, Endothelium, Vascular, F2-Isoprostanes, Female, Forearm, Genotype, Glutamic Acid, Hand, Homozygote, Humans, Male, Nitrates, Nitric Oxide, Nitric Oxide Synthase, Nitric Oxide Synthase Type III, Nitrites, Oxidative Stress, Polymorphism, Single Nucleotide, Regional Blood Flow, Vascular Resistance, Vasodilation
Show Abstract · Added December 10, 2013
Endothelial nitric oxide synthase catalyses the formation of the vasodilator nitric oxide, a major regulator of vascular tone. The Asp298 polymorphism of the nitric oxide synthase gene is associated with altered function and expression of the enzyme in vitro and myocardial infarction and coronary artery spasm in vivo. We examined the effect of the Glu298Asp polymorphism on: (1) local vascular responses to phenylephrine, acetylcholine, glyceryl trinitrate and prostaglandin E1 in the dorsal hand vein; (2) changes in forearm blood flow during mental stress, a measure of nitric oxide-mediated effect on resistance vessels; (3) excretion of urinary nitrite/nitrate as a measure of total body nitric oxide production; and (4) F2-isoprostane metabolite, a measure of oxidative stress, in healthy Glu298 (n = 12) and Asp298 (n = 13) homozygotes. There were no significant differences in acetylcholine dose responses (P = 0.29) in Glu298 and Asp298 homozygotes. Responses to glyceryl trinitrate, prostaglandin E1 and the alpha-adrenergic agonist phenylephrine did not differ by genotype. Forearm blood flow was similar at rest and increased significantly (from 7.5 ml/min/100 ml to 12.2 ml/min/100 ml; P = 0.003), but similarly (P = 0.2), during mental stress in both genotypes. Asp298 homozygotes excreted significantly less nitrate/nitrite than Glu298 homozygotes (nitrate + nitrite/creatinine ratio 0.05 +/- 0.01 vs. 0.09 +/- 0.01, respectively; P < 0.005). Urinary F2-isoprostane metabolite excretion did not differ (Glu298, 2.04 +/- 0.25 ng/mg creatinine; Asp298, 1.85 +/- 0.37 ng/mg creatinine; P = 0.7). We conclude that in healthy volunteers the Glu298Asp polymorphism affects endogenous nitric oxide production without affecting nitric oxide-mediated vascular responses. This polymorphism may only have clinical significance in the presence of endothelial dysfunction.
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22 MeSH Terms
Linkage disequilibrium at the Angelman syndrome gene UBE3A in autism families.
Nurmi EL, Bradford Y, Chen Y, Hall J, Arnone B, Gardiner MB, Hutcheson HB, Gilbert JR, Pericak-Vance MA, Copeland-Yates SA, Michaelis RC, Wassink TH, Santangelo SL, Sheffield VC, Piven J, Folstein SE, Haines JL, Sutcliffe JS
(2001) Genomics 77: 105-13
MeSH Terms: Alleles, Angelman Syndrome, Autistic Disorder, Base Sequence, Chromosome Deletion, Chromosomes, Human, Pair 15, DNA, DNA Mutational Analysis, Family Health, Female, Gene Frequency, Genotype, Humans, Ligases, Linkage Disequilibrium, Male, Microsatellite Repeats, Molecular Sequence Data, Polymorphism, Single Nucleotide, Protein Subunits, Receptors, GABA-A, Sequence Deletion, Ubiquitin-Protein Ligases
Show Abstract · Added February 20, 2014
Autistic disorder is a neurodevelopmental disorder with a complex genetic etiology. Observations of maternal duplications affecting chromosome 15q11-q13 in patients with autism and evidence for linkage and linkage disequilibrium to markers in this region in chromosomally normal autism families indicate the existence of a susceptibility locus. We have screened the families of the Collaborative Linkage Study of Autism for several markers spanning a candidate region covering approximately 2 Mb and including the Angelman syndrome gene (UBE3A) and a cluster of gamma-aminobutyric acid (GABA(A)) receptor subunit genes (GABRB3, GABRA5, and GABRG3). We found significant evidence for linkage disequilibrium at marker D15S122, located at the 5' end of UBE3A. This is the first report, to our knowledge, of linkage disequilibrium at UBE3A in autism families. Characterization of null alleles detected at D15S822 in the course of genetic studies of this region showed a small (approximately 5-kb) genomic deletion, which was present at somewhat higher frequencies in autism families than in controls.
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23 MeSH Terms
Identification of functionally variant MDR1 alleles among European Americans and African Americans.
Kim RB, Leake BF, Choo EF, Dresser GK, Kubba SV, Schwarz UI, Taylor A, Xie HG, McKinsey J, Zhou S, Lan LB, Schuetz JD, Schuetz EG, Wilkinson GR
(2001) Clin Pharmacol Ther 70: 189-99
MeSH Terms: ATP Binding Cassette Transporter, Subfamily B, Member 1, Africa, African Continental Ancestry Group, Alleles, Anti-Allergic Agents, Area Under Curve, Cloning, Molecular, DNA Primers, Digoxin, Enzyme Inhibitors, Europe, European Continental Ancestry Group, Genes, MDR, Genetic Variation, Genotype, Haplotypes, Humans, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Terfenadine, Time Factors
Show Abstract · Added March 27, 2014
MDR1 (P-glycoprotein) is an important factor in the disposition of many drugs, and the involved processes often exhibit considerable interindividual variability that may be genetically determined. Single-strand conformational polymorphism analysis and direct sequencing of exonic MDR1 deoxyribonucleic acid from 37 healthy European American and 23 healthy African American subjects identified 10 single nucleotide polymorphisms (SNPs), including 6 nonsynonymous variants, occurring in various allelic combinations. Population frequencies of the 15 identified alleles varied according to racial background. Two synonymous SNPs (C1236T in exon 12 and C3435T in exon 26) and a nonsynonymous SNP (G2677T, Ala893Ser) in exon 21 were found to be linked (MDR1*2 ) and occurred in 62% of European Americans and 13% of African Americans. In vitro expression of MDR1 encoding Ala893 (MDR1*1 ) or a site-directed Ser893 mutation (MDR1*2 ) indicated enhanced efflux of digoxin by cells expressing the MDR1-Ser893 variant. In vivo functional relevance of this SNP was assessed with the known P-glycoprotein drug substrate fexofenadine as a probe of the transporter's activity. In humans, MDR1*1 and MDR1*2 variants were associated with differences in fexofenadine levels, consistent with the in vitro data, with the area under the plasma level-time curve being almost 40% greater in the *1/*1 genotype compared with the *2/*2 and the *1/*2 heterozygotes having an intermediate value, suggesting enhanced in vivo P-glycoprotein activity among subjects with the MDR1*2 allele. Thus allelic variation in MDR1 is more common than previously recognized and involves multiple SNPs whose allelic frequencies vary between populations, and some of these SNPs are associated with altered P-glycoprotein function.
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22 MeSH Terms
Conserved worldwide linkage disequilibrium in the human factor XI gene.
Tarumi T, Martincic D, Whitlock JA, Addy JH, Williams SM, Gailani D
(2000) Genomics 70: 269-72
MeSH Terms: Factor XI, Humans, Linkage Disequilibrium, Polymorphism, Single Nucleotide
Show Abstract · Added May 19, 2014
We have identified, in four diverse human populations, five common single-nucleotide polymorphisms (SNPs) in the coding region of the gene for the blood coagulation protease factor XI. Each SNP has an allele frequency >5% in at least one population. Three of the SNPs (C472T, A844G, and T1234C), spread out over approximately 10 kb of genomic DNA, are in marked linkage disequilibrium (LD) with one another (P < 10(-4)). Interestingly, haplotypes associated with the linked SNPs are conserved across all populations studied, despite significantly different allele frequencies between populations. The presence of such common, widely dispersed haplotypes could complicate the interpretation of LD studies and emphasizes the need for a better understanding of general patterns of LD to facilitate identification of genes for common disorders.
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4 MeSH Terms
A common polymorphism associated with antibiotic-induced cardiac arrhythmia.
Sesti F, Abbott GW, Wei J, Murray KT, Saksena S, Schwartz PJ, Priori SG, Roden DM, George AL, Goldstein SA
(2000) Proc Natl Acad Sci U S A 97: 10613-8
MeSH Terms: Amino Acid Sequence, Animals, Base Sequence, CHO Cells, Cricetinae, DNA Primers, Female, Humans, Long QT Syndrome, Male, Middle Aged, Molecular Sequence Data, Mutagenesis, Mutation, Missense, Polymorphism, Single Nucleotide, Potassium Channels, Potassium Channels, Voltage-Gated, Sulfamethoxazole
Show Abstract · Added January 20, 2015
Drug-induced long QT syndrome (LQTS) is a prevalent disorder of uncertain etiology that predisposes to sudden death. KCNE2 encodes MinK-related peptide 1 (MiRP1), a subunit of the cardiac potassium channel I(Kr) that has been associated previously with inherited LQTS. Here, we examine KCNE2 in 98 patients with drug-induced LQTS, identifying three individuals with sporadic mutations and a patient with sulfamethoxazole-associated LQTS who carried a single-nucleotide polymorphism (SNP) found in approximately 1.6% of the general population. While mutant channels showed diminished potassium flux at baseline and wild-type drug sensitivity, channels with the SNP were normal at baseline but inhibited by sulfamethoxazole at therapeutic levels that did not affect wild-type channels. We conclude that allelic variants of MiRP1 contribute to a significant fraction of cases of drug-induced LQTS through multiple mechanisms and that common sequence variations that increase the risk of life-threatening drug reactions can be clinically silent before drug exposure.
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18 MeSH Terms