551
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Brzustowicz LM, Simone J, Mohseni P, Hayter JE, Hodgkinson KA, Chow EWC, Bassett AS. Linkage disequilibrium mapping of schizophrenia susceptibility to the CAPON region of chromosome 1q22. Am J Hum Genet 2004; 74:1057-63. [PMID: 15065015 PMCID: PMC1181969 DOI: 10.1086/420774] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 02/20/2004] [Indexed: 11/03/2022] Open
Abstract
Previously, we have reported linkage of markers from chromosome 1q22 to schizophrenia, a finding supported by several independent studies. We have now examined the region of strongest linkage for evidence of linkage disequilibrium (LD) in a sample of 24 Canadian familial-schizophrenia pedigrees. Analysis of 14 microsatellites and 15 single-nucleotide polymorphisms (SNPs) from the 5.4-Mb region between D1S1653 and D1S1677 produced significant evidence (nominal P<.05) of LD between schizophrenia and 2 microsatellites and 6 SNPs. All of the markers exhibiting significant LD to schizophrenia fall within the genomic extent of the gene for carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase (CAPON), making it a prime positional candidate for the schizophrenia-susceptibility locus on 1q22, although initial mutation analysis of this gene has not identified any schizophrenia-associated changes within exons. Consistent with several recently identified candidate genes for schizophrenia, CAPON is involved in signal transduction in the NMDA receptor system, highlighting the potential importance of this pathway in the etiology of schizophrenia.
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552
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Arai M, Itokawa M, Yamada K, Toyota T, Arai M, Haga S, Ujike H, Sora I, Ikeda K, Yoshikawa T. Association of neural cell adhesion molecule 1 gene polymorphisms with bipolar affective disorder in Japanese individuals. Biol Psychiatry 2004; 55:804-10. [PMID: 15050861 DOI: 10.1016/j.biopsych.2004.01.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2003] [Revised: 11/20/2003] [Accepted: 01/09/2004] [Indexed: 11/22/2022]
Abstract
BACKGROUND Although the pathogenesis of mood disorders remains unclear, heritable factors have been shown to be involved. Neural cell adhesion molecule 1 (NCAM1) is known to play important roles in cell migration, neurite growth, axonal guidance, and synaptic plasticity. Disturbance of these neurodevelopmental processes is proposed as one etiology for mood disorder. We therefore undertook genetic analysis of NCAM1 in mood disorders. METHODS We determined the complete genomic organization of human NCAM1 gene by comparing complementary deoxyribonucleic acid and genomic sequences; mutation screening detected 11 polymorphisms. The genotypic, allelic, and haplotype distributions of these variants were analyzed in unrelated control individuals (n = 357) and patients with bipolar disorder (n = 151) and unipolar disorder (n = 78), all from central Japan. RESULTS Three single nucleotide polymorphisms, IVS6+32T>C, IVS7+11G>C and IVS12+21C>A, displayed significant associations with bipolar disorder (for allelic associations, nominal p =.04, p =.02, and p =.004, respectively, all p >.05 after Bonferroni corrections). Furthermore, the haplotype located in a linkage disequilibrium block was strongly associated with bipolar disorder (the p value of the most significant three-marker haplotype is .005). CONCLUSIONS Our results suggest that genetic variations in NCAM1 or nearby genes could confer risks associated with bipolar affective disorder in Japanese individuals.
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Affiliation(s)
- Makoto Arai
- Department of Schizophrenia Research, Tokyo Metropolitan Organization for Medical Research, Tokyo Institute of Psychiatry, 2-1-8 Kamikitazawa, Setagaya-ku, Tokyo 156-8585, Japan
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553
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Zhang K, Qin ZS, Liu JS, Chen T, Waterman MS, Sun F. Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res 2004; 14:908-16. [PMID: 15078859 PMCID: PMC479119 DOI: 10.1101/gr.1837404] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed by regions of low LD. A small fraction of SNPs (tag SNPs) is sufficient to capture most of the haplotype structure of the human genome. In this paper, we develop a method to partition haplotypes into blocks and to identify tag SNPs based on genotype data by combining a dynamic programming algorithm for haplotype block partitioning and tag SNP selection based on haplotype data with a variation of the expectation maximization (EM) algorithm for haplotype inference. We assess the effects of using either haplotype or genotype data in haplotype block identification and tag SNP selection as a function of several factors, including sample size, density or number of SNPs studied, allele frequencies, fraction of missing data, and genotyping error rate, using extensive simulations. We find that a modest number of haplotype or genotype samples will result in consistent block partitions and tag SNP selection. The power of association studies based on tag SNPs using genotype data is similar to that using haplotype data.
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Affiliation(s)
- Kui Zhang
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-1113, USA
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554
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Nyholt DR. A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. Am J Hum Genet 2004; 74:765-9. [PMID: 14997420 PMCID: PMC1181954 DOI: 10.1086/383251] [Citation(s) in RCA: 1384] [Impact Index Per Article: 69.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2003] [Accepted: 01/29/2004] [Indexed: 11/03/2022] Open
Abstract
In this report, we describe a simple correction for multiple testing of single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between SNPs. This method provides a useful alternative to more computationally intensive permutation tests. A user-friendly interface (SNPSpD) for performing this correction is available online (http://genepi.qimr.edu.au/general/daleN/SNPSpD/). Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor "loadings" after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.
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Affiliation(s)
- Dale R Nyholt
- Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
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555
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Hamilton SP, Slager SL, Mayo D, Heiman GA, Klein DF, Hodge SE, Fyer AJ, Weissman MM, Knowles JA. Investigation of polymorphisms in the CREM gene in panic disorder. Am J Med Genet B Neuropsychiatr Genet 2004; 126B:111-5. [PMID: 15048659 DOI: 10.1002/ajmg.b.20121] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Clinical and animal studies suggest a role for pathways regulated by cyclic-AMP in anxiety. Mouse gene deletion studies, our own linkage findings on chromosome 10, and a recently published genetic association study by Domschke et al. [2003: Am J Med Genet 117B:70-78] suggest that the cAMP responsive element modulator (CREM) may be involved in panic disorder. We have employed a family-based design to investigate the role of DNA sequence variations in the gene for CREM in panic disorder. We have genotyped 613 individuals in 70 panic disorder pedigrees, as well as 42 parent/offspring triads. Subjects were genotyped at two informative single nucleotide polymorphisms (SNPs) and three polymorphic microsatellites in the CREM genomic region; and the data were analyzed for genetic association and linkage. Linkage analysis employing several diagnostic/genetic models produced a maximum lod score of 0.63 for SNP-1, located in the 5' UTR of CREM, under a dominant model with a broad diagnostic definition of panic disorder. Non-parametric analysis, using the NPL statistic or FBAT, also did not support any linkage or association between the markers and panic disorder. All five markers (spanning 77 kb) used in the study showed modest, but significant linkage disequilibrium. Analysis of 2-, 3-, 4-, or 5-marker haplotypes using TRANSMIT failed to find any globally significant results; however, individual haplotypes containing a single allele of MS-3 were nominally associated with panic disorder. These findings provide little additional evidence for a susceptibility locus for panic disorder either within the CREM gene or in a nearby region of chromosome 10p11 in our sample.
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Affiliation(s)
- Steven P Hamilton
- Department of Psychiatry, College of Physicians and Surgeons at Columbia University and the New York State Psychiatric Institute, 1051 Riverside Drive, New York, NY 10032, USA
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556
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Silander K, Mohlke KL, Scott LJ, Peck EC, Hollstein P, Skol AD, Jackson AU, Deloukas P, Hunt S, Stavrides G, Chines PS, Erdos MR, Narisu N, Conneely KN, Li C, Fingerlin TE, Dhanjal SK, Valle TT, Bergman RN, Tuomilehto J, Watanabe RM, Boehnke M, Collins FS. Genetic variation near the hepatocyte nuclear factor-4 alpha gene predicts susceptibility to type 2 diabetes. Diabetes 2004; 53:1141-9. [PMID: 15047633 DOI: 10.2337/diabetes.53.4.1141] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Finland-United States Investigation Of NIDDM Genetics (FUSION) study aims to identify genetic variants that predispose to type 2 diabetes by studying affected sibling pair families from Finland. Chromosome 20 showed our strongest initial evidence for linkage. It currently has a maximum logarithm of odds (LOD) score of 2.48 at 70 cM in a set of 495 families. In this study, we searched for diabetes susceptibility variant(s) at 20q13 by genotyping single nucleotide polymorphism (SNP) markers in case and control DNA pools. Of 291 SNPs successfully typed in a 7.5-Mb interval, the strongest association confirmed by individual genotyping was with SNP rs2144908, located 1.3 kb downstream of the primary beta-cell promoter P2 of hepatocyte nuclear factor-4 alpha (HNF4A). This SNP showed association with diabetes disease status (odds ratio [OR] 1.33, 95% CI 1.06-1.65, P = 0.011) and with several diabetes-related traits. Most of the evidence for linkage at 20q13 could be attributed to the families carrying the risk allele. We subsequently found nine additional associated SNPs spanning a 64-kb region, including the P2 and P1 promoters and exons 1-3. Our results and the independent observation of association of SNPs near the P2 promoter with diabetes in a separate study population of Ashkenazi Jewish origin suggests that variant(s) located near or within HNF4A increases susceptibility to type 2 diabetes.
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Affiliation(s)
- Kaisa Silander
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
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557
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Edenberg HJ, Dick DM, Xuei X, Tian H, Almasy L, Bauer LO, Crowe RR, Goate A, Hesselbrock V, Jones K, Kwon J, Li TK, Nurnberger JI, O'Connor SJ, Reich T, Rice J, Schuckit MA, Porjesz B, Foroud T, Begleiter H. Variations in GABRA2, encoding the alpha 2 subunit of the GABA(A) receptor, are associated with alcohol dependence and with brain oscillations. Am J Hum Genet 2004; 74:705-14. [PMID: 15024690 PMCID: PMC1181946 DOI: 10.1086/383283] [Citation(s) in RCA: 474] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2003] [Accepted: 02/02/2004] [Indexed: 12/13/2022] Open
Abstract
Alcoholism is a complex disease with both genetic and environmental risk factors. To identify genes that affect the risk for alcoholism, we systematically ascertained and carefully assessed individuals in families with multiple alcoholics. Linkage and association analyses suggested that a region of chromosome 4p contained genes affecting a quantitative endophenotype, brain oscillations in the beta frequency range (13-28 Hz), and the risk for alcoholism. To identify the individual genes that affect these phenotypes, we performed linkage disequilibrium analyses of 69 single-nucleotide polymorphism (SNPs) within a cluster of four GABA(A) receptor genes, GABRG1, GABRA2, GABRA4, and GABRB1, at the center of the linked region. GABA(A) receptors mediate important effects of alcohol and also modulate beta frequencies. Thirty-one SNPs in GABRA2, but only 1 of the 20 SNPs in the flanking genes, showed significant association with alcoholism. Twenty-five of the GABRA2 SNPs, but only one of the SNPs in the flanking genes, were associated with the brain oscillations in the beta frequency. The region of strongest association with alcohol dependence extended from intron 3 past the 3' end of GABRA2; all 43 of the consecutive three-SNP haplotypes in this region of GABRA2 were highly significant. A three-SNP haplotype was associated with alcoholism, with P=.000000022. No coding differences were found between the high-risk and low-risk haplotypes, suggesting that the effect is mediated through gene regulation. The very strong association of GABRA2 with both alcohol dependence and the beta frequency of the electroencephalogram, combined with biological evidence for a role of this gene in both phenotypes, suggest that GABRA2 might influence susceptibility to alcohol dependence by modulating the level of neural excitation.
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558
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Rubio JP, Bahlo M, Tubridy N, Stankovich J, Burfoot R, Butzkueven H, Chapman C, Johnson L, Marriott M, Mraz G, Tait B, Wilkinson C, Taylor B, Speed TP, Foote SJ, Kilpatrick TJ. Extended haplotype analysis in the HLA complex reveals an increased frequency of the HFE-C282Y mutation in individuals with multiple sclerosis. Hum Genet 2004; 114:573-80. [PMID: 15014978 DOI: 10.1007/s00439-004-1095-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Accepted: 01/23/2003] [Indexed: 02/02/2023]
Abstract
In order to resolve a multiple sclerosis (MS) susceptibility locus that we had identified in earlier work at the telomeric end of the HLA complex, we genotyped another 34 microsatellite markers (47 in total) across the class I/extended class I region in 166 Tasmanian MS case and 104 control families (D6S299-D6S265). Extended MS susceptibility haplotypes, up to 9 Mb in length, were observed in 11% of MS cases and 4% of controls. Direct comparison of the telomerically extended portion of the MS susceptibility haplotype in HFE-Cys282Tyr (C282Y)-homozygous haemochromatosis patients identified a common ancestry for this genomic segment, which translated into an increased frequency of the C282Y allele in 489 MS cases from Tasmania and Victoria (10.2%) compared with controls (6.7%). Six C282Y homozygotes (1.2%), a three-fold increased rate over the general population, and 88 heterozygotes (18%) were identified. One C282Y-homozygous female was identified who had MS and was being treated for symptoms of iron overload. Interestingly, for 71 Victorian MS cases not of north western European (NWE) ancestry, a DR15-independent reduction in the frequency of the C282Y allele was observed, supporting the theory of a NWE origin for the C282Y-variant of the DR15 ancestral haplotype (C282Y-HLA-A*0301-B*0702-DRB1*1501-DQB1*0602). The results of linkage disequilibrium (LD) and log linear modelling analyses suggest that C282Y is increased in MS cases of NWE ancestry because it is in LD with the ancestral DR15 susceptibility haplotype (7.1) and that it does not play an independent role in predisposition to MS. However, our findings provide the impetus for further investigations into the role of iron metabolism in the severity of MS.
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Affiliation(s)
- Justin P Rubio
- Walter and Eliza Hall Institute of Medical Research, 3050 Parkville, Victoria, Australia.
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559
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Winsey S, Lonie L, Allen J, Bunce M, Marshall SE, Wojnarowska F. Genetic variation in COL17A1 and the development of bullous pemphigoid. Exp Dermatol 2004; 13:140-7. [PMID: 14987253 DOI: 10.1111/j.0906-6705.2004.0138.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Bullous pemphigoid (BP) is an autoimmune blistering disease of the skin characterized by autoantibody attack on collagen XVII. OBJECTIVES To characterize the genetic complexity of COL17A1, the gene which encodes for the autoantigen collagen XVII. The data will be used to determine whether there is an association between polymorphisms and haplotypes of COL17A1 and genetic susceptibility to development of BP. METHODS The genetic complexity in COL17A1 was deduced by screening and then sequencing the gene. Haplotypes were constructed from the resulting polymorphisms using the statistical programme PHASE. The linkage disequilibrium (D') between the polymorphisms was deduced from haplotypic data using the statistical programme GOLD. Association of the polymorphisms and haplotypes was tested for, in a cohort of BP patients and controls. RESULTS Screening of COL17A1 for genetic variation was carried out in 29 individuals of North European caucasoid origin, and it revealed 19 single-nucleotide polymorphisms in approximately 14.7 kb of sequence. These variants resulted in 60 different haplotypes in 191 individuals, of which 13 occurred above 1% in the population. D' between the variants was found to be extensive, have a low correlation with physical distance and to extend over 33.8 kb. No association was found with any of the polymorphisms or haplotypes and development of BP, when tested for, in a cohort of patients and controls. CONCLUSION This study provides an extensive description of the genetic variation in COL17A1 and shows no association of the genetic variants with susceptibility to BP.
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Affiliation(s)
- Samantha Winsey
- Department of Dermatology, University of Oxford, Churchill Hospital, Oxford, UK
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560
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Lappalainen J, Kranzler HR, Petrakis I, Somberg LK, Page G, Krystal JH, Gelernter J. Confirmation and fine mapping of the chromosome 1 alcohol dependence risk locus. Mol Psychiatry 2004; 9:312-9. [PMID: 15094791 DOI: 10.1038/sj.mp.4001429] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Two previous large genetic linkage studies in the US population have implicated an area in chromosome 1p to contain a susceptibility gene for alcohol dependence. The 1-LOD support interval of the linkage signal spans about 30 cM and contains >30000000 DNA base pairs (bp) and 700 predicted genes. In order to reduce the size of the candidate area and potentially identify novel candidate genes within this region, we fine-mapped this area using closely spaced short tandem repeat (STR) markers and the transmission disequilibrium test (TDT) in small nuclear families. The subjects were 87 European-American families including one or more alcohol-dependent offspring (93 children and 174 parents). The initial marker set consisted of 30 STR markers, spanning the Marshfield map interval between 101.48 and 130.73 cM. Using the TDTPHASE program, we identified three markers in the distal part of this region (125-126 cM), which showed evidence of transmission disequilibrium. On the basis of this result, an additional 12 STR markers were genotyped in this region; some of these markers provided additional evidence for linkage disequilibrium. The strongest evidence for transmission disequilibrium was obtained at the marker D1S406 (P=0.005, 126.16 cM), with supporting evidence from three neighboring STR markers D1S424 (126.16 cM, P=0.01), D1S2804 (126.16 cM, P=0.04), and D1S2776 (126.16 cM, P=0.02), which are all located within a <350000 bp interval. These findings suggest that a gene (or genes) causing susceptibility to alcohol dependence resides near location 126.16 cM on chromosome 1. In addition, these results provide independent confirmation of the linkage finding regarding the identification of at least one gene in this region increasing the risk for alcohol dependence.
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Affiliation(s)
- J Lappalainen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06516, USA
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561
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Hamilton SP, Slager SL, De Leon AB, Heiman GA, Klein DF, Hodge SE, Weissman MM, Fyer AJ, Knowles JA. Evidence for genetic linkage between a polymorphism in the adenosine 2A receptor and panic disorder. Neuropsychopharmacology 2004; 29:558-65. [PMID: 14666117 DOI: 10.1038/sj.npp.1300311] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Data from clinical and behavioral pharmacological studies have implicated adenosine in anxiety behaviors, while genetic studies have suggested that adenosine receptors may be associated with panic disorder. We have undertaken an analysis of several DNA sequence variations in the adenosine 2A receptor (ADORA2A) in a large sample of panic disorder pedigrees. Individuals from 70 panic disorder pedigrees, and 83 child-parent 'trios', were genotyped at five single-nucleotide polymorphisms (SNPs) in and near the ADORA2A gene and were analyzed for genetic linkage and association. Linkage analysis revealed elevated LOD scores for a silent substitution (1083C/T, SNP-4) in the second coding exon. This SNP has been previously reported to be associated with panic disorder. We observed a maximal heterogeneity LOD score of 2.98 (theta=0) under a recessive genetic model and narrow diagnostic model. Other SNPs showed no evidence for linkage. Association tests were not significant for any of the five ADORA2A SNPs. When SNP haplotypes were assessed in the triads with TRANSMIT, one 3-marker haplotype (SNPs 1, 4, 5) was nominally significantly associated with panic disorder (p=0.029). Pairwise estimations of linkage disequilibrium between the SNPs showed strong patterns of linkage disequilibrium across the ADORA2A locus. Analyses carried out by broadening the panic disorder phenotype to include agoraphobia continued to support linkage to ADORA2A. Our findings provide evidence for a susceptibility locus for panic disorder, and possibly including agoraphobia, either within the ADORA2A gene or in a nearby region of chromosome 22, and serves as the first successful candidate gene replication study in panic disorder.
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Affiliation(s)
- Steven P Hamilton
- Department of Psychiatry, College of Physicians and Surgeons at Columbia University and the New York State Psychiatric Institute, New York City, NY 10032, USA
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562
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Raiford KL, Shao Y, Allen IC, Martin ER, Menold MM, Wright HH, Abramson RK, Worley G, DeLong GR, Vance JM, Cuccaro ML, Gilbert JR, Pericak-Vance MA. No association between the APOE gene and autism. Am J Med Genet B Neuropsychiatr Genet 2004; 125B:57-60. [PMID: 14755445 DOI: 10.1002/ajmg.b.20104] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Autism is a neurodevelopmental disorder characterized by stereotypic and repetitive behavior and interests, together with social and communicative deficiencies. The results of several genomic screens suggest the presence of an autism susceptibility locus on chromosome 19p13.2-q13.4. The apolipoprotein E (APOE) gene on chromosome 19 encodes for a protein, apoE, whose different isoforms (E2, E3, E4) influence neuronal growth. APOE participates in lipid transport and metabolism, repair, growth, and maintenance of axons and myelin during neuronal development. The APOE protein competes with the Reelin protein for VLDL/APOER2 receptor binding. Several studies have reported evidence for an association between autism and the Reelin gene. Based on these data we tested for association between APOE and autism using family-based association methods in a data set of 322 autism families. Three promoter, one intronic, and one 3' UTR single nucleotide polymorphisms (SNPs) in the APOE gene (-491a/t, -427c/t, -219g/t, 113c/g, and 5361c/t) as well as the APOE functional polymorphism (E2, E3, E4) were examined and failed to reveal significant evidence that autism is associated with APOE.
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Affiliation(s)
- K L Raiford
- Department of Medicine and Center for Human Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
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563
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Nabi R, Serajee FJ, Chugani DC, Zhong H, Huq AHMM. Association of tryptophan 2,3 dioxygenase gene polymorphism with autism. Am J Med Genet B Neuropsychiatr Genet 2004; 125B:63-8. [PMID: 14755447 DOI: 10.1002/ajmg.b.20147] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although elevation of blood and platelet serotonin has been documented in autism, genetic analyses of serotonin transporter gene have given conflicting results. Tryptophan 2,3 dioxygenase (TDO2) is the rate-limiting enzyme in the catabolism of tryptophan, the precursor of serotonin. A mutation that results in decreased activity of the TDO2 can decrease catabolism of tryptophan and increase the level of whole body serotonin. As such it is a potential candidate gene for autism. We have investigated five single nucleotide polymorphisms in the TDO2 gene for association with autistic disorder. One hundred and ninety six multiplex autistic disorder families were tested using transmission disequilibrium test. There was a significant difference in the transmission of a promoter variant to autistic subjects (P = 0.0006). Haplotype analysis also demonstrated significant difference in the transmission of TDO2 haplotypes to autistic subjects (P = 0.0027). Our results suggest the presence of a susceptibility mutation in the TDO2 or a nearby gene, but may also represent a chance finding.
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Affiliation(s)
- Rafiqun Nabi
- Department of Pediatrics, Wayne State University, Detroit, Michigan, USA
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564
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Hull J, Rowlands K, Lockhart E, Sharland M, Moore C, Hanchard N, Kwiatkowski DP. Haplotype mapping of the bronchiolitis susceptibility locus near IL8. Hum Genet 2004; 114:272-9. [PMID: 14605870 DOI: 10.1007/s00439-003-1038-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2003] [Accepted: 09/15/2003] [Indexed: 10/26/2022]
Abstract
Susceptibility to viral bronchiolitis, the commonest cause of infant admissions to hospital in the industrialised world, is associated with polymorphism at the IL8 locus. Here we map the genomic boundaries of the disease association by case-control analysis and TDT in 580 affected UK infants. Markers for association mapping were chosen after determining patterns of linkage disequilibrium across the surrounding region of chromosome 4q, a 550-kb segment containing nine genes, extending from AFP to PPBP. The region has three major clusters of high linkage disequilibrium and is notable for its low haplotypic diversity. We exclude adjacent chemokine genes as the cause of the association, and identify a disease-associated haplotype that spans a 250-kb region from AFM to IL8. In between these two genes there is only one structural feature of interest, a novel gene RASSF6, which is predicted to encode a Ras effector protein.
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Affiliation(s)
- Jeremy Hull
- University Department of Paediatrics, Level 4, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK.
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565
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Wen G, Mahata SK, Cadman P, Mahata M, Ghosh S, Mahapatra NR, Rao F, Stridsberg M, Smith DW, Mahboubi P, Schork NJ, O’Connor DT, Hamilton BA. Both rare and common polymorphisms contribute functional variation at CHGA, a regulator of catecholamine physiology. Am J Hum Genet 2004; 74:197-207. [PMID: 14740315 PMCID: PMC1181918 DOI: 10.1086/381399] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Accepted: 11/11/2003] [Indexed: 11/03/2022] Open
Abstract
The chromogranin/secretogranin proteins are costored and coreleased with catecholamines from secretory vesicles in chromaffin cells and noradrenergic neurons. Chromogranin A (CHGA) regulates catecholamine storage and release through intracellular (vesiculogenic) and extracellular (catecholamine release-inhibitory) mechanisms. CHGA is a candidate gene for autonomic dysfunction syndromes, including intermediate phenotypes that contribute to human hypertension. Here, we show a surprising pattern of CHGA variants that alter the expression and function of this gene, both in vivo and in vitro. Functional variants include both common alleles that quantitatively alter gene expression and rare alleles that qualitatively change the encoded product to alter the signaling potency of CHGA-derived catecholamine release-inhibitory catestatin peptides.
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Affiliation(s)
- Gen Wen
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Sushil K. Mahata
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Peter Cadman
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Manjula Mahata
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Sajalendu Ghosh
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Nitish R. Mahapatra
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Fangwen Rao
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Mats Stridsberg
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Douglas W. Smith
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Payam Mahboubi
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Nicholas J. Schork
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Daniel T. O’Connor
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
| | - Bruce A. Hamilton
- Department of Medicine, Division of Biology, Department of Psychiatry, and John and Rebecca Moores University of California San Diego Cancer Center, University of California San Diego School of Medicine, La Jolla; VA San Diego Healthcare System, San Diego; and Department of Medical Sciences, University Hospital, Uppsala, Sweden
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566
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Mira MT, Alcaïs A, Nguyen VT, Moraes MO, Di Flumeri C, Vu HT, Mai CP, Nguyen TH, Nguyen NB, Pham XK, Sarno EN, Alter A, Montpetit A, Moraes ME, Moraes JR, Doré C, Gallant CJ, Lepage P, Verner A, Van De Vosse E, Hudson TJ, Abel L, Schurr E. Susceptibility to leprosy is associated with PARK2 and PACRG. Nature 2004; 427:636-40. [PMID: 14737177 DOI: 10.1038/nature02326] [Citation(s) in RCA: 324] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Accepted: 01/07/2004] [Indexed: 11/09/2022]
Abstract
Leprosy is caused by Mycobacterium leprae and affects about 700,000 individuals each year. It has long been thought that leprosy has a strong genetic component, and recently we mapped a leprosy susceptibility locus to chromosome 6 region q25-q26 (ref. 3). Here we investigate this region further by using a systematic association scan of the chromosomal interval most likely to harbour this leprosy susceptibility locus. In 197 Vietnamese families we found a significant association between leprosy and 17 markers located in a block of approx. 80 kilobases overlapping the 5' regulatory region shared by the Parkinson's disease gene PARK2 and the co-regulated gene PACRG. Possession of as few as two of the 17 risk alleles was highly predictive of leprosy. This was confirmed in a sample of 975 unrelated leprosy cases and controls from Brazil in whom the same alleles were strongly associated with leprosy. Variants in the regulatory region shared by PARK2 and PACRG therefore act as common risk factors for leprosy.
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Affiliation(s)
- Marcelo T Mira
- McGill Centre for the Study of Host Resistance and Department of Human Genetics, McGill University, 1650 Cedar Avenue, Montreal, PQ H3G1A4, Canada
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567
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Jamieson SE, Miller EN, Black GF, Peacock CS, Cordell HJ, Howson JMM, Shaw MA, Burgner D, Xu W, Lins-Lainson Z, Shaw JJ, Ramos F, Silveira F, Blackwell JM. Evidence for a cluster of genes on chromosome 17q11–q21 controlling susceptibility to tuberculosis and leprosy in Brazilians. Genes Immun 2004; 5:46-57. [PMID: 14735149 DOI: 10.1038/sj.gene.6364029] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The region of conserved synteny on mouse chromosome 11/human 17q11-q21 is known to carry a susceptibility gene(s) for intramacrophage pathogens. The region is rich in candidates including NOS2A, CCL2/MCP-1, CCL3/MIP-1alpha, CCL4/MIP-1beta, CCL5/RANTES, CCR7, STAT3 and STAT5A/5B. To examine the region in man, we studied 92 multicase tuberculosis (627 individuals) and 72 multicase leprosy (372 individuals) families from Brazil. Multipoint nonparametric analysis (ALLEGRO) using 16 microsatellites shows two peaks of linkage for leprosy at D17S250 (Z(lr) score 2.34; P=0.01) and D17S1795 (Z(lr) 2.67; P=0.004) and a single peak for tuberculosis at D17S250 (Z(lr) 2.04; P=0.02). Combined analysis shows significant linkage (peak Z(lr) 3.38) at D17S250, equivalent to an allele sharing LOD score 2.48 (P=0.0004). To determine whether one or multiple genes contribute, 49 informative single nucleotide polymorphisms were typed in candidate genes. Family-based allelic association testing that was robust to family clustering demonstrated significant associations with tuberculosis susceptibility at four loci separated by intervals (NOS2A-8.4 Mb-CCL18-32.3 kb-CCL4-6.04 Mb-STAT5B) up to several Mb. Stepwise conditional logistic regression analysis using a case/pseudo-control data set showed that the four genes contributed separate main effects, consistent with a cluster of susceptibility genes across 17q11.2.
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Affiliation(s)
- S E Jamieson
- Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Addenbrookes Hospital, Cambridge, UK
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568
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Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, Ghori J, Whittaker P, Collins A, Morris AP, Bentley D, Cardon LR, Deloukas P. The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum Mol Genet 2004; 13:577-88. [PMID: 14734624 DOI: 10.1093/hmg/ddh060] [Citation(s) in RCA: 165] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Linkage disequilibrium (LD) is a measure of the degree of association between alleles in a population. The detection of disease-causing variants by association with neighbouring single nucleotide polymorphisms (SNPs) depends on the existence of strong LD between them. Previous studies have indicated that the extent of LD is highly variable in different chromosome regions and different populations, demonstrating the importance of genome-wide accurate measurement of LD at high resolution throughout the human genome. A uniform feature of these studies has been the inability to detect LD in regions of low marker density. To investigate the dependence of LD patterns on marker selection we performed a high-resolution study in African-American, Asian and UK Caucasian populations. We selected over 5000 SNPs with an average spacing of approximately 1 SNP per 2 kb after validating ca 12 000 SNPs derived from a dense SNP collection (1 SNP per 0.3 kb on average). Applications of different statistical methods of LD assessment highlight similar areas of high and low LD. However, at high resolution, features such as overall sequence coverage in LD blocks and block boundaries vary substantially with respect to marker density. Model-based linkage disequilibrium unit (LDU) maps appear robust to marker density and consistently influenced by marker allele frequency. The results suggest that very dense marker sets will be required to yield stable views of fine-scale LD in the human genome.
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Affiliation(s)
- Xiayi Ke
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK
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569
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Barkley RA, Chakravarti A, Cooper RS, Ellison RC, Hunt SC, Province MA, Turner ST, Weder AB, Boerwinkle E. Positional identification of hypertension susceptibility genes on chromosome 2. Hypertension 2004; 43:477-82. [PMID: 14732741 DOI: 10.1161/01.hyp.0000111585.76299.f7] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chromosome 2 has been consistently identified as a genomic region with genetic linkage evidence suggesting that one or more loci contributes to blood pressure and hypertension status. As with all complex disease traits, following-up linkage evidence to identify the underlying susceptibility gene(s) is an arduous yet biologically and clinically important task. Using combined positional candidate gene methods, the Family Blood Pressure Program (FBPP) has concentrated efforts in narrowing a large region of chromosome 2, demonstrating evidence for linkage in several populations, and identifying underlying candidate hypertension susceptibility gene(s). Initial informatics efforts identified the boundaries of the region and the known genes within it. A total of 82 polymorphic sites in 8 genes were genotyped in a large hypothesis-generating sample consisting of 1640 African Americans, 1339 whites, and 1616 Mexican Americans. After resampling-based false discovery adjustment, SLC4A5, a sodium bicarbonate transporter, was identified as a primary candidate gene for hypertension. Polymorphisms in SLC4A5 were subsequently genotyped and analyzed for validation in two other subcomponents of the FBPP, each contributing African Americans (N=461; N=778) and whites (N=550; N=967). Again, single nucleotide polymorphisms within this gene were significantly associated with blood pressure levels and hypertension status. Although not identifying a single causal gene variant that is significantly associated with blood pressure levels and hypertension status across all samples, the results further implicate SLC4A5 as a candidate hypertension susceptibility gene. Moreover, the present study validates previous evidence for one or more genes on chromosome 2 that influence hypertension-related phenotypes in the population-at-large.
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Affiliation(s)
- Ruth Ann Barkley
- Human Genetics Center and Institute of Molecular Medicine, of Texas Health Science Center at Houston, USA
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570
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Loh EW, Fann CSJ, Chang YT, Chang CJ, Cheng ATA. Endogenous Opioid Receptor Genes and Alcohol Dependence Among Taiwanese Han. Alcohol Clin Exp Res 2004; 28:15-9. [PMID: 14745298 DOI: 10.1097/01.alc.0000106303.41755.b8] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Nonselective opioid antagonists reduce alcohol consumption under various experimental situations, and several association studies have examined possible roles of opioid receptor mu (OPRM), delta (OPRD), and kappa (OPRK) genes in the development of alcohol dependence. METHODS We examined 20 single nucleotide polymorphisms (SNPs) across the OPRM, OPRD, and OPRK genes in 158 alcohol-dependent subjects and 149 controls. Differences in allele frequency and genotype distribution between case subjects and controls, as well as the deviation from Hardy-Weinberg equilibrium, were examined using Fisher's exact tests. RESULTS No significant difference in either allele or genotype frequency was found between case subjects and controls for each of the SNPs. CONCLUSIONS Our findings do not support a possible role of the opioid receptor genes for the proclivity to alcohol dependence in the Taiwanese Han.
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Affiliation(s)
- El Wui Loh
- National Genotyping Center at Academia Sinica, Academia Sinica, Taipei, Taiwan
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571
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Haines J, Camarata S. Examination of candidate genes in language disorder: A model of genetic association for treatment studies. ACTA ACUST UNITED AC 2004; 10:208-17. [PMID: 15611983 DOI: 10.1002/mrdd.20035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The purpose of this review is to provide a model for studying genetic association of response to intervention in child language disorders. In addition to a theoretical overview and review of different approaches to studying candidate genes, a specific methodology for completing this type of analysis is presented. The goal of the analysis is to provide detail beyond simple broad phenotyping for affected and nonaffected individuals and to take advantage of data yielded from concise behavioral phenotyping often available in treatment studies.
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Affiliation(s)
- Jonathan Haines
- Kennedy Center Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
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572
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Chen YS, Akula N, Detera-Wadleigh SD, Schulze TG, Thomas J, Potash JB, DePaulo JR, McInnis MG, Cox NJ, McMahon FJ. Findings in an independent sample support an association between bipolar affective disorder and the G72/G30 locus on chromosome 13q33. Mol Psychiatry 2004; 9:87-92; image 5. [PMID: 14699445 DOI: 10.1038/sj.mp.4001453] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Markers near the nested genes G72 and G30 on chromosome 13q33 have been implicated in the etiology of schizophrenia and, recently, bipolar affective disorder (BPAD). Hattori et al (2003) reported that single-nucleotide polymorphisms (SNPs) near the G72/G30 locus were associated with BPAD in a sample of 22 pedigrees, and that SNP haplotypes were associated in a second, larger sample of triads. The present study attempts to replicate this finding in an independent case-control sample. Six SNPs near the G72/G30 locus, including the most strongly associated markers in the previous study, were tested in 139 cases and 113 ethnically matched controls. Significant association was detected between BPAD and two adjacent SNPs (smallest P=0.007; global P=0.024). Haplotype analysis produced additional support for association (smallest P=0.004; global P=0.004). Analysis of 31 unlinked microsatellite markers detected no population stratification in the cases or controls studied. Although the associated alleles and haplotypes differ from those previously reported, these new results provide further evidence, in an independent sample, for an association between BPAD and genetic variation in the vicinity of the genes G72 and G30.
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Affiliation(s)
- Y-S Chen
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
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573
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Dick DM, Edenberg HJ, Xuei X, Goate A, Kuperman S, Schuckit M, Crowe R, Smith TL, Porjesz B, Begleiter H, Foroud T. Association of GABRG3 With Alcohol Dependence. Alcohol Clin Exp Res 2004; 28:4-9. [PMID: 14745296 DOI: 10.1097/01.alc.0000108645.54345.98] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Evidence from human, animal, and in vitro cell models suggests that gamma-aminobutyric acid (GABA), the major inhibitory neurotransmitter in the human central nervous system, is involved in many of the neurochemical pathways that affect alcohol use, abuse, and dependence. Both linkage and association to the region on chromosome 15q that contains a cluster of GABAA receptor genes have previously been reported, but the role of these genes in alcoholism remains inconclusive. METHODS We conducted family-based association analyses by using a large sample of multiplex alcoholic families collected as part of the Collaborative Study on the Genetics of Alcoholism, to test for an association between alcohol dependence and the GABAA receptor genes clustered on chromosome 15q. Multiple single-nucleotide polymorphisms were tested in each of the three chromosome 15q GABAA receptor genes: GABRA5, GABRB3, and GABRG3. RESULTS Using both classic trio-based analyses and extended-family analyses, we found consistent evidence of association between alcohol dependence and GABRG3. Nearly all single-nucleotide polymorphisms across the gene yielded evidence of association, and haplotype analyses were highly significant. No consistent evidence of association was observed with either GABRA5 or GABRB3, nor was there evidence for parent-of-origin effects with any of the genes. CONCLUSIONS These analyses suggest that GABRG3 may be involved in the risk for alcohol dependence. These findings support the theory that the predisposition to alcoholism may be inherited as a general state of central nervous system disinhibition/hyperexcitability that results from an altered responsiveness to GABA.
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Affiliation(s)
- Danielle M Dick
- Indiana University School of Medicine, Indianapolis, Indiana, USA
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574
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Sharan K, Surrey S, Ballas S, Borowski M, Devoto M, Wang KF, Sandler E, Keller M. Association of T-786C
eNOS gene polymorphism with increased susceptibility to acute chest syndrome in females with sickle cell disease. Br J Haematol 2003; 124:240-3. [PMID: 14687036 DOI: 10.1046/j.1365-2141.2003.04762.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Acute chest syndrome (ACS) is a life-threatening complication of sickle cell disease (SCD). A retrospective study was performed to evaluate the role of endothelial nitric oxide synthase (eNOS) gene polymorphisms (E298D and T-786C) in African-American SCD patients. The D298 allele showed no association; the C-786 allele showed a statistically significant association (P = 0.0061) in female ACS cases. Multiple logistic regression analysis showed that relative risk of ACS was 8.695 (P = 0.0076, 95% confidence interval 1.761-42.920) for female carriers of C-786. eNOS T-786C is a gender-specific genetic modifier that is associated with increased susceptibility to ACS in female SCD patients.
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Affiliation(s)
- K Sharan
- Division of Hematology and Cardeza Foundation for Hematologic Research, Department of Medicine, Jefferson Medical College, 7th Floor Curtis Building, 1015 Walnut Street, Philadelphia, PA 19107, USA
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575
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Schulze TG, Zhang K, Chen YS, Akula N, Sun F, McMahon FJ. Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome. Hum Mol Genet 2003; 13:335-42. [PMID: 14681300 DOI: 10.1093/hmg/ddh035] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent studies suggest that the genome is organized into blocks of haplotypes, and efforts to create a genome-wide haplotype map of single-nucleotide polymorphisms (SNPs) are already underway. Haplotype blocks are defined algorithmically and to date several algorithms have been proposed. However, little is known about their relative performance in real data or about the impact of allele frequencies and parameter choices on the detection of haplotype blocks and the markers that tag them. Here we present a formal comparison of two major algorithms, a linkage disequilibrium (LD)-based method and a dynamic programming algorithm (DPA), in three chromosomal regions differing in gene content and recombination rate. The two methods produced strikingly different results. DPA identified fewer and larger haplotype blocks as well as a smaller set of tag SNPs than the LD method. For both methods, the results were strongly dependent on the allele frequency. Decreasing the minor allele frequency led to an up to 3.7-fold increase in the number of haplotype blocks and tag SNPs. Definition of haploytpe blocks and tag SNPs was also sensitive to parameter changes, but the results could not be reconciled simply by parameter adjustment. These results show that two major methods for detecting haplotype blocks and tag SNPs can produce different results in the same data and that these results are sensitive to marker allele frequencies and parameter choices. More information is needed to guide the choice of method, marker allele frequencies, and parameters in the development of a haplotype map.
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Affiliation(s)
- Thomas G Schulze
- Dicvision of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health (ZI), 68159 Mannheim, Germany.
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576
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Bacchelli E, Blasi F, Biondolillo M, Lamb JA, Bonora E, Barnby G, Parr J, Beyer KS, Klauck SM, Poustka A, Bailey AJ, Monaco AP, Maestrini E. Screening of nine candidate genes for autism on chromosome 2q reveals rare nonsynonymous variants in the cAMP-GEFII gene. Mol Psychiatry 2003; 8:916-24. [PMID: 14593429 DOI: 10.1038/sj.mp.4001340] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The results from several genome scans indicate that chromosome 2q21-q33 is likely to contain an autism susceptibility locus. We studied the potential contribution of nine positional and functional candidate genes: TBR-1; GAD1; DLX1; DLX2; cAMP-GEFII; CHN1; ATF2; HOXD1 and NEUROD1. Screening these genes for DNA variants and association analysis using intragenic single nucleotide polymorphisms did not provide evidence for a major role in the aetiology of autism. Four rare nonsynonymous variants were identified, however, in the cAMP-GEFII gene. These variants were present in five families, where they segregate with the autistic phenotype, and were not observed in control individuals. The significance of these variants is unclear, as their low frequency in IMGSAC families does not account for the relatively strong linkage signal at the 2q locus. Further studies are needed to clarify the contribution of cAMP-GEFII gene variants to autism susceptibility.
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Affiliation(s)
- E Bacchelli
- Dipartimento di Biologia Evoluzionistica Sperimentale, University of Bologna, Bologna, Italy
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577
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Duan J, Sanders AR, Molen JEV, Martinolich L, Mowry BJ, Levinson DF, Crowe RR, Silverman JM, Gejman PV. Polymorphisms in the 5'-untranslated region of the human serotonin receptor 1B (HTR1B) gene affect gene expression. Mol Psychiatry 2003; 8:901-10. [PMID: 14593427 DOI: 10.1038/sj.mp.4001403] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We present evidence of complex balancing regulation of HTR1B transcription by common polymorphisms in its promoter. Computational analysis of the HTR1B gene predicted that a 5' segment, spanning common DNA sequence variations, T-261G, A-161T, and -182INS/DEL-181, contained a putative functional promoter. Using a secreted alkaline phosphatase (SEAP) reporter gene system, we found that the haplotype -261G_-182INS-181_A-161 enhanced transcriptional activity 2.3-fold compared with the haplotype T-261_-182INS-181_A-161. Conversely, -161T reversed this, and the net effect when -261G and -161T were in the same haplotype (-261G_-182INS-181_-161T) was equivalent to the major haplotype (T-261_-182INS-181_A-161). Electrophoretic mobility shift experiments showed that -261G and -161T modify the binding of transcription factors (TFs): -261G generates a new AP2 binding site, while alleles A-161 and -161T exhibit different binding characteristics to AP1. T-261G and A-161T were found to be in linkage disequilibrium (LD) with G861C in a European ancestry population. Interestingly, G861C has been reported to be associated with several psychiatric disorders. Our results indicate that HTR1B is the target of substantial transcriptional genetic regulation by common haplotypes, which are in LD with the HTR1B single-nucleotide polymorphism (SNP) most commonly used in association studies.
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Affiliation(s)
- J Duan
- Center for Psychiatric Genetics, Evanston Northwestern Healthcare (ENH) Research Institute, ENH & Northwestern University, Evanston, IL 60206, USA
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578
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Allen M, Heinzmann A, Noguchi E, Abecasis G, Broxholme J, Ponting CP, Bhattacharyya S, Tinsley J, Zhang Y, Holt R, Jones EY, Lench N, Carey A, Jones H, Dickens NJ, Dimon C, Nicholls R, Baker C, Xue L, Townsend E, Kabesch M, Weiland SK, Carr D, von Mutius E, Adcock IM, Barnes PJ, Lathrop GM, Edwards M, Moffatt MF, Cookson WOCM. Positional cloning of a novel gene influencing asthma from chromosome 2q14. Nat Genet 2003; 35:258-63. [PMID: 14566338 DOI: 10.1038/ng1256] [Citation(s) in RCA: 250] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2003] [Accepted: 09/29/2003] [Indexed: 12/20/2022]
Abstract
Asthma is a common disease in children and young adults. Four separate reports have linked asthma and related phenotypes to an ill-defined interval between 2q14 and 2q32 (refs. 1-4), and two mouse genome screens have linked bronchial hyper-responsiveness to the region homologous to 2q14 (refs. 5,6). We found and replicated association between asthma and the D2S308 microsatellite, 800 kb distal to the IL1 cluster on 2q14. We sequenced the surrounding region and constructed a comprehensive, high-density, single-nucleotide polymorphism (SNP) linkage disequilibrium (LD) map. SNP association was limited to the initial exons of a solitary gene of 3.6 kb (DPP10), which extends over 1 Mb of genomic DNA. DPP10 encodes a homolog of dipeptidyl peptidases (DPPs) that cleave terminal dipeptides from cytokines and chemokines, and it presents a potential new target for asthma therapy.
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579
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Traherne JA, Hill MR, Hysi P, D'Amato M, Broxholme J, Mott R, Moffatt MF, Cookson WOCM. LD mapping of maternally and non-maternally derived alleles and atopy in FcepsilonRI-beta. Hum Mol Genet 2003; 12:2577-85. [PMID: 12944417 DOI: 10.1093/hmg/ddg290] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Polymorphisms in the beta chain of the high affinity receptor for IgE (Fc epsilon RI-beta, MS4A2) are consistently associated with traits underlying asthma and atopy (immunoglobulin E-mediated allergy). However, the causal variants and haplotypes underlying disease have not yet been identified. Maternal effects, with association confined to maternally derived alleles, have been shown in some studies but not in others. We have therefore extended the known sequence and systematically detected polymorphisms across an 18.1 Kb genomic region that includes Fc epsilon RI-beta. Association testing in two panels of subjects showed the presence of single-nucleotide polymorphisms (SNPs) affecting prick skin tests and specific IgE responses in several clusters. Stepwise analyses indicated that the clusters represent independent effects. Interferon regulatory factor 2 (IRF-2) sites were altered by significantly associated SNPs in two regions. Strong association to maternally derived alleles was seen in one panel of subjects and not in the other. Maternal and non-maternally derived associations tended to share the same SNP clusters, but associations were stronger in the presence of maternal effects. Two regions of increased CpG concentration were identified in Fc epsilon RI-beta. One of these approximated a SNP cluster that showed strong association and maternal effects, providing a potential substrate for epigenetic effects.
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Affiliation(s)
- James A Traherne
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, UK
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580
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Ertekin-Taner N, Ronald J, Asahara H, Younkin L, Hella M, Jain S, Gnida E, Younkin S, Fadale D, Ohyagi Y, Singleton A, Scanlin L, de Andrade M, Petersen R, Graff-Radford N, Hutton M, Younkin S. Fine mapping of the alpha-T catenin gene to a quantitative trait locus on chromosome 10 in late-onset Alzheimer's disease pedigrees. Hum Mol Genet 2003; 12:3133-43. [PMID: 14559775 PMCID: PMC2836540 DOI: 10.1093/hmg/ddg343] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Using plasma amyloid beta protein (Abeta42) levels as an intermediate, quantitative phenotype for late onset Alzheimer's disease (LOAD), we previously obtained significant linkage at approximately 80 cM on chromosome 10. Linkage to the same region was obtained independently in a study of affected LOAD sib-pairs. Together, these two studies provide strong evidence for a novel LOAD locus on chromosome 10 that acts to increase Abeta42. VR22 is a large (1.7 Mb) gene located at 80 cM that encodes alpha-T catenin, which is a binding partner of beta catenin. This makes VR22 an attractive candidate gene because beta catenin interacts with presenilin 1, which has many mutations that elevate Abeta42 and cause early onset familial AD. We identified two intronic VR22 SNPs (4360 and 4783) in strong linkage disequilibrium (LD) that showed highly significant association (P=0.0001 and 0.0006) with plasma Abeta42 in 10 extended LOAD families. This association clearly contributed to the linkage at approximately 80 cM because the lod scores decreased when linkage analysis was performed conditional upon the VR22 association. This association replicated in another independent set of 12 LOAD families (P=0.04 for 4783 and P=0.08 for 4360). Bounding of the association region using multiple SNPs showed VR22 to be the only confirmed gene within the region of association. These findings indicate that VR22 has variant(s) which influence Abeta42 and contribute to the previously reported linkage for plasma Abeta42 in LOAD families.
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Affiliation(s)
| | - James Ronald
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Hideaki Asahara
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Linda Younkin
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Maria Hella
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Shushant Jain
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Eugene Gnida
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Samuel Younkin
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Daniel Fadale
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Yasumasa Ohyagi
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Adam Singleton
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Leah Scanlin
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Division of Biostatistics, Mayo Clinic Rochester, Rochester, MN, USA
| | - Ronald Petersen
- Department of Neurology, Mayo Clinic Rochester, Rochester, MN, USA
| | | | - Michael Hutton
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Steven Younkin
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
- To whom correspondence should be addressed at: Mayo Clinic Jacksonville, 4500 San Pablo Road, Birdsall 2, Jacksonville, FL 32224, USA. Tel: +1 9049537356; Fax: +1 9049537370;
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581
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Johansson S, Lie BA, Cambon-Thomsen A, Pociot F, Nerup J, Kockum I, Thorsby E, Undlien DE. No evidence of type 1 diabetes susceptibility genes in the region centromeric of the HLA complex. Hum Immunol 2003; 64:951-9. [PMID: 14522092 DOI: 10.1016/s0198-8859(03)00172-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There is strong evidence that DQB1, DQA1, and DRB1 alleles are not the only contributors to the human leukocyte antigen (HLA) linked type 1 diabetes (T1D) predisposition. Although the HLA complex is much studied for disease association, little is known about the neighboring centromeric region. We have previously found suggestive association on DQ2-DR3 haplotypes for marker D6S291, located 3.6-Mb centromeric of HLA-DQB1. This region on human chromosome 6 is syntenic to a part of the region adjacent to the mouse major histocompatibility complex (MHC) on chromosome 17, which has been suggested to harbor a susceptibility gene in mouse (Idd16). To evaluate a possible role of the region centromeric of HLA-DQB1 in human T1D, we have scanned the region with nine microsatellite markers in 267 T1D families from five different populations. Our results indicate that the characteristic strong linkage disequilibrium in the HLA complex does not extend into this region. Furthermore, we did not detect any consistent T1D association for the markers analyzed in the study. In conclusion, our data argue against the presence of any strong genetic susceptibility factors for T1D in the region centromeric of the HLA complex.
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Affiliation(s)
- Stefan Johansson
- Institute of Immunology, Rikshospitalet University Hospital, Oslo, Norway.
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582
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Campbell SJ, Sabeti P, Fielding K, Sillah J, Bah B, Gustafson P, Manneh K, Lisse I, Sirugo G, Bellamy R, Bennett S, Aaby P, McAdam KPWJ, Bah-Sow O, Lienhardt C, Hill AVS. Variants of the CD40 ligand gene are not associated with increased susceptibility to tuberculosis in West Africa. Immunogenetics 2003; 55:502-7. [PMID: 12955358 DOI: 10.1007/s00251-003-0602-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2003] [Revised: 07/31/2003] [Indexed: 10/26/2022]
Abstract
Evidence for linkage between tuberculosis and human chromosomal region Xq26 has previously been described. The costimulatory molecule CD40 ligand, encoded by TNFSF5 and located at Xq26.3, is a promising positional candidate. Interactions between CD40 ligand and CD40 are involved in the development of humoral- and cell-mediated immunity, as well as the activation of macrophages, which are the primary host and effector cells for Mycobacterium tuberculosis. We hypothesised that common variation within TNFSF5 might affect susceptibility to tuberculosis disease and, thus, might be responsible for the observed linkage to Xq26. Sequencing 32 chromosomes from a Gambian population identified nine common polymorphisms within the coding, 3' and 5' regulatory sequences of the gene. Six single nucleotide polymorphisms (SNPs) and a 3' microsatellite were genotyped in 121 tuberculosis patients and their available parents. No association with tuberculosis was detected for these variants using a transmission disequilibrium test, although one SNP at -726 showed some evidence of association in males. This finding, however, did not replicate in a separate case control study of over 1,200 West African individuals. We conclude that common genetic variation in TNFSF5 is not likely to affect tuberculosis susceptibility in West Africa and the linkage observed in this region is not due to variation in TNFSF5.
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Affiliation(s)
- Sarah J Campbell
- The Henry Wellcome Building of Genomic Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, UK
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583
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Bonora E, Beyer KS, Lamb JA, Parr JR, Klauck SM, Benner A, Paolucci M, Abbott A, Ragoussis I, Poustka A, Bailey AJ, Monaco AP. Analysis of reelin as a candidate gene for autism. Mol Psychiatry 2003; 8:885-92. [PMID: 14515139 DOI: 10.1038/sj.mp.4001310] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic studies indicate that chromosome 7q is likely to contain an autism susceptibility locus (AUTS1). We have followed a positional candidate gene approach to identify relevant gene(s) and report here the analysis of reelin (RELN), a gene located under our peak of linkage. Screening RELN for DNA changes identified novel missense variants absent in a large control group; however, the low frequency of these mutations does not explain the relatively strong linkage results on 7q. Furthermore, analysis of a previously reported triplet repeat polymorphism and intragenic single nucleotide polymorphisms, using the transmission disequilibrium test, provided no evidence for association with autism in IMGSAC and German singleton families. The analysis of RELN suggests that it probably does not play a major role in autism aetiology, although further analysis of several missense mutations is warranted in additional affected individuals.
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Affiliation(s)
- E Bonora
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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584
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Rankinen T, Rice T, Boudreau A, Leon AS, Skinner JS, Wilmore JH, Rao DC, Bouchard C. Titin is a candidate gene for stroke volume response to endurance training: the HERITAGE Family Study. Physiol Genomics 2003; 15:27-33. [PMID: 12865504 DOI: 10.1152/physiolgenomics.00147.2002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A genome-wide linkage scan for endurance training-induced changes in submaximal exercise stroke volume (DeltaSV50) in the HERITAGE Family Study revealed two chromosomal regions (2q31-q32 and 10p11.2) with at least suggestive evidence of linkage among white families. Here we report a further characterization of the quantitative trait locus (QTL) in chromosome 2q31 and provide evidence that titin (TTN) is likely a candidate gene involved. The original linkage was detected with two markers (D2S335 and D2S1391), and the QTL covered approximately 25 million base pairs (Mb). We added 12 microsatellite markers resulting in an average marker density of one marker per 2.3 Mb. The evidence of linkage increased from P = 0.006 to P = 0.0002 and 0.00002 in the multi- and single-point analyses, respectively. The strongest evidence of linkage was seen with two markers in and near the TTN gene. Transmission/disequilibrium test (TDT) with the same marker set provided evidence for association with one of the TTN markers (D2S385; P = 0.004). TTN is a major contributor to the elasticity of cardiomyocytes and a key regulator of the Frank-Starling mechanism. Since TTN is the largest gene in the human genome, the challenge is to identify the DNA sequence variants contributing to the interindividual differences in cardiac adaptation to endurance training.
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Affiliation(s)
- Tuomo Rankinen
- Pennington Biomedical Research Center, Human Genomics Laboratory, Baton Rouge, Louisiana 70808-4124, USA.
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585
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Lu X, Niu T, Liu JS. Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms. Genome Res 2003; 13:2112-7. [PMID: 12952879 PMCID: PMC403705 DOI: 10.1101/gr.586803] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Single nucleotide polymorphisms in the human genome have become an increasingly popular topic in that their analyses promise to be a key step toward personalized medicine. We investigate two related questions, how much the haplotype information contributes to linkage disequilibrium (LD) mapping and whether an in silico haplotype construction preceding the LD analysis can help. For disease gene mapping, using both simulated and real data sets on cystic fibrosis and the Alzheimer disease, we reached the following conclusions: (1) for simple Mendelian diseases, in which case a tractable full statistical model can be developed, the loss of haplotype information for either control or disease data do not have a great impact on LD fine mapping, and haplotype inference should be carried out jointly with LD mapping; (2) for complex diseases, inferring haplotype phases for individuals prior to LD mapping helps achieve a better accuracy. An improved version of the linkage disequilibrium mapping program, BLADE v2, is available at http://www.fas.harvard.edu/junliu/TechRept/03folder/bladev2.tgz.
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Affiliation(s)
- Xin Lu
- Department of Statistics, Harvard University, Cambridge, Massachusetts 02138, USA
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586
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Shi M, Caprau D, Romitti P, Christensen K, Murray JC. Genotype frequencies and linkage disequilibrium in the CEPH human diversity panel for variants in folate pathway genesMTHFR,MTHFD,MTRR,RFC1, andGCP2. ACTA ACUST UNITED AC 2003; 67:545-9. [PMID: 14632302 DOI: 10.1002/bdra.10076] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Genetic variation in enzymes involved in vitamin metabolism is a candidate for analysis in studies of how nutritional covariates may impact a disease state. The role of folate pathway genes in birth defects and cardiovascular disease in humans has been widely studied. Since incidence rates for these disorders vary by geographic origins, it is useful to know which variants are the best candidates for studies based on genotype and allele frequency, as well as linkage disequilibrium (LD) in founder populations. METHODS Six polymorphisms in five folate metabolism-related genes (MTHFR, MTHFD, MTRR, GCP2, and RFC1) were genotyped on a collection of 1064 DNA samples from populations around the world, which were made available by the Centre d'Etude du Polymorphisme Humain (CEPH) consortium for analysis. RESULTS In this study we report the genotype frequencies for variants in the MTHFR, MTHFD, MTRR, GCP2, and RFC1 genes, and the LD for two variants (C677T and A1298C) in MTHFR. CONCLUSIONS The rare allele frequency for each of the five genes studied varied widely. LD is strongest in Pakistani and Brazilian populations (D' = 1.0) and weakest in Mexican populations (D' = 0.45). These findings will allow the selection of variants that will provide the most power in studies of folate pathway genes involving different ancestral populations, and contribute to our knowledge of the population distribution of selected nutritional gene variants.
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Affiliation(s)
- Min Shi
- Biology Department, University of Iowa, Iowa City, Iowa 52242, USA
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587
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Ranade SS, Mansour H, Wood J, Chowdari KV, Brar LK, Kupfer DJ, Nimgaonkar VL. Linkage and association between serotonin 2A receptor gene polymorphisms and bipolar I disorder. Am J Med Genet B Neuropsychiatr Genet 2003; 121B:28-34. [PMID: 12898571 DOI: 10.1002/ajmg.b.20070] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Several inconsistent associations between bipolar I disorder (BD1) and polymorphisms of the genes encoding the serotonin 2A receptor (HTR2A) have been published. We conducted the Transmission Disequilibrium Test (TDT) and case-control comparisons involving nine single nucleotide polymorphisms at the serotonin 2A receptor gene (four SNPs of HTR2A exons and five flanking SNPs). Comparison of BD1 cases (n = 93) with a group of unrelated population based controls (n = 92) revealed associations with SNPs on exons 2 and 3 (516C/T and 1354C/T, respectively), consistent with haplotype-based differences. Analysis of the cases and their available parents using the TDT suggested significant linkage and associations with 1354C/T, as well as haplotypes bearing this SNP. Our results support an etiological role for HTR2A in BD1. In view of the relatively small sample, replicate studies using large samples are needed.
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Affiliation(s)
- Swati S Ranade
- Departments of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
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588
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Wang Y, Ng MCY, Lee SC, So WY, Tong PCY, Cockram CS, Critchley JAJH, Chan JCN. Phenotypic heterogeneity and associations of two aldose reductase gene polymorphisms with nephropathy and retinopathy in type 2 diabetes. Diabetes Care 2003; 26:2410-5. [PMID: 12882871 DOI: 10.2337/diacare.26.8.2410] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE We investigated the phenotypic features of diabetic microvascular complications and their association with a (CA)(n) microsatellite and a C/T polymorphism at the 5' region of the aldose reductase gene (ALR2) in a consecutive cohort of 738 Chinese type 2 diabetic patients. RESEARCH DESIGN AND METHODS Of the entire patient cohort, 392 were free of diabetes complications, or uncomplicated, 159 had diabetic nephropathy, 66 had diabetic retinopathy, and 121 had both diabetic nephropathy and retinopathy. Nephropathy was defined as urinary albumin excretion rate (AER) >or=20 micro g/min and albumin-to-creatinine ratio >or=3.5 mg/mmol in two urine collections. Retinopathy was defined by the presence of hemorrhages, exudates, laser marks, and fibrous proliferation or by a history of vitrectomy. (CA)(n) and C/T polymorphisms were examined by PCR followed by capillary electrophoresis and digestion with BfaI, respectively. RESULTS In the whole cohort, patients with diabetic retinopathy (n = 187) had higher blood pressure and lower BMI, while those with diabetic nephropathy (n = 280) had higher blood pressure, waist-to-hip ratio, and lipid profile than those without the respective complications. The z+6 carriers of the (CA)(n) polymorphism were less common in patients with diabetic retinopathy than those without diabetic retinopathy (n = 551) (4.3 vs. 9.3%, P = 0.04). The CT/TT carriers had a higher AER than the CC carriers (30.2 x/divided by 7.2 vs. 21.9 x/divided by 6.9 micro g/min, P = 0.03). Further subgroup analysis was performed after excluding uncomplicated patients with <5 years disease duration. The group with both diabetic nephropathy and retinopathy had higher frequencies of the z-2 allele (25.7 vs. 16.9%, P = 0.03) and T allele (26.4 vs. 18.5%, P = 0.04) and a lower frequency of the z+6 allele (1.7 vs. 5.5%, P = 0.054) than the uncomplicated group. Multiple logistic regression analysis confirmed that z-2 carrying (odds ratio 2.6, 95% CI 1.20-5.83, P = 0.02) and CT/TT genotypes (OR 2.5, 95% CI 1.19-5.19, P = 0.02) were independent predictors for both diabetic nephropathy and retinopathy. CONCLUSIONS Chinese type 2 diabetic patients exhibited phenotypic differences in terms of risk factors for both diabetic nephropathy and diabetic retinopathy. Both the z-2 allele of (CA)(n) polymorphism and T allele of ALR2 were independently associated with severe diabetic microvascular complications.
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Affiliation(s)
- Ying Wang
- Division of Clinical Pharmacology, Department of Medicine and Therapeutics, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, Hong Kong SAR
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589
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Edland SD, Wavrant-De Vriesé F, Compton D, Smith GE, Ivnik R, Boeve BF, Tangalos EG, Petersen RC. Insulin degrading enzyme (IDE) genetic variants and risk of Alzheimer's disease: evidence of effect modification by apolipoprotein E (APOE). Neurosci Lett 2003; 345:21-4. [PMID: 12809979 DOI: 10.1016/s0304-3940(03)00488-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Insulin degrading enzyme (IDE) is a protease that degrades insulin and the beta-amyloid peptide implicated in Alzheimer's disease (AD). We reexamined data on five previously reported IDE polymorphisms stratifying the analysis by the presence or absence of an apolipoprotein E (APOE) epsilon4 allele. Three IDE variants were associated with AD within epsilon4-negative subjects (genotype exact test P-values < or =0.02). A haplotype containing the minor variant at each of these sites represented an estimated 4.2% of case haplotypes versus 12.3% of control haplotypes among epsilon4-negative subjects. Lack of this minor haplotype may be predictive of AD, potentially explaining some fraction of disease within subjects without the APOE epsilon4 risk allele. Confirmation of this finding with a larger sample of cases and controls is warranted.
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Affiliation(s)
- S D Edland
- Division of Clinical Epidemiology, Mayo Clinic and Foundation, 200 First Street SW, Rochester, MN 55905, USA.
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590
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Cruciani F, Bernardini L, Santolamazza P, Modiano D, Torroni A, Scozzari R. Linkage disequilibrium analysis of the human adenosine deaminase (ada) gene provides evidence for a lack of correlation between hot spots of equal and unequal homologous recombination. Genomics 2003; 82:20-33. [PMID: 12809673 DOI: 10.1016/s0888-7543(03)00096-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The linkage disequilibrium (LD) pattern within the adenosine deaminase (ADA) gene was analyzed by studying 13 polymorphic loci in 137 families from two European and three African populations. Evidence for the presence of a 12-kb meiotic crossover hot spot, spanning part of the first and the second intron and flanked by regions of reduced recombination activity, was obtained. Moreover, segregation analysis of 113 informative meioses revealed two recombination events that are internal or overlap the 12-kb region, thus suggesting a recombination rate for the hot-spot region about 50-fold higher than the mean rate across the human genome. Within the hot spot, a 144-bp palindromic sequence was also identified and its possible involvement in the recombination process is discussed. The 12-kb region characterized by the low degree of LD does not include the 3.2-kb region that is deleted, as a result of recurrent unequal homologous recombination between two Alu elements, in patients affected by autosomal severe combined immunodeficiency. This observation provides the first evidence for an absence of correlation between hot spots of equal and unequal homologous recombination.
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Affiliation(s)
- Fulvio Cruciani
- Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, P.le Aldo Moro 5, 00185 Rome, Italy.
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591
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Aucan C, Walley AJ, Hennig BJW, Fitness J, Frodsham A, Zhang L, Kwiatkowski D, Hill AVS. Interferon-alpha receptor-1 (IFNAR1) variants are associated with protection against cerebral malaria in the Gambia. Genes Immun 2003; 4:275-82. [PMID: 12761564 DOI: 10.1038/sj.gene.6363962] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The chromosome 21q22.11 cytokine receptor cluster contains four genes that encode subunits of the receptors for the cytokines interleukin-10 and interferon-alpha, -beta and -gamma that may have a role in malaria pathogenesis. A total of 15 polymorphic markers located within these genes were initially genotyped in 190 controls and 190 severe malaria cases from The Gambia. Two interferon-alpha receptor-1 (IFNAR1) gene SNPs (17470 and L168 V) showed evidence for an association with severe malaria phenotypes and were typed in a larger series of samples comprising 538 severe malaria cases, 338 mild malaria cases and 562 controls. Both the 17470-G/G and L168V-G/G genotypes were associated with protection against severe malaria, in general, and cerebral malaria, in particular (P=0.004 and 0.003, respectively). IFNAR1 diplotypes were then constructed for these two markers using the PHASE software package. The (17470-G L168V-G/17470-G L168V-G) diplotype was found to be associated with a reduced risk of cerebral malaria and the (17470-C L168V-C/17470-G L168V-G) diplotype with an increased risk of cerebral malaria (overall 3 x 2 chi(2)=12.8, d.f.=2, P=0.002 and 3 x 2 chi(2)=15.2, d.f.=2, P=0.0005, respectively). These data suggest a role for the type I interferon pathway in resistance to cerebral malaria.
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Affiliation(s)
- C Aucan
- Wellcome Trust Centre for Human Genetics, Henry Wellcome Building of Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK.
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592
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Stern AG, de Carvalho MRC, Buck GA, Adler RA, Rao TPS, Disler D, Moxley G. Association of erosive hand osteoarthritis with a single nucleotide polymorphism on the gene encoding interleukin-1 beta. Osteoarthritis Cartilage 2003; 11:394-402. [PMID: 12801479 DOI: 10.1016/s1063-4584(03)00054-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Certain forms of primary osteoarthritis (OA), particularly those affecting hand joints, have a genetic component. Recent studies have shown suggestive evidence that hand and knee OA are linked with the interleukin-1 (IL-1) region on human chromosome 2q. This study was undertaken to assess the association of primary OA of the hand (hand OA) with IL-1 region markers. METHODS Sixty-eight US Caucasoid cases and 51 US Caucasoid controls aged 60 years or older were recruited from the Mid-Atlantic region of the United States. Hand OA was classified by American College of Rheumatology (ACR) Clinical Criteria, and cases were subjected to radiographic examination for subgrouping. Genotyping was done for seven previously described single nucleotide polymorphisms (SNPs) of genes for IL-1alpha (encoded by IL1A), IL-1beta (IL1B), and the IL-1 receptor antagonist (IL1RN), as well as an IL1RN variable number of tandem repeat (VNTR) marker. Six microsatellite markers on other chromosomes (null loci) were also typed. RESULTS The IL1B 5810 G>A SNP genotypes marker were not in Hardy-Weinberg equilibrium (p<0.05 in both non-erosive and erosive hand OA subgroups). Statistically significant association with the IL1B 5810 AA genotype was found in the erosive hand OA subgroup (relative risk 3.8, p=0.007). This IL1B 5810 AA genotype association was also significant between erosive and non-erosive hand OA subjects (relative risk 4.01, p=0.008). As expected, significant linkage disequilibrium was present between IL1B 5810 SNP and IL1A (-)889 SNP, other IL1B SNPs, and the nearest IL1RN SNP examined. The IL1B 5810A allele occurs most frequently on haplotypes with the SNP alleles IL1B 1423C, IL1B 1903T, IL1B 5887C, and IL1A (-)889C. Genotypes at null loci failed to show evidence suggesting population stratification that might account for spurious association. CONCLUSION Statistical evidence shows association between erosive hand OA and a genomic region containing the IL1B 5810 SNP in a US Caucasoid population. This supports a potential role for IL-1 in the pathogenesis of a severe phenotype of hand OA.
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Affiliation(s)
- A G Stern
- Rheumatology Section, Hunter Holmes McGuire Veteran Affairs Medical Center and the Division of Rheumatology, Allergy, and Immunology, Virginia Commonwealth University, Richmond, VA, USA.
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593
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Nurmi EL, Amin T, Olson LM, Jacobs MM, McCauley JL, Lam AY, Organ EL, Folstein SE, Haines JL, Sutcliffe JS. Dense linkage disequilibrium mapping in the 15q11-q13 maternal expression domain yields evidence for association in autism. Mol Psychiatry 2003; 8:624-34, 570. [PMID: 12851639 DOI: 10.1038/sj.mp.4001283] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Autism [MIM 209850] is a neurodevelopmental disorder exhibiting a complex genetic etiology with clinical and locus heterogeneity. Chromosome 15q11-q13 has been proposed to harbor a gene for autism susceptibility based on (1) maternal-specific chromosomal duplications seen in autism and (2) positive evidence for linkage disequilibrium (LD) at 15q markers in chromosomally normal autism families. To investigate and localize a potential susceptibility variant, we developed a dense single nucleotide polymorphism (SNP) map of the maternal expression domain in proximal 15q. We analyzed 29 SNPs spanning the two known imprinted, maternally expressed genes in the interval (UBE3A and ATP10C) and putative imprinting control regions. With a marker coverage of 1/10 kb in coding regions and 1/15 kb in large 5' introns, this map was employed to thoroughly dissect LD in autism families. Two SNPs within ATP10C demonstrated evidence for preferential allelic transmission to affected offspring. The signal detected at these SNPs was stronger in singleton families, and an adjacent SNP demonstrated transmission distortion in this subset. All SNPs showing allelic association lie within islands of sequence homology between human and mouse genomes that may be part of an ancestral haplotype containing a functional susceptibility allele. The region was further explored for recombination hot spots and haplotype blocks to evaluate haplotype transmission. Five haplotype blocks were defined within this region. One haplotype within ATP10C displayed suggestive evidence for preferential transmission. Interpretation of these data will require replication across data sets, evaluation of potential functional effects of associated alleles, and a thorough assessment of haplotype transmission within ATP10C and neighboring genes. Nevertheless, these findings are consistent with the presence of an autism susceptibility locus in 15q11-q13.
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Affiliation(s)
- E L Nurmi
- Department of Molecular Physiology and Biophysics, Program in Human Genetics, Vanderbilt University, Nashville, TN 37232-0615, USA
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594
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Jezewski PA, Vieira AR, Nishimura C, Ludwig B, Johnson M, O'Brien SE, Daack-Hirsch S, Schultz RE, Weber A, Nepomucena B, Romitti PA, Christensen K, Orioli IM, Castilla EE, Machida J, Natsume N, Murray JC. Complete sequencing shows a role for MSX1 in non-syndromic cleft lip and palate. J Med Genet 2003; 40:399-407. [PMID: 12807959 PMCID: PMC1735501 DOI: 10.1136/jmg.40.6.399] [Citation(s) in RCA: 218] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
MSX1 has been proposed as a gene in which mutations may contribute to non-syndromic forms of cleft lip and/or cleft palate. Support for this comes from human linkage and linkage disequilibrium studies, chromosomal deletions resulting in haploinsufficiency, a large family with a stop codon mutation that includes clefting as a phenotype, and the Msx1 phenotype in a knockout mouse. This report describes a population based scan for mutations encompassing the sense and antisense transcribed sequence of MSX1 (two exons, one intron). We compare the completed genomic sequence of MSX1 to the mouse Msx1 sequence to identify non-coding homology regions, and sequence highly conserved elements. The samples studied were drawn from a panethnic collection including people of European, Asian, and native South American ancestry. The gene was sequenced in 917 people and potentially aetiological mutations were identified in 16. These included missense mutations in conserved amino acids and point mutations in conserved regions not identified in any of 500 controls sequenced. Five different missense mutations in seven unrelated subjects with clefting are described. Evolutionary sequence comparisons of all known Msx1 orthologues placed the amino acid substitutions in context. Four rare mutations were found in non-coding regions that are highly conserved and disrupt probable regulatory regions. In addition, a panel of 18 population specific polymorphic variants were identified that will be useful in future haplotype analyses of MSX1. MSX1 mutations are found in 2% of cases of clefting and should be considered for genetic counselling implications, particularly in those families in which autosomal dominant inheritance patterns or dental anomalies appear to be cosegregating with the clefting phenotype.
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Affiliation(s)
- P A Jezewski
- Department of Periodontics, College of Dentistry, University of Iowa, Iowa City 52242, USA
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595
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Zhang Y, Leaves NI, Anderson GG, Ponting CP, Broxholme J, Holt R, Edser P, Bhattacharyya S, Dunham A, Adcock IM, Pulleyn L, Barnes PJ, Harper JI, Abecasis G, Cardon L, White M, Burton J, Matthews L, Mott R, Ross M, Cox R, Moffatt MF, Cookson WOCM. Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma. Nat Genet 2003; 34:181-6. [PMID: 12754510 DOI: 10.1038/ng1166] [Citation(s) in RCA: 195] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2002] [Accepted: 04/18/2003] [Indexed: 01/27/2023]
Abstract
Atopic or immunoglobulin E (IgE)-mediated diseases include the common disorders of asthma, atopic dermatitis and allergic rhinitis. Chromosome 13q14 shows consistent linkage to atopy and the total serum IgE concentration. We previously identified association between total serum IgE levels and a novel 13q14 microsatellite (USAT24G1; ref. 7) and have now localized the underlying quantitative-trait locus (QTL) in a comprehensive single-nucleotide polymorphism (SNP) map. We found replicated association to IgE levels that was attributed to several alleles in a single gene, PHF11. We also found association with these variants to severe clinical asthma. The gene product (PHF11) contains two PHD zinc fingers and probably regulates transcription. Distinctive splice variants were expressed in immune tissues and cells.
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Affiliation(s)
- Youming Zhang
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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596
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Ahmadi KR, Lanchbury JS, Reed P, Chiano M, Thompson D, Galley M, Line A, Lank E, Wong HJ, Strachan D, Spector TD. Novel association suggests multiple independent QTLs within chromosome 5q21-33 region control variation in total humans IgE levels. Genes Immun 2003; 4:289-97. [PMID: 12761566 DOI: 10.1038/sj.gene.6363968] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Asthma is a common, heterogeneous, complex disease accompanied by raised total and specific immunoglobulin-E (IgE) antibody levels. Despite numerous previous reports of linkage and association of asthma, atopy and serum IgE levels to genes within the 5q21-33 region, definitive, replicable results are still not available. We used the classical twin design to (i) estimate the relative contributions of genes and environment to variation in total IgE levels, (ii) assess genetic linkage, and (iii) examine allelic association of 11 microsatellite markers spanning the 5q21-33 region to total IgE. Variation in total IgE level was shown to be highly heritable (65%). Although evidence for linkage of the 11 microsatellites to IgE was not observed, the omnibus test of association, not confounded by population substructure, showed positive association of D5S393 and D5S673 to IgE. Genes in the vicinity of D5S673 include hepatitis A virus receptor (HAVCR-1) and IL-12B. Recently, the mouse orthologue of HAVCR-1, the T-cell membrane family of proteins, have been shown to be in strong association with expression of airway hyperactivity in a mouse model of human asthma and atopy. IL-12B subserves many proinflammatory functions and also induces B cells proliferation.
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Affiliation(s)
- K R Ahmadi
- Twin Research & Genetic Epidemiology Unit, St Thomas' Hospital, and Molecular Immunogenetics Unit, Department of Rheumatology, GKT School of Medicine, King's College London, UK.
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597
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O’Brien EK, Zhang X, Nishimura C, Tomblin JB, Murray JC. Association of specific language impairment (SLI) to the region of 7q31. Am J Hum Genet 2003; 72:1536-43. [PMID: 12721956 PMCID: PMC1180313 DOI: 10.1086/375403] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2002] [Accepted: 03/04/2003] [Indexed: 11/03/2022] Open
Abstract
FOXP2 (forkhead box P2) was the first gene characterized in which a mutation affects human speech and language abilities. A common developmental language disorder, specific language impairment (SLI), affects 6%-7% of children with normal nonverbal intelligence and has evidence of a genetic basis in familial and twin studies. FOXP2 is located on chromosome 7q31, and studies of other disorders with speech and language impairment, including autism, have found linkage to this region. In the present study, samples from children with SLI and their family members were used to study linkage and association of SLI to markers within and around FOXP2, and samples from 96 probands with SLI were directly sequenced for the mutation in exon 14 of FOXP2. No mutations were found in exon 14 of FOXP2, but strong association was found to a marker within the CFTR gene and another marker on 7q31, D7S3052, both adjacent to FOXP2, suggesting that genetic factors for regulation of common language impairment reside in the vicinity of FOXP2.
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Affiliation(s)
- Erin K. O’Brien
- Departments of Otolaryngology, Speech Pathology and Audiology, and Pediatrics, University of Iowa, Iowa City
| | - Xuyang Zhang
- Departments of Otolaryngology, Speech Pathology and Audiology, and Pediatrics, University of Iowa, Iowa City
| | - Carla Nishimura
- Departments of Otolaryngology, Speech Pathology and Audiology, and Pediatrics, University of Iowa, Iowa City
| | - J. Bruce Tomblin
- Departments of Otolaryngology, Speech Pathology and Audiology, and Pediatrics, University of Iowa, Iowa City
| | - Jeffrey C. Murray
- Departments of Otolaryngology, Speech Pathology and Audiology, and Pediatrics, University of Iowa, Iowa City
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598
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Monti LD, Barlassina C, Citterio L, Galluccio E, Berzuini C, Setola E, Valsecchi G, Lucotti P, Pozza G, Bernardinelli L, Casari G, Piatti P. Endothelial nitric oxide synthase polymorphisms are associated with type 2 diabetes and the insulin resistance syndrome. Diabetes 2003; 52:1270-5. [PMID: 12716763 DOI: 10.2337/diabetes.52.5.1270] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Endothelial nitric oxide synthase (eNOS) variants were previously demonstrated in cardiovascular disease. To evaluate whether eNOS gene variants are associated with insulin resistance and type 2 diabetes, we evaluated polymorphisms in Exon7 (E298D), intron 18 (IVS18 + 27A-->C), and intron 23 (IVS23 + 10G-->T) in 159 type 2 diabetic patients without macrovascular complications and in 207 healthy control subjects. Samples for all hormonal and metabolic variables were obtained after an overnight fast. The D298 and IVS18 + 27C alleles, but not the IVS23 + 10G-->T variant, were significantly more frequent in type 2 diabetic patients than in control subjects. The two- and three-loci haplotype analysis showed that there is a statistically significant association between the eNOS variants and type 2 diabetes. No significant differences were observed in the clinical characteristics of type 2 diabetic patients according to genotypes (except for visceral obesity [waist-to-hip ratio], which was significantly more present in D298 homozygotes). Healthy control subjects homozygous for both D298 and IVS18 + 27C presented higher insulin, C-peptide, and nitric oxide levels, as well as higher HOMA (homeostasis model assessment) values than the double wild-type homozygotes, with values superimposable on those found in type 2 diabetic patients. In conclusion, we described a significant association between eNOS gene polymorphisms and type 2 diabetes, suggesting a new genetic susceptibility factor for hyperinsulinemia, insulin resistance, and type 2 diabetes.
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Affiliation(s)
- Lucilla D Monti
- Diabetology, Endocrinology and Metabolic Disease Unit, Medicine Division, San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milan, Italy.
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599
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Abstract
Mitochondrial DNA (mtDNA) is a widely employed molecular tool in phylogeography, in the inference of human evolutionary history, in dating the domestication of livestock and in forensic science. In humans and other vertebrates the popularity of mtDNA can be partially attributed to an assumption of strict maternal inheritance, such that there is no recombination between mitochondrial lineages. The recent demonstration that linkage disequilibrium (LD) declines as a function of distance between polymorphic sites in hominid mitochondrial genomes has been interpreted as evidence of recombination between mtDNA haplotypes, and hence nonclonal inheritance. However, critics of mtDNA recombination have suggested that this association is an artefact of an inappropriate measure of LD or of sequencing error, and subsequent studies of other populations have failed to replicate the initial finding. Here we report the analysis of 16 ruminant populations and present evidence that LD significantly declines with distance in five of them. A meta-analysis of the data indicates a nonsignificant trend of LD declining with distance. Most of the earlier criticisms of patterns between LD and distance in hominid mtDNA are not applicable to this data set. Our results suggest that either ruminant mtDNA is not strictly clonal or that compensatory selection has influenced patterns of variation at closely linked sites within the mitochondrial control region. The potential impact of these processes should be considered when using mtDNA as a tool in vertebrate population genetic, phylogenetic and forensic studies.
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Affiliation(s)
- J Slate
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand.
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600
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Tenesa A, Knott SA, Ward D, Smith D, Williams JL, Visscher PM. Estimation of linkage disequilibrium in a sample of the United Kingdom dairy cattle population using unphased genotypes. J Anim Sci 2003; 81:617-23. [PMID: 12661641 DOI: 10.2527/2003.813617x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The association between genetic marker alleles was estimated for two regions of the bovine genome from a random sample of 50 young dairy bulls born in the United Kingdom between 1988 and 1995. Microsatellite marker genotypes were obtained for six markers on chromosome 2 and seven markers on chromosome 6, spanning 38 and 20 cM, respectively. Two different methods, which do not require family information, were used to estimate population haplotype frequencies. Haplotype frequencies were estimated for pairs of loci using the expectation-maximization algorithm and for all linked loci using a Bayesian approach via a Markov chain-Monte Carlo algorithm. Significant (P = 0.0007) linkage disequilibrium was detected between pairs of loci in syntenic groups (that is, loci in the same linkage group), extending to about 10 cM. No significant linkage disequilibrium was detected between markers in nonsyntenic regions. Given the observed level of linkage disequilibrium, mapping methods based on population-wide association might provide a better resolution than traditional quantitative trait loci mapping methods in the U.K. dairy cattle population and may reduce the required sample sizes of the experiments.
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Affiliation(s)
- A Tenesa
- Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT, Scotland, UK.
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