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  • 1
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    Whole-genome patterns of common DNA variation in three human populations (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-19
    Description: Individual differences in DNA sequence are the genetic basis of human variability. We have characterized whole-genome patterns of common human DNA variation by genotyping 1,586,383 single-nucleotide polymorphisms (SNPs) in 71 Americans of European, African, and Asian ancestry. Our results indicate that these SNPs capture most common genetic variation as a result of linkage disequilibrium, the correlation among common SNP alleles. We observe a strong correlation between extended regions of linkage disequilibrium and functional genomic elements. Our data provide a tool for exploring many questions that remain regarding the causal role of common human DNA variation in complex human traits and for investigating the nature of genetic variation within and between human populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hinds, David A -- Stuve, Laura L -- Nilsen, Geoffrey B -- Halperin, Eran -- Eskin, Eleazar -- Ballinger, Dennis G -- Frazer, Kelly A -- Cox, David R -- New York, N.Y. -- Science. 2005 Feb 18;307(5712):1072-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Perlegen Sciences Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15718463" target="_blank"〉PubMed〈/a〉
    Keywords: African Americans/*genetics ; Algorithms ; Asian Continental Ancestry Group/*genetics ; Case-Control Studies ; Chromosome Mapping ; Databases, Genetic ; European Continental Ancestry Group/*genetics ; Female ; Gene Frequency ; Genetic Markers ; Genetic Predisposition to Disease ; *Genetic Variation ; *Genome, Human ; Genotype ; Haplotypes ; Humans ; Linkage Disequilibrium ; Male ; Multifactorial Inheritance ; *Polymorphism, Single Nucleotide ; Recombination, Genetic ; Risk Factors ; Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    9p21 DNA variants associated with coronary artery disease impair interferon-gamma signalling response (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-02-11
    Description: Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) in the 9p21 gene desert associated with coronary artery disease (CAD) and type 2 diabetes. Despite evidence for a role of the associated interval in neighbouring gene regulation, the biological underpinnings of these genetic associations with CAD or type 2 diabetes have not yet been explained. Here we identify 33 enhancers in 9p21; the interval is the second densest gene desert for predicted enhancers and six times denser than the whole genome (P 〈 6.55 x 10(-33)). The CAD risk alleles of SNPs rs10811656 and rs10757278 are located in one of these enhancers and disrupt a binding site for STAT1. Lymphoblastoid cell lines homozygous for the CAD risk haplotype show no binding of STAT1, and in lymphoblastoid cell lines homozygous for the CAD non-risk haplotype, binding of STAT1 inhibits CDKN2BAS (also known as CDKN2B-AS1) expression, which is reversed by short interfering RNA knockdown of STAT1. Using a new, open-ended approach to detect long-distance interactions, we find that in human vascular endothelial cells the enhancer interval containing the CAD locus physically interacts with the CDKN2A/B locus, the MTAP gene and an interval downstream of IFNA21. In human vascular endothelial cells, interferon-gamma activation strongly affects the structure of the chromatin and the transcriptional regulation in the 9p21 locus, including STAT1-binding, long-range enhancer interactions and altered expression of neighbouring genes. Our findings establish a link between CAD genetic susceptibility and the response to inflammatory signalling in a vascular cell type and thus demonstrate the utility of genome-wide association study findings in directing studies to novel genomic loci and biological processes important for disease aetiology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079517/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079517/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harismendy, Olivier -- Notani, Dimple -- Song, Xiaoyuan -- Rahim, Nazli G -- Tanasa, Bogdan -- Heintzman, Nathaniel -- Ren, Bing -- Fu, Xiang-Dong -- Topol, Eric J -- Rosenfeld, Michael G -- Frazer, Kelly A -- 1R21CA152613-01/CA/NCI NIH HHS/ -- 1U54RR025204/RR/NCRR NIH HHS/ -- 1UL1RR025774/RR/NCRR NIH HHS/ -- 1UL1RR031980-01/RR/NCRR NIH HHS/ -- CA97134/CA/NCI NIH HHS/ -- DK018477/DK/NIDDK NIH HHS/ -- DK074868/DK/NIDDK NIH HHS/ -- DK39949/DK/NIDDK NIH HHS/ -- DK74686/DK/NIDDK NIH HHS/ -- HL065445/HL/NHLBI NIH HHS/ -- L65445/PHS HHS/ -- NS34934/NS/NINDS NIH HHS/ -- P01 AG025204/AG/NIA NIH HHS/ -- P01 AG025204-01/AG/NIA NIH HHS/ -- R01 CA097134/CA/NCI NIH HHS/ -- R01 DK018477/DK/NIDDK NIH HHS/ -- R01 DK018477-35/DK/NIDDK NIH HHS/ -- R01 DK039949/DK/NIDDK NIH HHS/ -- R01 DK039949-29/DK/NIDDK NIH HHS/ -- R01 HL065445/HL/NHLBI NIH HHS/ -- R01 HL065445-12/HL/NHLBI NIH HHS/ -- R01 NS034934/NS/NINDS NIH HHS/ -- R21 CA152613/CA/NCI NIH HHS/ -- R21 CA152613-01/CA/NCI NIH HHS/ -- R21 CA152613-02/CA/NCI NIH HHS/ -- R37 DK039949/DK/NIDDK NIH HHS/ -- U01 HL107442/HL/NHLBI NIH HHS/ -- UL1 RR025774/RR/NCRR NIH HHS/ -- UL1 RR025774-01/RR/NCRR NIH HHS/ -- UL1 RR031980/RR/NCRR NIH HHS/ -- UL1 RR031980-01/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Feb 10;470(7333):264-8. doi: 10.1038/nature09753.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pediatrics and Rady's Children's Hospital, University of California at San Diego, School of Medicine, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21307941" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Cell Line ; Chromatin/drug effects/genetics/metabolism ; Chromosomes, Human, Pair 9/*genetics ; Conserved Sequence/genetics ; Coronary Artery Disease/*genetics ; Cyclin-Dependent Kinase Inhibitor p15/genetics ; Diabetes Mellitus, Type 2/genetics ; Endothelial Cells/drug effects/metabolism ; Enhancer Elements, Genetic/*genetics ; European Continental Ancestry Group/genetics ; Gene Expression Regulation/drug effects/genetics ; Gene Knockdown Techniques ; Genetic Predisposition to Disease/*genetics ; *Genetic Variation ; Genome-Wide Association Study ; Haplotypes/genetics ; HeLa Cells ; Humans ; Interferon-alpha/genetics ; Interferon-gamma/*pharmacology ; Linkage Disequilibrium ; Male ; Polymorphism, Single Nucleotide/genetics ; Protein Binding/drug effects ; Purine-Nucleoside Phosphorylase/genetics ; STAT1 Transcription Factor/biosynthesis/deficiency/genetics/metabolism ; Signal Transduction/*drug effects
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-21
    Description: The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and approximately 4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clark, Richard M -- Schweikert, Gabriele -- Toomajian, Christopher -- Ossowski, Stephan -- Zeller, Georg -- Shinn, Paul -- Warthmann, Norman -- Hu, Tina T -- Fu, Glenn -- Hinds, David A -- Chen, Huaming -- Frazer, Kelly A -- Huson, Daniel H -- Scholkopf, Bernhard -- Nordborg, Magnus -- Ratsch, Gunnar -- Ecker, Joseph R -- Weigel, Detlef -- New York, N.Y. -- Science. 2007 Jul 20;317(5836):338-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17641193" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Arabidopsis/*genetics ; Base Sequence ; Chromosomes, Plant/genetics ; Computational Biology ; Gene Frequency ; Genes, Plant ; *Genetic Variation ; *Genome, Plant ; Molecular Sequence Data ; *Polymorphism, Genetic ; *Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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