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Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies

Keating, Brendan J ; Tischfield, Sam ; Murray, Sarah S ; Bhangale, Tushar ; Price, Thomas S ; Glessner, Joseph T ; Galver, Luana ; Barrett, Jeffrey C ; Grant, Struan F A ; Farlow, Deborah N ; Chandrupatla, Hareesh R ; Hansen, Mark ; Ajmal, Saad ; Papanicolaou, George J ; Guo, Yiran ; Li, Mingyao ; Derohannessian, Stephanie ; de Bakker, Paul I W ; Bailey, Swneke D ; Montpetit, Alexandre ; Edmondson, Andrew C ; Taylor, Kent ; Gai, Xiaowu ; Wang, Susanna S ; Fornage, Myriam ; Shaikh, Tamim ; Groop, Leif ; Boehnke, Michael ; Hall, Alistair S ; Hattersley, Andrew T ; Frackelton, Edward ; Patterson, Nick ; Chiang, Charleston W K ; Kim, Cecelia E ; Fabsitz, Richard R ; Ouwehand, Willem ; Price, Alkes L ; Munroe, Patricia ; Caulfield, Mark ; Drake, Thomas ; Boerwinkle, Eric ; Reich, David ; Whitehead, A Stephen ; Cappola, Thomas P ; Samani, Nilesh J ; Lusis, A Jake ; Schadt, Eric ; Wilson, James G ; Koenig, Wolfgang ; McCarthy, Mark I ; Kathiresan, Sekar ; Gabriel, Stacey B ; Hakonarson, Hakon ; Anand, Sonia S ; Reilly, Muredach ; Engert, James C ; Nickerson, Deborah A ; Rader, Daniel J ; Hirschhorn, Joel N ; Fitzgerald, Garret A Reitsma, Pieter H.

PloS one, 2008-10, Vol.3 (10), p.e3583-e3583 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies
Autor: Keating, Brendan J ; Tischfield, Sam ; Murray, Sarah S ; Bhangale, Tushar ; Price, Thomas S ; Glessner, Joseph T ; Galver, Luana ; Barrett, Jeffrey C ; Grant, Struan F A ; Farlow, Deborah N ; Chandrupatla, Hareesh R ; Hansen, Mark ; Ajmal, Saad ; Papanicolaou, George J ; Guo, Yiran ; Li, Mingyao ; Derohannessian, Stephanie ; de Bakker, Paul I W ; Bailey, Swneke D ; Montpetit, Alexandre ; Edmondson, Andrew C ; Taylor, Kent ; Gai, Xiaowu ; Wang, Susanna S ; Fornage, Myriam ; Shaikh, Tamim ; Groop, Leif ; Boehnke, Michael ; Hall, Alistair S ; Hattersley, Andrew T ; Frackelton, Edward ; Patterson, Nick ; Chiang, Charleston W K ; Kim, Cecelia E ; Fabsitz, Richard R ; Ouwehand, Willem ; Price, Alkes L ; Munroe, Patricia ; Caulfield, Mark ; Drake, Thomas ; Boerwinkle, Eric ; Reich, David ; Whitehead, A Stephen ; Cappola, Thomas P ; Samani, Nilesh J ; Lusis, A Jake ; Schadt, Eric ; Wilson, James G ; Koenig, Wolfgang ; McCarthy, Mark I ; Kathiresan, Sekar ; Gabriel, Stacey B ; Hakonarson, Hakon ; Anand, Sonia S ; Reilly, Muredach ; Engert, James C ; Nickerson, Deborah A ; Rader, Daniel J ; Hirschhorn, Joel N ; Fitzgerald, Garret A
Reitsma, Pieter H.
Assuntos: Arteriosclerosis ; Atherosclerosis ; Biotechnology ; Cardiovascular disease ; Cardiovascular Diseases - ethnology ; Cardiovascular Diseases - genetics ; Cardiovascular Disorders ; Concept Formation ; Coronary vessels ; Deoxyribonucleic acid ; Diabetes ; DNA ; Encyclopedias ; Endocrinology ; Environment models ; Epistasis ; Gene expression ; Gene Frequency ; Gene polymorphism ; Genes ; Genetic aspects ; Genetic diversity ; Genetics ; Genetics and Genomics ; Genome-Wide Association Study - instrumentation ; Genome-Wide Association Study - methods ; Genomes ; Genomics ; Genotype ; Hospitals ; Humans ; Interrogation ; Loci ; Medical research ; Medical schools ; Medicine ; Medicine, Experimental ; Oligonucleotide Array Sequence Analysis - methods ; Pediatrics ; Polymorphism ; Polymorphism, Single Nucleotide ; Population Groups - genetics ; Populations ; Quality Control ; Quantitative genetics ; Quantitative trait loci ; Research Design ; Saturation ; Science ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Tagging ; Type 2 diabetes
É parte de: PloS one, 2008-10, Vol.3 (10), p.e3583-e3583
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
Conceived and designed the experiments: BJK ST SSM TB TSP LG JCB DNF GJP PdB MF CWKC RRF EB JGW MIM SG MR JCE DAN JH. Performed the experiments: BJK MH SDB AM EF CEK WK HH SSA JCE. Analyzed the data: BJK ST SSM TB JTG LG JCB SFAG HC MH WK HH JCE DAN JH. Contributed reagents/materials/analysis tools: BJK ST SSM TB LG HC MH GJP SA YG ML SD PdB SDB AM ACE KDT XG SSW TS LCG MB ASH AH NP CWKC WHO ALP PM MC TAD DR ASW TC NJS AJL EES WK MIM SK HH SSA MR JCE DAN DJR JH. Wrote the paper: BJK ST TSP SFAG DNF GJP YG EB JGW MIM HH JCE DAN DJR JH GAF.
Descrição: A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS). True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a "cosmopolitan" tagging approach to capture the genetic diversity across approximately 2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions.
Editor: United States: Public Library of Science
Idioma: Inglês

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Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies

United States: Public Library of Science

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