title: Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array.
abstract: The success of genome-wide association studies has paralleled the development of efficient genotyping technologies. We describe the development of a next-generation microarray based on the new highly-efficient Affymetrix Axiom genotyping technology that we are using to genotype individuals of European ancestry from the Kaiser Permanente Research Program on Genes, Environment and Health (RPGEH). The array contains 674,517 SNPs, and provides excellent genome-wide as well as gene-based and candidate-SNP coverage. Coverage was calculated using an approach based on imputation and cross validation. Preliminary results for the first 80,301 saliva-derived DNA samples from the RPGEH demonstrate very high quality genotypes, with sample success rates above 94% and over 98% of successful samples having SNP call rates exceeding 98%. At steady state, we have produced 462 million genotypes per week for each Axiom system. The new array provides a valuable addition to the repertoire of tools for large scale genome-wide association studies.
authors.affiliation: Institute for Human Genetics, University of California, San Francisco 94143-0794, CA, USA. tjhoffm@gmail.com
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Hoffmann
authors.forename: Mark N
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authors.forename: Stephanie E
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authors.lastname: Hesselson
authors.forename: Yiping
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authors.lastname: Chung
authors.forename: Sheryl
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authors.lastname: Hubbell
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authors.lastname: Kaufman
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authors.forename: Yontao
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authors.lastname: Ludwig
authors.forename: Gurpreet K
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authors.forename: William
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authors.lastname: Mei
authors.forename: Sunita
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authors.lastname: Quesenberry
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authors.lastname: Rowell
authors.forename: Marianne
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authors.lastname: Sadler
authors.forename: Michael H
authors.initials: MH
authors.lastname: Shapero
authors.forename: Ling
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authors.lastname: Shen
authors.forename: Tanushree R
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authors.lastname: Shenoy
authors.forename: David
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authors.lastname: Smethurst
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authors.lastname: Van den Eeden
authors.forename: Larry
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authors.lastname: Walter
authors.forename: Eunice
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authors.forename: Reid
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authors.lastname: Wearley
authors.forename: Teresa
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authors.lastname: Webster
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Wen
authors.forename: Li
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authors.lastname: Weng
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Whitmer
authors.forename: Alan
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authors.lastname: Williams
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authors.initials: SC
authors.lastname: Wong
authors.forename: Chia
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authors.lastname: Zau
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authors.lastname: Finn
authors.forename: Catherine
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authors.lastname: Schaefer
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authors.lastname: Kwok
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authors.lastname: Risch
mesh_terms: D055106:Genome-Wide Association Study / Q000379:methods*; D057166:High-Throughput Screening Assays; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D044465:White People / Q000235:genetics*