title: Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm.
abstract: Four custom Axiom genotyping arrays were designed for a genome-wide association (GWA) study of 100,000 participants from the Kaiser Permanente Research Program on Genes, Environment and Health. The array optimized for individuals of European race/ethnicity was previously described. Here we detail the development of three additional microarrays optimized for individuals of East Asian, African American, and Latino race/ethnicity. For these arrays, we decreased redundancy of high-performing SNPs to increase SNP capacity. The East Asian array was designed using greedy pairwise SNP selection. However, removing SNPs from the target set based on imputation coverage is more efficient than pairwise tagging. Therefore, we developed a novel hybrid SNP selection method for the African American and Latino arrays utilizing rounds of greedy pairwise SNP selection, followed by removal from the target set of SNPs covered by imputation. The arrays provide excellent genome-wide coverage and are valuable additions for large-scale GWA studies.
authors: Institute for Human Genetics, University of California, San Francisco, CA 94143-0794, USA. hoffmannt@humgen.ucsf.edu
authors: Thomas J
authors: TJ
authors: Hoffmann
authors: Yiping
authors: Y
authors: Zhan
authors: Mark N
authors: MN
authors: Kvale
authors: Stephanie E
authors: SE
authors: Hesselson
authors: Jeremy
authors: J
authors: Gollub
authors: Carlos
authors: C
authors: Iribarren
authors: Yontao
authors: Y
authors: Lu
authors: Gangwu
authors: G
authors: Mei
authors: Matthew M
authors: MM
authors: Purdy
authors: Charles
authors: C
authors: Quesenberry
authors: Sarah
authors: S
authors: Rowell
authors: Michael H
authors: MH
authors: Shapero
authors: David
authors: D
authors: Smethurst
authors: Carol P
authors: CP
authors: Somkin
authors: Stephen K
authors: SK
authors: Van den Eeden
authors: Larry
authors: L
authors: Walter
authors: Teresa
authors: T
authors: Webster
authors: Rachel A
authors: RA
authors: Whitmer
authors: Andrea
authors: A
authors: Finn
authors: Catherine
authors: C
authors: Schaefer
authors: Pui-Yan
authors: PY
authors: Kwok
authors: Neil
authors: N
authors: Risch
mesh_terms: D001741:Black or African American / Q000235:genetics*; D000465:Algorithms; D044466:Asian People / Q000235:genetics*; D005202:Asia, Eastern; D015894:Genome, Human; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D006630:Hispanic or Latino / Q000235:genetics*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D010865:Pilot Projects; D020641:Polymorphism, Single Nucleotide; D044465:White People / Q000235:genetics