Elsevier

Genomics

Volume 98, Issue 6, December 2011, Pages 422-430
Genomics

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

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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.

Highlights

► European, East Asian, African American and Latino race/ethnicity optimized arrays. ► High density genotyping arrays for large-scale genome-wide association studies. ► Novel design alternates rounds of pairwise SNP selection and imputation coverage. ► Increased SNP density achieved by reduced redundancy of high performing SNPs.

Abbreviations

GWA
genome-wide association
MAF
minor allele frequency
KGP
1000 Genomes Project
RPGEH
Research Program on Genes, Environment and Health
EUR
European and West Asian
EAS
East Asian
AFR
African American
LAT
Latino
2-rep
2 features
1-rep
1 feature
ASW
African Ancestry in Southwest USA
CEU
Utah residents with ancestry from Northern and Western Europe from Centre d'Etude du Polymorphisme Humain
CHB
Han Chinese in Beijing
CHS
Han Chinese South
CLM
Colombian in Medellin, Colombia
Fin
Finnish from Finland
GBR
British individuals from England and Scotland
IBS
Iberians in Spain
JPT
Japanese in Tokyo
LWK
Luhya in Webuye Kenya
MXL
Mexican in Los Angeles, CA
PUR
Puerto Rican in Puerto Rico
TSI
Toscani in Italia
YRI
Yoruba in Ibadan, Nigeria
KGHP
1000 Genomes High Pass
KPNC
Kaiser Permanente Northern California
AIMs
Ancestry Informative Markers
KG2011
1000 Genomes interim June 2011 release

Keywords

Microarray
Genome-wide association study
Coverage
Imputation
Single nucleotide polymorphism
Throughput

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1

These authors contributed equally to this work.