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

Thomas J. Hoffmann, Yiping Zhan, Mark N. Kvale, Stephanie E. Hesselson, Jeremy Gollub, Carlos Iribarren, Yontao Lu, Gangwu Mei, Matthew M. Purdy, Charles Quesenberry, Sarah Rowell, Michael H. Shapero, David Smethurst, Carol P. Somkin, Stephen K. Van den Eeden, Larry Walter, Teresa Webster, Rachel Whitmer, Andrea Finn, Catherine SchaeferPui Yan Kwok, Neil Risch

Research output: Contribution to journalArticle

85 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)422-430
Number of pages9
JournalGenomics
Volume98
Issue number6
DOIs
StatePublished - Dec 1 2011
Externally publishedYes

Fingerprint

Asian Americans
Hispanic Americans
African Americans
Single Nucleotide Polymorphism
Genome-Wide Association Study
Genome
Health
Research
Genes

Keywords

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

ASJC Scopus subject areas

  • Genetics

Cite this

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. / Hoffmann, Thomas J.; Zhan, Yiping; Kvale, Mark N.; Hesselson, Stephanie E.; Gollub, Jeremy; Iribarren, Carlos; Lu, Yontao; Mei, Gangwu; Purdy, Matthew M.; Quesenberry, Charles; Rowell, Sarah; Shapero, Michael H.; Smethurst, David; Somkin, Carol P.; Van den Eeden, Stephen K.; Walter, Larry; Webster, Teresa; Whitmer, Rachel; Finn, Andrea; Schaefer, Catherine; Kwok, Pui Yan; Risch, Neil.

In: Genomics, Vol. 98, No. 6, 01.12.2011, p. 422-430.

Research output: Contribution to journalArticle

Hoffmann, TJ, Zhan, Y, Kvale, MN, Hesselson, SE, Gollub, J, Iribarren, C, Lu, Y, Mei, G, Purdy, MM, Quesenberry, C, Rowell, S, Shapero, MH, Smethurst, D, Somkin, CP, Van den Eeden, SK, Walter, L, Webster, T, Whitmer, R, Finn, A, Schaefer, C, Kwok, PY & Risch, N 2011, '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', Genomics, vol. 98, no. 6, pp. 422-430. https://doi.org/10.1016/j.ygeno.2011.08.007
Hoffmann, Thomas J. ; Zhan, Yiping ; Kvale, Mark N. ; Hesselson, Stephanie E. ; Gollub, Jeremy ; Iribarren, Carlos ; Lu, Yontao ; Mei, Gangwu ; Purdy, Matthew M. ; Quesenberry, Charles ; Rowell, Sarah ; Shapero, Michael H. ; Smethurst, David ; Somkin, Carol P. ; Van den Eeden, Stephen K. ; Walter, Larry ; Webster, Teresa ; Whitmer, Rachel ; Finn, Andrea ; Schaefer, Catherine ; Kwok, Pui Yan ; Risch, Neil. / 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. In: Genomics. 2011 ; Vol. 98, No. 6. pp. 422-430.
@article{649df5c18128407eb5fc837b9e6a158c,
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.",
keywords = "Coverage, Genome-wide association study, Imputation, Microarray, Single nucleotide polymorphism, Throughput",
author = "Hoffmann, {Thomas J.} and Yiping Zhan and Kvale, {Mark N.} and Hesselson, {Stephanie E.} and Jeremy Gollub and Carlos Iribarren and Yontao Lu and Gangwu Mei and Purdy, {Matthew M.} and Charles Quesenberry and Sarah Rowell and Shapero, {Michael H.} and David Smethurst and Somkin, {Carol P.} and {Van den Eeden}, {Stephen K.} and Larry Walter and Teresa Webster and Rachel Whitmer and Andrea Finn and Catherine Schaefer and Kwok, {Pui Yan} and Neil Risch",
year = "2011",
month = "12",
day = "1",
doi = "10.1016/j.ygeno.2011.08.007",
language = "English (US)",
volume = "98",
pages = "422--430",
journal = "Genomics",
issn = "0888-7543",
publisher = "Academic Press Inc.",
number = "6",

}

TY - JOUR

T1 - 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

AU - Hoffmann, Thomas J.

AU - Zhan, Yiping

AU - Kvale, Mark N.

AU - Hesselson, Stephanie E.

AU - Gollub, Jeremy

AU - Iribarren, Carlos

AU - Lu, Yontao

AU - Mei, Gangwu

AU - Purdy, Matthew M.

AU - Quesenberry, Charles

AU - Rowell, Sarah

AU - Shapero, Michael H.

AU - Smethurst, David

AU - Somkin, Carol P.

AU - Van den Eeden, Stephen K.

AU - Walter, Larry

AU - Webster, Teresa

AU - Whitmer, Rachel

AU - Finn, Andrea

AU - Schaefer, Catherine

AU - Kwok, Pui Yan

AU - Risch, Neil

PY - 2011/12/1

Y1 - 2011/12/1

N2 - 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.

AB - 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.

KW - Coverage

KW - Genome-wide association study

KW - Imputation

KW - Microarray

KW - Single nucleotide polymorphism

KW - Throughput

UR - http://www.scopus.com/inward/record.url?scp=81955167912&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=81955167912&partnerID=8YFLogxK

U2 - 10.1016/j.ygeno.2011.08.007

DO - 10.1016/j.ygeno.2011.08.007

M3 - Article

C2 - 21903159

AN - SCOPUS:81955167912

VL - 98

SP - 422

EP - 430

JO - Genomics

JF - Genomics

SN - 0888-7543

IS - 6

ER -