Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

Consortia CAAPA Consortium

Research output: Contribution to journalArticle

Abstract

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (∼30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

Original languageEnglish (US)
Article number46398
JournalScientific Reports
Volume7
DOIs
StatePublished - Jan 1 2017

Fingerprint

Single Nucleotide Polymorphism
Genome
Population
Asthma
Genome-Wide Association Study
Cataloging
Exome
Research Personnel

ASJC Scopus subject areas

  • General

Cite this

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome. / Consortia CAAPA Consortium.

In: Scientific Reports, Vol. 7, 46398, 01.01.2017.

Research output: Contribution to journalArticle

@article{0d5eca72cda04a3e9944c94aecde5e0d,
title = "Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome",
abstract = "A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (∼30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.",
author = "{Consortia CAAPA Consortium} and Johnston, {Henry Richard} and Hu, {Yi Juan} and Jingjing Gao and O'Connor, {Timothy D.} and Abecasis, {Gon{\cc}alo R.} and Wojcik, {Genevieve L.} and Gignoux, {Christopher R.} and Gourraud, {Pierre Antoine} and Antoine Lizee and Mark Hansen and Rob Genuario and Dave Bullis and Cindy Lawley and Kenny, {Eimear E.} and Carlos Bustamante and Beaty, {Terri H.} and Mathias, {Rasika A.} and Barnes, {Kathleen C.} and Qin, {Zhaohui S.} and Boorgula, {Meher Preethi} and Monica Campbell and Sameer Chavan and Ford, {Jean G.} and Cassandra Foster and Li Gao and Hansel, {Nadia N.} and Edward Horowitz and Lili Huang and Romina Ortiz and Joseph Potee and Nicholas Rafaels and Ingo Ruczinski and Scott, {Alan F.} and Taub, {Margaret A.} and Candelaria Vergara and Levin, {Albert M.} and Badri Padhukasahasram and Williams, {L. Keoki} and Dunston, {Georgia M.} and Faruque, {Mezbah U.} and Kimberly Gietzen and Aniket Deshpande and Grus, {Wendy E.} and Locke, {Devin P.} and Foreman, {Marilyn G.} and Avila, {Pedro C.} and Leslie Grammer and Kim, {Kwang Youn A.} and Rajesh Kumar and Robert Schleimer",
year = "2017",
month = "1",
day = "1",
doi = "10.1038/srep46398",
language = "English (US)",
volume = "7",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

AU - Consortia CAAPA Consortium

AU - Johnston, Henry Richard

AU - Hu, Yi Juan

AU - Gao, Jingjing

AU - O'Connor, Timothy D.

AU - Abecasis, Gonçalo R.

AU - Wojcik, Genevieve L.

AU - Gignoux, Christopher R.

AU - Gourraud, Pierre Antoine

AU - Lizee, Antoine

AU - Hansen, Mark

AU - Genuario, Rob

AU - Bullis, Dave

AU - Lawley, Cindy

AU - Kenny, Eimear E.

AU - Bustamante, Carlos

AU - Beaty, Terri H.

AU - Mathias, Rasika A.

AU - Barnes, Kathleen C.

AU - Qin, Zhaohui S.

AU - Boorgula, Meher Preethi

AU - Campbell, Monica

AU - Chavan, Sameer

AU - Ford, Jean G.

AU - Foster, Cassandra

AU - Gao, Li

AU - Hansel, Nadia N.

AU - Horowitz, Edward

AU - Huang, Lili

AU - Ortiz, Romina

AU - Potee, Joseph

AU - Rafaels, Nicholas

AU - Ruczinski, Ingo

AU - Scott, Alan F.

AU - Taub, Margaret A.

AU - Vergara, Candelaria

AU - Levin, Albert M.

AU - Padhukasahasram, Badri

AU - Williams, L. Keoki

AU - Dunston, Georgia M.

AU - Faruque, Mezbah U.

AU - Gietzen, Kimberly

AU - Deshpande, Aniket

AU - Grus, Wendy E.

AU - Locke, Devin P.

AU - Foreman, Marilyn G.

AU - Avila, Pedro C.

AU - Grammer, Leslie

AU - Kim, Kwang Youn A.

AU - Kumar, Rajesh

AU - Schleimer, Robert

PY - 2017/1/1

Y1 - 2017/1/1

N2 - A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (∼30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

AB - A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (∼30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

UR - http://www.scopus.com/inward/record.url?scp=85038807070&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85038807070&partnerID=8YFLogxK

U2 - 10.1038/srep46398

DO - 10.1038/srep46398

M3 - Article

C2 - 28429804

AN - SCOPUS:85038807070

VL - 7

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 46398

ER -