Dataset Information

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.

SUBMITTER: Johnston HR

PROVIDER: S-EPMC5399604 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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

Johnston Henry Richard HR Hu Yi-Juan YJ Gao Jingjing J O'Connor Timothy D TD Abecasis Gonçalo R GR Wojcik Genevieve L GL Gignoux Christopher R CR Gourraud Pierre-Antoine PA Lizee Antoine A Hansen Mark M Genuario Rob R Bullis Dave D Lawley Cindy C Kenny Eimear E EE Bustamante Carlos C Beaty Terri H TH Mathias Rasika A RA Barnes Kathleen C KC Qin Zhaohui S ZS

Scientific reports 20170421

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 cata ...[more]

PMID: 28429804

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Dataset Information

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

Publications

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

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