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

Henry Richard Johnston, Yi-Juan Hu, Jingjing Gao, Timoty D. O’Connor, Goncalo Abecasis, Genevieve L Wojcik, Christopher R. Gignoux, Pierre-Antoine Gourraud, Antoine Lizee, Mark Hansen, Rob Genuario, Dave Bullis, Cindy Lawley, Eimear E. Kenny, Carlos Bustamante, Terri H. Beaty, Rasika A. Mathias, Kathleen C. Barnes, Zhaohui Steve Qin, CAAPA Consortium
doi: https://doi.org/10.1101/112235
Henry Richard Johnston
Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA
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Yi-Juan Hu
Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA
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Jingjing Gao
Data and Statistical Sciences, AbbVie, North Chicago, IL
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Timoty D. O’Connor
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MDProgram in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MDDepartment of Medicine, University of Maryland School of Medicine, Baltimore, MD
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Goncalo Abecasis
Department of Biostatistics, SPH II, University of Michigan, Ann Arbor, MI
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Genevieve L Wojcik
Department of Genetics, Stanford University School of Medicine, Stanford, CA
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Christopher R. Gignoux
Department of Genetics, Stanford University School of Medicine, Stanford, CA
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Pierre-Antoine Gourraud
Department of Neurology, University of California, San Francisco, San Francisco, CA
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Antoine Lizee
Department of Neurology, University of California, San Francisco, San Francisco, CA
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Mark Hansen
Illumina, Inc., San Diego, CA
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Rob Genuario
Illumina, Inc., San Diego, CA
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Dave Bullis
Illumina, Inc., San Diego, CA
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Cindy Lawley
Illumina, Inc., San Diego, CA
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Eimear E. Kenny
Department of Genetics, Stanford University School of Medicine, Stanford, CADepartment of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY
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Carlos Bustamante
Department of Genetics, Stanford University School of Medicine, Stanford, CA
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Terri H. Beaty
Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, MD
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Rasika A. Mathias
Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, MDDepartment of Medicine, Johns Hopkins University, Baltimore, MD
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Kathleen C. Barnes
Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, MDDepartment of Medicine, Johns Hopkins University, Baltimore, MD
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  • For correspondence: kathleen.barnes@ucdenver.edu
Zhaohui Steve Qin
Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA
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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 (~30x 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 study1 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 27, 2017.
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Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome
Henry Richard Johnston, Yi-Juan Hu, Jingjing Gao, Timoty D. O’Connor, Goncalo Abecasis, Genevieve L Wojcik, Christopher R. Gignoux, Pierre-Antoine Gourraud, Antoine Lizee, Mark Hansen, Rob Genuario, Dave Bullis, Cindy Lawley, Eimear E. Kenny, Carlos Bustamante, Terri H. Beaty, Rasika A. Mathias, Kathleen C. Barnes, Zhaohui Steve Qin, CAAPA Consortium
bioRxiv 112235; doi: https://doi.org/10.1101/112235
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Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome
Henry Richard Johnston, Yi-Juan Hu, Jingjing Gao, Timoty D. O’Connor, Goncalo Abecasis, Genevieve L Wojcik, Christopher R. Gignoux, Pierre-Antoine Gourraud, Antoine Lizee, Mark Hansen, Rob Genuario, Dave Bullis, Cindy Lawley, Eimear E. Kenny, Carlos Bustamante, Terri H. Beaty, Rasika A. Mathias, Kathleen C. Barnes, Zhaohui Steve Qin, CAAPA Consortium
bioRxiv 112235; doi: https://doi.org/10.1101/112235

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