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Johnston HR, Hu YJ, Gao J, O’Connor TD, Abecasis GR, Wojcik GL, Gignoux CR, Gourraud PA, Lizee A, Hansen M, Genuario R, Bullis D, Lawley C, Kenny EE, Bustamante C, Beaty TH, Mathias RA, Barnes KC, Qin ZS. Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome. Sci Rep 2017; 7:46398. [PMID: 28429804 PMCID: PMC5399604 DOI: 10.1038/srep46398] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/17/2017] [Indexed: 12/15/2022] Open
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.
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Affiliation(s)
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Jingjing Gao
- Data and Statistical Sciences, AbbVie, North Chicago, IL, USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Gonçalo R. Abecasis
- Department of Biostatistics, SPH, University of Michigan, Ann Arbor, MI, USA
| | - Genevieve L Wojcik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Antoine Lizee
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Eimear E. Kenny
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Rasika A. Mathias
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen C. Barnes
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Zhaohui S. Qin
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
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