Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry

Michael D. Kessler, Laura Yerges-Armstrong, Margaret A. Taub, Amol C. Shetty, Kristin Maloney, Linda Jo Bone Jeng, Ingo Ruczinski, Albert M. Levin, L. Keoki Williams, Terri H. Beaty, Rasika A. Mathias, Kathleen C. Barnes and Timothy D. O’Connor ()
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Michael D. Kessler: Institute for Genome Sciences, University of Maryland School of Medicine
Laura Yerges-Armstrong: University of Maryland School of Medicine
Margaret A. Taub: Bloomberg School of Public Health, Johns Hopkins University
Amol C. Shetty: Institute for Genome Sciences, University of Maryland School of Medicine
Kristin Maloney: Program in Personalized and Genomic Medicine, University of Maryland School of Medicine
Linda Jo Bone Jeng: Program in Personalized and Genomic Medicine, University of Maryland School of Medicine
Ingo Ruczinski: Bloomberg School of Public Health, Johns Hopkins University
Albert M. Levin: Henry Ford Health System
L. Keoki Williams: Center for Health Policy & Health Services Research, Henry Ford Health System
Terri H. Beaty: Bloomberg School of Public Health, Johns Hopkins University
Rasika A. Mathias: Bloomberg School of Public Health, Johns Hopkins University
Kathleen C. Barnes: Bloomberg School of Public Health, Johns Hopkins University
Timothy D. O’Connor: Institute for Genome Sciences, University of Maryland School of Medicine

Nature Communications, 2016, vol. 7, issue 1, 1-8

Abstract: Abstract To characterize the extent and impact of ancestry-related biases in precision genomic medicine, we use 642 whole-genome sequences from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) project to evaluate typical filters and databases. We find significant correlations between estimated African ancestry proportions and the number of variants per individual in all variant classification sets but one. The source of these correlations is highlighted in more detail by looking at the interaction between filtering criteria and the ClinVar and Human Gene Mutation databases. ClinVar’s correlation, representing African ancestry-related bias, has changed over time amidst monthly updates, with the most extreme switch happening between March and April of 2014 (r=0.733 to r=−0.683). We identify 68 SNPs as the major drivers of this change in correlation. As long as ancestry-related bias when using these clinical databases is minimally recognized, the genetics community will face challenges with implementation, interpretation and cost-effectiveness when treating minority populations.

Date: 2016
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DOI: 10.1038/ncomms12521

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