Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry
Michael D. Kessler(University of Maryland, Baltimore), Laura M. Yerges-Armstrong(University of Maryland, Baltimore), Margaret A. Taub(Johns Hopkins University), Amol C. Shetty(University of Maryland, Baltimore), Kristin A. Maloney(University of Maryland, Baltimore), Linda Jo Bone Jeng(University of Maryland, Baltimore), Ingo Ruczinski(Johns Hopkins University), Albert M. Levin(Henry Ford Health System), L. Keoki Williams(Henry Ford Health System), Terri H. Beaty(Johns Hopkins University), Rasika A. Mathias(Johns Hopkins University), Kathleen C. Barnes(Johns Hopkins University), Meher Preethi Boorgula(Johns Hopkins University), Monica Campbell(Johns Hopkins University), Sameer Chavan(Johns Hopkins University), Jean G. Ford(Brooklyn Hospital Center), Cassandra Foster(Johns Hopkins University), Li Gao(Johns Hopkins University), Nadia N. Hansel(Johns Hopkins University), Edward A. Horowitz(Johns Hopkins University), Lili Huang(Johns Hopkins University), Romina Ortiz(Johns Hopkins University), Joseph Potee(Johns Hopkins University), Nicholas Rafaels(Johns Hopkins University), Alan F. Scott(Johns Hopkins University), Candelaria Vergara(Johns Hopkins University), Jingjing Gao(AbbVie (United States)), Yi‐Juan Hu(Emory University), H. Richard Johnston(Emory University), Zhaohui Qin(Emory University), Badri Padhukasahasram(Henry Ford Health System), Georgia M. Dunston(Howard University), Mezbah U. Faruque(Howard University), Eimear E. Kenny(Stanford University), Kimberly Gietzen(Illumina (United States)), Mark Hansen(Illumina (United States)), Rob Genuario(Illumina (United States)), Dave Bullis(Illumina (United States)), Cindy Lawley(Illumina (United States)), Aniket Deshpande(Cambridge Scientific (United States)), Wendy E. Grus(Cambridge Scientific (United States)), Devin P. Locke(Cambridge Scientific (United States)), Marilyn G. Foreman(Morehouse School of Medicine), Pedro C. Avila(Northwestern University), Leslie C. Grammer(Northwestern University), Kwang-YounA Kim(Northwestern University), Rajesh Kumar(Northwestern University), Robert P. Schleimer(Northwestern University), Carlos D. Bustamante(Stanford University), Francisco M. De La Vega(Stanford University), Chris Gignoux(Stanford University), Suyash Shringarpure(Stanford University), Shaila Musharoff(Stanford University), Genevieve L. Wojcik(Stanford University), Esteban Burchard(University of California, San Francisco), Celeste Eng(University of California, San Francisco), Pierre‐Antoine Gourraud(University of California, San Francisco), Ryan D. Hernandez(QB3), Antoine Lizée(University of California, San Francisco), Maria Pino‐Yanes(University of California, San Francisco), Dara G. Torgerson(University of California, San Francisco), Zachary A. Szpiech(University of California, San Francisco), Raúl Torres(University of California, San Francisco), Dan L. Nicolae(University of Chicago), Carole Ober(University of Chicago), Christopher O. Olopade(University of Chicago), Olufunmilayo I. Olopade(University of Chicago), Oluwafemi Oluwole(University of Chicago), Ganiyu Arinola(University of Ibadan), Wei Song(University of Maryland, Baltimore), Gonçalo R. Abecasis(University of Michigan), Adolfo Correa(University of Mississippi Medical Center), Solomon K. Musani(University of Mississippi Medical Center), James G. Wilson(Jackson Memorial Hospital), Leslie A. Lange(University of North Carolina at Chapel Hill), Joshua M. Akey(University of Washington), Michael J. Bamshad(University of Washington), Jessica X. Chong(University of Washington), Wenqing Fu(University of Washington), Deborah A. Nickerson(University of Washington), Alexander P. Reiner(University of Washington), Tina V. Hartert(Vanderbilt University), Lorraine B. Ware(Vanderbilt University), Eugene R. Bleecker(Wake Forest University), Deborah Meyers(Wake Forest University), Victor E. Ortega(Wake Forest University), Maul R. N. Pissamai(University of the West Indies), Maul R. N. Trevor(University of the West Indies), Harold Watson(University of the West Indies System), Maria Ilma Araújo(Universidade Federal da Bahia), Ricardo Riccio Oliveira, Luis Caraballo(Universidad Politécnica de Cartagena), Javier Marrugo(Universidad Politécnica de Cartagena), B. Martínez(Universidad Politécnica de Cartagena), Catherine Meza(Universidad Politécnica de Cartagena), Gerardo Ayestas(National Autonomous University of Honduras), Edwin Francisco Herrera-Paz(Universidad Católica de Honduras Nuestra Señora Reina de la Paz), Pamela Landaverde-Torres(Universidad Católica de Honduras Nuestra Señora Reina de la Paz), Said Omar Leiva Erazo(Universidad Católica de Honduras Nuestra Señora Reina de la Paz), Rosella Martinez(Universidad Católica de Honduras Nuestra Señora Reina de la Paz), Alvaro Mayorga(Honduras Foundation for Agricultural Research), L Mayorga(Universidad Católica de Honduras Nuestra Señora Reina de la Paz), Delmy-Aracely Mejia-Mejia(Honduras Foundation for Agricultural Research), Hector Ramos(Universidad Católica de Honduras Nuestra Señora Reina de la Paz), Allan Saenz(National Autonomous University of Honduras), Gloria Varela(National Autonomous University of Honduras), Olga Marina Vasquez(Honduras Foundation for Agricultural Research), Trevor S. Ferguson(University of the West Indies), Jennifer Knight‐Madden(University of the West Indies), Maureen Samms‐Vaughan(University of the West), Rainford Wilks(University of the West Indies), Akim Adegnika(Leiden University Medical Center), Ulysse Ateba-Ngoa(Leiden University Medical Center), Maria Yazdanbakhsh(Leiden University Medical Center), Timothy D. O’Connor(University of Maryland, Baltimore)
Cited by 80Open Access
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.
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