A population-specific reference panel for improved genotype imputation in African Americans
Jared O’Connell, Taedong Yun, Meghan E. Moreno, Helen Li, Nadia K. Litterman, Alexey Kolesnikov, Elizabeth S. Noblin, Pi-Chuan Chang, Anjali J. Shastri, Elizabeth H. Dorfman, Suyash Shringarpure, Stella Aslibekyan, Elizabeth Babalola, Robert K. Bell, Jessica Bielenberg, Katarzyna Bryc, Emily Bullis, Daniella Coker, Gabriel Cuéllar-Partida, Devika Dhamija, Sayantan Das, Sarah L. Elson, Teresa Filshtein, Kipper Fletez‐Brant, Pierre Fontanillas, Will Freyman, Pooja Gandhi, Karl Heilbron, Alejandro Hernandez, Barry Hicks, David A. Hinds, Ethan M. Jewett, Yunxuan Jiang, Katelyn Kukar, Keng-Han Lin, Maya Lowe, Jey C. McCreight, Matthew H. McIntyre, Steven J. Micheletti, Joanna L. Mountain, Priyanka Nandakumar, Aaron A. Petrakovitz, G. David Poznik, Morgan Schumacher, Janie F. Shelton, Jingchunzi Shi, Christophe Toukam Tchakouté, Vinh Tran, Joyce Y. Tung, Xin Wang, Wei Wang, Catherine H. Weldon, Peter Wilton, Corinna Wong, Adam Auton, Andrew Carroll, Cory Y. McLean
Abstract
There is currently a dearth of accessible whole genome sequencing (WGS) data for individuals residing in the Americas with Sub-Saharan African ancestry. We generated whole genome sequencing data at intermediate (15×) coverage for 2,294 individuals with large amounts of Sub-Saharan African ancestry, predominantly Atlantic African admixed with varying amounts of European and American ancestry. We performed extensive comparisons of variant callers, phasing algorithms, and variant filtration on these data to construct a high quality imputation panel containing data from 2,269 unrelated individuals. With the exception of the TOPMed imputation server (which notably cannot be downloaded), our panel substantially outperformed other available panels when imputing African American individuals. The raw sequencing data, variant calls and imputation panel for this cohort are all freely available via dbGaP and should prove an invaluable resource for further study of admixed African genetics.