A population-specific reference panel for improved genotype imputation in African Americans

• DOI: 10.1038/s42003-021-02777-9
• Publication Date: 2021-11-05T11:06:21Z
• Authors: Jared O’Connell; Taedong Yun; Meghan Moreno; Helen Li; Nadia Litterman; Alexey Kolesnikov; Elizabeth Noblin; Pi-Chuan Chang; Anjali Shastri; Elizabeth H. Dorfman; Suyash Shringarpure; ; Stella Aslibekyan; Elizabeth Babalola; Robert K. Bell; Jessica Bielenberg; Katarzyna Bryc; Emily Bullis; Daniella Coker; Gabriel Cuellar P...; Devika Dhamija; Sayantan Das; Sarah L. Elson; Teresa Filshtein; Kipper Fletez-Brant; Pierre Fontanillas; Will Freyman; Pooja M. Gandhi; Karl Heilbron; Alejandro Hernandez; Barry Hicks; David A. Hinds; Ethan M. Jewett; Yunxuan Jiang; Katelyn Kukar; Keng-Han Lin; Maya Lowe; Jey 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...; Vinh Tran; Joyce Y. Tung; Xin Wang; Wei Wang; Catherine H. Weldon; Peter Wilton; Corinna Wong; Adam Auton; Andrew Carroll; Cory Y. McLean
• Keywords: Imputation (statistics); 1000 Genomes Project; Genome-wide Association Study

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 at intermediate (15×) coverage 2,294 large amounts ancestry, predominantly Atlantic admixed varying European and American performed extensive comparisons variant callers, phasing algorithms, filtration on these to construct high quality imputation panel containing from 2,269 unrelated individuals. With exception TOPMed server (which notably cannot be downloaded), our substantially outperformed other available panels when imputing The raw data, calls this cohort are all freely via dbGaP should prove an invaluable resource further study genetics.