Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes
Qingbo S. Wang, Emma Pierce‐Hoffman, Beryl B. Cummings, Jessica Alföldi, Laurent C. Francioli, Laura D. Gauthier, Andrew Hill, Anne O’Donnell‐Luria, Genome Aggregation Database Production Team, Irina M. Armean, Eric Banks, Louis Bergelson, Kristian Cibulskis, Ryan L. Collins, Kristen M. Connolly, Miguel Covarrubias, Mark J. Daly, Stacey Donnelly, Yossi Farjoun, Steven Ferriera, Stacey Gabriel, Jeff Gentry, Namrata Gupta, Thibault Jeandet, Diane Kaplan, Kristen M. Laricchia, Christopher Llanwarne, Eric Vallabh Minikel, Ruchi Munshi, Benjamin M. Neale, Sam Novod, Nikelle Petrillo, Timothy Poterba, David Roazen, Valentín Ruano-Rubio, Andrea Saltzman, Kaitlin E. Samocha, Molly Schleicher, Cotton Seed, Matthew Solomonson, José Soto, Grace Tiao, Kathleen Tibbetts, Charlotte Tolonen, Christopher Vittal, Gordon Wade, Arcturus Wang, James S. Ware, Nicholas A. Watts, Ben Weisburd, Nicola Whiffin, Carlos A. Aguilar‐Salinas, Tariq Ahmad, Christine M. Albert, Diego Ardissino, Gil Atzmon, John Barnard, Laurent Beaugerie, Emelia J. Benjamin, Michael Boehnke, Lori L. Bonnycastle, Erwin P. Böttinger, Donald W. Bowden, Matthew J. Bown, John C. Chambers, Juliana C.N. Chan, Daniel I. Chasman, Judy H. Cho, Mina K. Chung, Bruce M. Cohen, Adolfo Correa, Dana Dabelea, Dawood Darbar, Ravindranath Duggirala, Josée Dupuis, Patrick T. Ellinor, Roberto Elosúa, Jeanette Erdmann, Tõnu Esko, Martti Färkkilâ, José C. Florez, André Franke, Gad Getz, Benjamin Gläser, Stephen J. Glatt, David Goldstein, Clicerio González, Leif Groop, Christopher Haiman, Craig L. Hanis, Matthew B. Harms, Mikko Hiltunen, Matti Holi, Christina M. Hultman, Mikko Kallela, Jaakko Kaprio, Sekar Kathiresan, Bong-Jo Kim, Young Jin Kim, George Kirov
Abstract
Multi-nucleotide variants (MNVs), defined as two or more nearby variants existing on the same haplotype in an individual, are a clinically and biologically important class of genetic variation. However, existing tools typically do not accurately classify MNVs, and understanding of their mutational origins remains limited. Here, we systematically survey MNVs in 125,748 whole exomes and 15,708 whole genomes from the Genome Aggregation Database (gnomAD). We identify 1,792,248 MNVs across the genome with constituent variants falling within 2 bp distance of one another, including 18,756 variants with a novel combined effect on protein sequence. Finally, we estimate the relative impact of known mutational mechanisms - CpG deamination, replication error by polymerase zeta, and polymerase slippage at repeat junctions - on the generation of MNVs. Our results demonstrate the value of haplotype-aware variant annotation, and refine our understanding of genome-wide mutational mechanisms of MNVs.