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Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

By Daniel Taliun, Daniel N. Harris, Michael D Kessler, Jedidiah Carlson, Zachary A. Szpiech, Raul Torres, Sarah A Gagliano Taliun, André Corvelo, Stephanie M. Gogarten, Hyun Min Kang, Achilleas N Pitsillides, Jonathon LeFaive, Seung-been Lee, Xiaowen Tian, Brian L Browning, Sayantan Das, Anne-Katrin Emde, Wayne E. Clarke, Douglas P. Loesch, Amol C Shetty, Thomas W Blackwell, Quenna Wong, François Aguet, Christine Albert, Alvaro Alonso, Kristin G Ardlie, Stella Aslibekyan, Paul L Auer, John Barnard, R. Graham Barr, Lewis C. Becker, Rebecca L Beer, Emelia J. Benjamin, Lawrence F Bielak, John Blangero, Michael Boehnke, Donald W. Bowden, Jennifer A Brody, Esteban G Burchard, Brian E Cade, James F. Casella, Brandon Chalazan, Yii-Der Ida Chen, Michael H Cho, Seung Hoan Choi, Mina K. Chung, Clary B Clish, Adolfo Correa, Joanne E. Curran, Brian Custer, Dawood Darbar, Michelle Daya, Mariza de Andrade, Dawn L DeMeo, Susan K Dutcher, Patrick T Ellinor, Leslie S Emery, Diane Fatkin, Lukas Forer, Myriam Fornage, Nora Franceschini, Christian Fuchsberger, Stephanie M Fullerton, Soren Germer, Mark T Gladwin, Daniel J Gottlieb, Xiuqing Guo, Michael E Hall, Jiang He, Nancy L. Heard-Costa, Susan R Heckbert, Marguerite R Irvin, Jill M Johnsen, Andrew D. Johnson, Sharon LR Kardia, Tanika Kelly, Shannon Kelly, Eimear E Kenny, Douglas P Kiel, Robert Klemmer, Barbara A Konkle, Charles Kooperberg, Anna Köttgen, Leslie A Lange, Jessica Lasky-Su, Daniel Levy, Xihong Lin, Keng-Han Lin, Chunyu Liu, Ruth JF Loos, Lori Garman, Robert Gerszten, Steven A. Lubitz, Kathryn L. Lunetta, Angel CY Mak, Ani Manichaikul, Alisa K Manning, Rasika A. Mathias, David D McManus, Stephen T McGarvey, James B Meigs, Deborah A Meyers, Julie L Mikulla, Mollie A Minear, Braxton Mitchell, Sanghamitra Mohanty, May E Montasser, Courtney Montgomery, Alanna C. Morrison, Joanne M. Murabito, Andrea Natale, Pradeep Natarajan, Sarah C. Nelson, Kari E. North, Jeffrey R. O’Connell, Nicholette D Palmer, Nathan Pankratz, Gina M Peloso, Patricia A Peyser, Wendy S. Post, Bruce M Psaty, DC Rao, Susan Redline, Alexander P Reiner, Dan Roden, Jerome I Rotter, Ingo Ruczinski, Chloé Sarnowski, Sebastian Schoenherr, Jeong-Sun Seo, Sudha Seshadri, Vivien A Sheehan, M Benjamin Shoemaker, Albert V Smith, Nicholas L Smith, Jennifer A. Smith, Nona Sotoodehnia, Adrienne M. Stilp, Weihong Tang, Kent D Taylor, Marilyn Telen, Timothy A Thornton, Russell P Tracy, David J. Van Den Berg, Ramachandran S Vasan, Karine A Viaud-Martinez, Scott Vrieze, Daniel E Weeks, Bruce S. Weir, Scott T Weiss, Lu-Chen Weng, Cristen J. Willer, Yingze Zhang, Xutong Zhao, Donna K. Arnett, Allison E Ashley-Koch, Kathleen C Barnes, Eric Boerwinkle, Stacey Gabriel, Richard Gibbs, Kenneth M Rice, Stephen S Rich, Edwin Silverman, Pankaj Qasba, Weiniu Gan, Trans-Omics for Precision Medicine (TOPMed) Program, TOPMed Population Genetics Working Group, George J Papanicolaou, Deborah A. Nickerson, Sharon R Browning, Michael C. Zody, Sebastian Zöllner, James G Wilson, L Adrienne Cupples, Cathy C. Laurie, Cashell E Jaquish, Ryan D. Hernandez, Timothy D. O’Connor, Gonçalo R Abecasis

Posted 06 Mar 2019
bioRxiv DOI: 10.1101/563866

The Trans-Omics for Precision Medicine (TOPMed) program seeks to elucidate the genetic architecture and disease biology of heart, lung, blood, and sleep disorders, with the ultimate goal of improving diagnosis, treatment, and prevention. The initial phases of the program focus on whole genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here, we describe TOPMed goals and design as well as resources and early insights from the sequence data. The resources include a variant browser, a genotype imputation panel, and sharing of genomic and phenotypic data via dbGaP. In 53,581 TOPMed samples, >400 million single-nucleotide and insertion/deletion variants were detected by alignment with the reference genome. Additional novel variants are detectable through assembly of unmapped reads and customized analysis in highly variable loci. Among the >400 million variants detected, 97% have frequency <1% and 46% are singletons. These rare variants provide insights into mutational processes and recent human evolutionary history. The nearly complete catalog of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and non-coding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and extends the reach of nearly all genome-wide association studies to include variants down to ~0.01% in frequency.

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