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

Pubmed ID: 33568819

Pubmed Central ID: PMC7875770

Journal: Nature

Publication Date: Feb. 1, 2021

Affiliation: Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA. goncalo@umich.edu.

MeSH Terms: Humans, United States, Heterozygote, Haplotypes, Polymorphism, Single Nucleotide, Sample Size, Phenotype, Genome, Human, Mutagenesis, Quality Control, Genetic Variation, National Heart, Lung, and Blood Institute (U.S.), Genomics, Precision Medicine, Loss of Function Mutation, Cytochrome P-450 CYP2D6, INDEL Mutation, Population Density, Whole Genome Sequencing

Grants: P50 HL118006, R01 HL120393, R21 HL123677, P30 DK020572, U01 HL120393, R01 HL117626, R01 HL113326, P30 ES010126, T32 HG000040, R01 AI132476, U01 HG009088, HHSN268201800001C, R01 DA037904, K01 HL135405, R01 HL142711, R03 HL154284, R35 HG010692, K08 HL141601, K24 HL148521, R01 HL131565, R01 DA044283, R01 HL123915, R03 HL141439, K01 AG059898, R01 HL155742, R01 DK117445, R01 HG005701, T32 HL007085, R01 MD012765, UM1 DK078616, UG3 HL151865, R01 HL149836, U01 CA182913, R01 HL163972, R01 AR072199, I01 BX005295, U01 HL137162, R01 HL090620, R01 HL111314, UH3 HL151865

Authors: Arking DE, Casella JF, Barron-Casella E, Gladwin MT, Custer B, Zhang Y, Smith J, Sankaran VG, Vaidya D, Sabino EC, Eng C, Abecasis GR, McGarvey ST, Natale A, Benjamin EJ, Murabito JM, Tracy RP, Vasan RS, Jackson R, Lee J, Li Y, Li X, Psaty BM, He J, Guo X, Wu J, Wallace R, Mitchell BD, Lee WJ, Williams K, Smith NL, Nickerson DA, Mathai S, Lewis J, Kramer H, Taylor S, Johnson C, Xu H, Hokanson J, Carlson J, Watson K, Becker D, Alonso A, Reiner AP, Rich SS, Heckbert SR, Boerwinkle E, Smith T, Herrington D, Martin L, Gupta N, Post WS, Zhu X, Weng LC, Tang W, Köttgen A, Johnson AD, Taylor KD, Lubitz SA, Rotter JI, Fullerton SM, Wilson JG, Morrison AC, Cupples LA, Brody JA, Liu X, Franceschini N, North KE, Correa A, Smith AV, Fornage M, Fornage M, Seshadri S, Auer PL, Lin H, Lin H, Pankratz N, Lange LA, Haessler J, Kooperberg C, Chasman DI, Gibbs R, Kathiresan S, Peters U, Sotoodehnia N, Manichaikul A, Liu Y, Liu Y, Arnett DK, Meigs JB, Aslibekyan S, Irvin MR, Zhi D, Liu C, Levy D, Hidalgo B, Rice KM, Smith JA, Zhao W, Barr RG, Gogarten SM, Laurie CC, Rao DC, Schwander K, Jain D, Fu M, Qin Z, Tinker L, Phillips LS, Wang H, Gao S, Sung YJ, Chen YI, Heard-Costa NL, Blangero J, Saleheen D, O'Connell JR, Willer CJ, Boehnke M, Loos RJF, Kang HM, Fuchsberger C, Taliun D, de Andrade M, Parsa A, Mychaleckyj JC, Peloso GM, Montasser ME, Hung YJ, Hsiung CA, Sheu WH, Sheu WH, Palmer ND, Bielak LF, Peyser PA, Preuss M, Pankow J, Carty C, Kiel DP, Lunetta KL, Garman L, Liu S, Konkle BA, Lin X, Luo J, Levine D, Cho MH, Ruczinski I, Ashley-Koch AE, Redline S, Zhao X, Barnard J, Hall ME, Choi SH, Ellinor PT, Barnes KC, Daya M, Rafaels N, Weiss ST, Lasky-Su J, Mathias RA, Becker LC, Johnsen JM, Sheehan VA, Curran JE, Peralta JM, Montgomery C, Chung RH, Meyers DA, Das S, LeFaive J, Forer L, Schoenherr S, Natarajan P, Hernandez RD, Burchard EG, Hwu CM, Kardia SLR, O'Connor TD, Emery LS, Blackwell TW, Cade BE, Conomos MP, Gao Y, Kim W, Mak ACY, Musani S, Qiao D, Shoemaker MB, Weeks DE, Harris DN, Kessler MD, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Pitsillides AN, Lee SB, Tian X, Browning BL, Emde AK, Clarke WE, Loesch DP, Shetty AC, Wong Q, Bobo DM, Aguet F, Albert C, Ardlie KG, Barwick L, Beer RL, Bowden DW, Chalazan B, Chung MK, Clish CB, Darbar D, DeMeo DL, Dutcher SK, Fatkin D, Fingerlin T, Germer S, Gottlieb DJ, Kaplan R, Kelly T, Kelly S, Kenny EE, Klemmer R, Lin KH, Lin KH, Gerszten R, Manning AK, McManus DD, Mikulla JL, Minear MA, Mohanty S, Nelson SC, Pleiness J, Roden D, Sarnowski C, Schwartz DA, Seo JS, Stilp AM, Telen M, Thornton TA, Van Den Berg DJ, Viaud-Martinez KA, Vrieze S, Weir BS, Gabriel S, Silverman EK, Qasba P, Gan W, Papanicolaou GJ, Browning SR, Zody MC, Zöllner S, Jaquish CE, Abe N, Almasy L, Ament S, Anderson P, Anugu P, Applebaum-Bowden D, Assimes T, Avramopoulos D, Beaty T, Beck G, Beitelshees A, Benos T, Bezerra M, Bis J, Bowler R, Broeckel U, Broome J, Bunting K, Bustamante C, Buth E, Cardwell J, Carey V, Casaburi R, Castaldi P, Chaffin M, Chang C, Chang YC, Chavan S, Chen BJ, Chen WM, Chuang LM, Comhair S, Cornell E, Crandall C, Crapo J, Curtis J, Damcott C, David S, Davis C, Fuentes LL, DeBaun M, Deka R, Devine S, Duan Q, Duggirala R, Durda JP, Eaton C, Ekunwe L, El Boueiz A, Erzurum S, Farber C, Flickinger M, Frazar C, Fulton L, Gass M, Gelb B, Geng XP, Geraci M, Ghosh A, Gignoux C, Glahn D, Gong DW, Goring H, Graw S, Grine D, Gu CC, Guan Y, Hawley NL, Heavner B, Hersh C, Hixson J, Hobbs B, Hong E, Hoth K, Huston H, Jhun MA, Johnston R, Jones K, Khan A, Kinney G, Lange C, Lange E, Lange L, Laurie C, LeBoff M, Lee SS, Mahaney M, Make B, Manson J, Margolin L, May S, McArdle P, McDonald ML, McFarland S, McGoldrick D, McHugh C, Mei H, Mestroni L, Min N, Minster RL, Moll M, Moscati A, Mwasongwe S, Nadkarni G, Naik R, Naseri T, Nekhai S, Neltner B, Ochs-Balcom H, Paik D, Perez M, Perry J, Pollin T, Becker JP, Boorgula MP, Raffield L, Rasmussen-Torvik L, Ratan A, Reed R, Regan E, Reupena MS, Roselli C, Russell P, Ruuska S, Ryan K, Salimi S, Salzberg S, Sandow K, Scheller C, Schmidt E, Sciurba F, Seidman C, Seidman J, Sherman SL, Shetty A, Silver B, Smoller S, Snively B, Snyder M, Sofer T, Storm G, Streeten E, Sylvia J, Szpiro A, Sztalryd C, Tang H, Taub M, Taylor M, Threlkeld M, Tirschwell D, Tishkoff S, Tiwari H, Tong C, Tsai M, VandeHaar P, Walker T, Walts A, Wang FF, Wessel J, Williams LK, Wilson C, Yanek L, Yang I, Yang R, Zaghloul N, Zekavat M, Zhao SX, Zhou X

Cite As: Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM, Kang HM, Pitsillides AN, LeFaive J, Lee SB, Tian X, Browning BL, Das S, Emde AK, Clarke WE, Loesch DP, Shetty AC, Blackwell TW, Smith AV, Wong Q, Liu X, Conomos MP, Bobo DM, Aguet F, Albert C, Alonso A, Ardlie KG, Arking DE, Aslibekyan S, Auer PL, Barnard J, Barr RG, Barwick L, Becker LC, Beer RL, Benjamin EJ, Bielak LF, Blangero J, Boehnke M, Bowden DW, Brody JA, Burchard EG, Cade BE, Casella JF, Chalazan B, Chasman DI, Chen YI, Cho MH, Choi SH, Chung MK, Clish CB, Correa A, Curran JE, Custer B, Darbar D, Daya M, de Andrade M, DeMeo DL, Dutcher SK, Ellinor PT, Emery LS, Eng C, Fatkin D, Fingerlin T, Forer L, Fornage M, Franceschini N, Fuchsberger C, Fullerton SM, Germer S, Gladwin MT, Gottlieb DJ, Guo X, Hall ME, He J, Heard-Costa NL, Heckbert SR, Irvin MR, Johnsen JM, Johnson AD, Kaplan R, Kardia SLR, Kelly T, Kelly S, Kenny EE, Kiel DP, Klemmer R, Konkle BA, Kooperberg C, Köttgen A, Lange LA, Lasky-Su J, Levy D, Lin X, Lin KH, Liu C, Loos RJF, Garman L, Gerszten R, Lubitz SA, Lunetta KL, Mak ACY, Manichaikul A, Manning AK, Mathias RA, McManus DD, McGarvey ST, Meigs JB, Meyers DA, Mikulla JL, Minear MA, Mitchell BD, Mohanty S, Montasser ME, Montgomery C, Morrison AC, Murabito JM, Natale A, Natarajan P, Nelson SC, North KE, O'Connell JR, Palmer ND, Pankratz N, Peloso GM, Peyser PA, Pleiness J, Post WS, Psaty BM, Rao DC, Redline S, Reiner AP, Roden D, Rotter JI, Ruczinski I, Sarnowski C, Schoenherr S, Schwartz DA, Seo JS, Seshadri S, Sheehan VA, Sheu WH, Shoemaker MB, Smith NL, Smith JA, Sotoodehnia N, Stilp AM, Tang W, Taylor KD, Telen M, Thornton TA, Tracy RP, Van Den Berg DJ, Vasan RS, Viaud-Martinez KA, Vrieze S, Weeks DE, Weir BS, Weiss ST, Weng LC, Willer CJ, Zhang Y, Zhao X, Arnett DK, Ashley-Koch AE, Barnes KC, Boerwinkle E, Gabriel S, Gibbs R, Rice KM, Rich SS, Silverman EK, Qasba P, Gan W, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Papanicolaou GJ, Nickerson DA, Browning SR, Zody MC, Zöllner S, Wilson JG, Cupples LA, Laurie CC, Jaquish CE, Hernandez RD, O'Connor TD, Abecasis GR. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature 2021 Feb;590(7845):290-299. Epub 2021 Feb 10.

Studies:

Abstract

The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)<sup>1</sup>. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%.