A draft human pangenome reference
Author:
Liao Wen-WeiORCID, Asri Mobin, Ebler Jana, Doerr DanielORCID, Haukness MarinaORCID, Hickey Glenn, Lu ShuangjiaORCID, Lucas Julian K., Monlong Jean, Abel Haley J., Buonaiuto Silvia, Chang Xian H., Cheng Haoyu, Chu Justin, Colonna VincenzaORCID, Eizenga Jordan M., Feng Xiaowen, Fischer Christian, Fulton Robert S., Garg Shilpa, Groza Cristian, Guarracino AndreaORCID, Harvey William T., Heumos Simon, Howe KerstinORCID, Jain MitenORCID, Lu Tsung-YuORCID, Markello Charles, Martin Fergal J.ORCID, Mitchell Matthew W.ORCID, Munson Katherine M.ORCID, Mwaniki Moses Njagi, Novak Adam M.ORCID, Olsen Hugh E., Pesout Trevor, Porubsky DavidORCID, Prins PjotrORCID, Sibbesen Jonas A., Sirén JouniORCID, Tomlinson ChadORCID, Villani FlaviaORCID, Vollger Mitchell R.ORCID, Antonacci-Fulton Lucinda L., Baid Gunjan, Baker Carl A., Belyaeva Anastasiya, Billis KonstantinosORCID, Carroll Andrew, Chang Pi-Chuan, Cody Sarah, Cook Daniel E., Cook-Deegan Robert M., Cornejo Omar E.ORCID, Diekhans MarkORCID, Ebert PeterORCID, Fairley Susan, Fedrigo OlivierORCID, Felsenfeld Adam L., Formenti GiulioORCID, Frankish Adam, Gao Yan, Garrison Nanibaa’ A.ORCID, Giron Carlos Garcia, Green Richard E.ORCID, Haggerty Leanne, Hoekzema Kendra, Hourlier ThibautORCID, Ji Hanlee P.ORCID, Kenny Eimear E., Koenig Barbara A., Kolesnikov Alexey, Korbel Jan O.ORCID, Kordosky Jennifer, Koren SergeyORCID, Lee HoJoonORCID, Lewis Alexandra P., Magalhães HugoORCID, Marco-Sola SantiagoORCID, Marijon Pierre, McCartney Ann, McDaniel JenniferORCID, Mountcastle JacquelynORCID, Nattestad Maria, Nurk Sergey, Olson Nathan D.ORCID, Popejoy Alice B., Puiu Daniela, Rautiainen Mikko, Regier Allison A., Rhie ArangORCID, Sacco Samuel, Sanders Ashley D., Schneider Valerie A., Schultz Baergen I., Shafin KishwarORCID, Smith Michael W., Sofia Heidi J., Abou Tayoun Ahmad N., Thibaud-Nissen FrançoiseORCID, Tricomi Francesca FlorianaORCID, Wagner Justin, Walenz BrianORCID, Wood Jonathan M. D.ORCID, Zimin Aleksey V., Bourque GuillaumeORCID, Chaisson Mark J. P.ORCID, Flicek PaulORCID, Phillippy Adam M.ORCID, Zook Justin M.ORCID, Eichler Evan E.ORCID, Haussler DavidORCID, Wang TingORCID, Jarvis Erich D.ORCID, Miga Karen H.ORCID, Garrison ErikORCID, Marschall TobiasORCID, Hall Ira M.ORCID, Li HengORCID, Paten BenedictORCID
Abstract
AbstractHere the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.
Publisher
Springer Science and Business Media LLC
Subject
Multidisciplinary
Cited by
157 articles.
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