A Draft Human Pangenome Reference

Author:

Liao Wen-WeiORCID,Asri Mobin,Ebler Jana,Doerr Daniel,Haukness Marina,Hickey GlennORCID,Lu ShuangjiaORCID,Lucas Julian K.,Monlong JeanORCID,Abel Haley J.,Buonaiuto Silvia,Chang Xian H.ORCID,Cheng Haoyu,Chu Justin,Colonna Vincenza,Eizenga Jordan M.ORCID,Feng Xiaowen,Fischer Christian,Fulton Robert S.,Garg Shilpa,Groza Cristian,Guarracino Andrea,Harvey William T,Heumos Simon,Howe Kerstin,Jain Miten,Lu Tsung-Yu,Markello CharlesORCID,Martin Fergal J.ORCID,Mitchell Matthew W.,Munson Katherine M.ORCID,Mwaniki Moses Njagi,Novak Adam M.ORCID,Olsen Hugh E.ORCID,Pesout TrevorORCID,Porubsky DavidORCID,Prins PjotrORCID,Sibbesen Jonas A.ORCID,Tomlinson Chad,Villani FlaviaORCID,Vollger Mitchell R.ORCID,Bourque GuillaumeORCID,Chaisson Mark JPORCID,Flicek PaulORCID,Phillippy Adam M.,Zook Justin M.,Eichler Evan E.ORCID,Haussler DavidORCID,Jarvis Erich D.,Miga Karen H.ORCID,Wang Ting,Garrison ErikORCID,Marschall Tobias,Hall IraORCID,Li HengORCID,Paten BenedictORCID,

Abstract

AbstractThe Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence and are more than 99% accurate at the structural and base-pair levels. Based on alignments of the assemblies, we generated a draft pangenome that captures known variants and haplotypes, reveals novel alleles at structurally complex loci, and adds 119 million base pairs of euchromatic polymorphic sequence and 1,529 gene duplications relative to the existing reference, GRCh38. Roughly 90 million of the additional base pairs derive from structural variation. Using our draft pangenome to analyze short-read data reduces errors when discovering small variants by 34% and boosts the detected structural variants per haplotype by 104% compared to GRCh38-based workflows, and by 34% compared to using previous diversity sets of genome assemblies.

Publisher

Cold Spring Harbor Laboratory

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