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A draft human pangenome reference

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Item Type:Article
Title:A draft human pangenome reference
Creators Name:Liao, W.W. and Asri, M. and Ebler, J. and Doerr, D. and Haukness, M. and Hickey, G. and Lu, S. and Lucas, J.K. and Monlong, J. and Abel, H.J. and Buonaiuto, S. and Chang, X.H. and Cheng, H. and Chu, J. and Colonna, V. and Eizenga, J.M. and Feng, X. and Fischer, C. and Fulton, R.S. and Garg, S. and Groza, C. and Guarracino, A. and Harvey, W.T. and Heumos, S. and Howe, K. and Jain, M. and Lu, T.Y. and Markello, C. and Martin, F.J. and Mitchell, M.W. and Munson, K.M. and Mwaniki, M.N. and Novak, A.M. and Olsen, H.E. and Pesout, T. and Porubsky, D. and Prins, P. and Sibbesen, J.A. and Sirén, J. and Tomlinson, C. and Villani, F. and Vollger, M.R. and Antonacci-Fulton, L.L. and Baid, G. and Baker, C.A. and Belyaeva, A. and Billis, K. and Carroll, A. and Chang, P.C. and Cody, S. and Cook, D.E. and Cook-Deegan, R.M. and Cornejo, O.E. and Diekhans, M. and Ebert, P. and Fairley, S. and Fedrigo, O. and Felsenfeld, A.L. and Formenti, G. and Frankish, A. and Gao, Yan and Garrison, N.A. and Giron, C.G. and Green, R.E. and Haggerty, L. and Hoekzema, K. and Hourlier, T. and Ji, H.P. and Kenny, E.E. and Koenig, B.A. and Kolesnikov, A. and Korbel, J.O. and Kordosky, J. and Koren, S. and Lee, H.J. and Lewis, A.P. and Magalhães, H. and Marco-Sola, S. and Marijon, P. and McCartney, A. and McDaniel, J. and Mountcastle, J. and Nattestad, M. and Nurk, S. and Olson, N.D. and Popejoy, A.B. and Puiu, D. and Rautiainen, M. and Regier, A.A. and Rhie, A. and Sacco, S. and Sanders, A.D. and Schneider, V.A. and Schultz, B.I. and Shafin, K. and Smith, M.W. and Sofia, H.J. and Abou Tayoun, A.N. and Thibaud-Nissen, F. and Tricomi, F.F. and Wagner, J. and Walenz, B. and Wood, J.M.D. and Zimin, A.V. and Bourque, G. and Chaisson, M.J P and Flicek, Paul and Phillippy, A.M. and Zook, J.M. and Eichler, E.E. and Haussler, D. and Wang, T. and Jarvis, E.D. and Miga, K.H. and Garrison, E. and Marschall, T. and Hall, I.M. and Li, H. and Paten, B.
Abstract:Here 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 individuals. 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.
Keywords:Alleles, Cohort Studies, Diploidy, Genetic Variation, Human Genome, Genomics, Haplotypes, Reference Standards, DNA Sequence Analysis
Publisher:Nature Publishing Group
Page Range:312-324
Date:11 May 2023
Official Publication:https://doi.org/10.1038/s41586-023-05896-x
PubMed:View item in PubMed

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