A draft human pangenome reference

Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison (), Tobias Marschall (), Ira M. Hall (), Heng Li () and Benedict Paten ()
Additional contact information
Wen-Wei Liao: Yale University School of Medicine
Mobin Asri: University of California
Jana Ebler: Heinrich Heine University
Daniel Doerr: Heinrich Heine University
Marina Haukness: University of California
Glenn Hickey: University of California
Shuangjia Lu: Yale University School of Medicine
Julian K. Lucas: University of California
Jean Monlong: University of California
Haley J. Abel: Washington University School of Medicine
Silvia Buonaiuto: National Research Council
Xian H. Chang: University of California
Haoyu Cheng: Dana-Farber Cancer Institute
Justin Chu: Dana-Farber Cancer Institute
Vincenza Colonna: National Research Council
Jordan M. Eizenga: University of California
Xiaowen Feng: Dana-Farber Cancer Institute
Christian Fischer: University of Tennessee Health Science Center
Robert S. Fulton: Washington University School of Medicine
Shilpa Garg: Technical University of Denmark
Cristian Groza: McGill University
Andrea Guarracino: University of Tennessee Health Science Center
William T. Harvey: University of Washington School of Medicine
Simon Heumos: University of Tübingen
Kerstin Howe: Wellcome Sanger Institute, Hinxton
Miten Jain: Northeastern University
Tsung-Yu Lu: University of Southern California
Charles Markello: University of California
Fergal J. Martin: Wellcome Genome Campus, Hinxton
Matthew W. Mitchell: Coriell Institute for Medical Research
Katherine M. Munson: University of Washington School of Medicine
Moses Njagi Mwaniki: University of Pisa
Adam M. Novak: University of California
Hugh E. Olsen: University of California
Trevor Pesout: University of California
David Porubsky: University of Washington School of Medicine
Pjotr Prins: University of Tennessee Health Science Center
Jonas A. Sibbesen: University of Copenhagen
Jouni Sirén: University of California
Chad Tomlinson: Washington University School of Medicine
Flavia Villani: University of Tennessee Health Science Center
Mitchell R. Vollger: University of Washington School of Medicine
Lucinda L. Antonacci-Fulton: Washington University School of Medicine
Gunjan Baid: Google
Carl A. Baker: University of Washington School of Medicine
Anastasiya Belyaeva: Google
Konstantinos Billis: Wellcome Genome Campus, Hinxton
Andrew Carroll: Google
Pi-Chuan Chang: Google
Sarah Cody: Washington University School of Medicine
Daniel E. Cook: Google
Robert M. Cook-Deegan: Barrett and O’Connor Washington Center, Arizona State University
Omar E. Cornejo: University of California
Mark Diekhans: University of California
Peter Ebert: Heinrich Heine University
Susan Fairley: Wellcome Genome Campus, Hinxton
Olivier Fedrigo: The Rockefeller University
Adam L. Felsenfeld: National Institutes of Health (NIH)–National Human Genome Research Institute
Giulio Formenti: The Rockefeller University
Adam Frankish: Wellcome Genome Campus, Hinxton
Yan Gao: The Children’s Hospital of Philadelphia
Nanibaa’ A. Garrison: University of California
Carlos Garcia Giron: Wellcome Genome Campus, Hinxton
Richard E. Green: University of California
Leanne Haggerty: Wellcome Genome Campus, Hinxton
Kendra Hoekzema: University of Washington School of Medicine
Thibaut Hourlier: Wellcome Genome Campus, Hinxton
Hanlee P. Ji: Stanford University School of Medicine
Eimear E. Kenny: Icahn School of Medicine at Mount Sinai
Barbara A. Koenig: University of California
Alexey Kolesnikov: Google
Jan O. Korbel: Wellcome Genome Campus, Hinxton
Jennifer Kordosky: University of Washington School of Medicine
Sergey Koren: National Human Genome Research Institute, National Institutes of Health
HoJoon Lee: Stanford University School of Medicine
Alexandra P. Lewis: University of Washington School of Medicine
Hugo Magalhães: Heinrich Heine University
Santiago Marco-Sola: Barcelona Supercomputing Center
Pierre Marijon: Heinrich Heine University
Ann McCartney: National Human Genome Research Institute, National Institutes of Health
Jennifer McDaniel: National Institute of Standards and Technology
Jacquelyn Mountcastle: The Rockefeller University
Maria Nattestad: Google
Sergey Nurk: National Human Genome Research Institute, National Institutes of Health
Nathan D. Olson: National Institute of Standards and Technology
Alice B. Popejoy: University of California
Daniela Puiu: Johns Hopkins University
Mikko Rautiainen: National Human Genome Research Institute, National Institutes of Health
Allison A. Regier: Washington University School of Medicine
Arang Rhie: National Human Genome Research Institute, National Institutes of Health
Samuel Sacco: University of California
Ashley D. Sanders: Max Delbrück Center for Molecular Medicine in the Helmholtz Association
Valerie A. Schneider: National Library of Medicine, National Institutes of Health
Baergen I. Schultz: National Institutes of Health (NIH)–National Human Genome Research Institute
Kishwar Shafin: Google
Michael W. Smith: National Institutes of Health (NIH)–National Human Genome Research Institute
Heidi J. Sofia: National Institutes of Health (NIH)–National Human Genome Research Institute
Ahmad N. Abou Tayoun: Al Jalila Children’s Specialty Hospital
Françoise Thibaud-Nissen: National Library of Medicine, National Institutes of Health
Francesca Floriana Tricomi: Wellcome Genome Campus, Hinxton
Justin Wagner: National Institute of Standards and Technology
Brian Walenz: National Human Genome Research Institute, National Institutes of Health
Jonathan M. D. Wood: Wellcome Sanger Institute, Hinxton
Aleksey V. Zimin: Johns Hopkins University
Guillaume Bourque: McGill University
Mark J. P. Chaisson: University of Southern California
Paul Flicek: Wellcome Genome Campus, Hinxton
Adam M. Phillippy: National Human Genome Research Institute, National Institutes of Health
Justin M. Zook: National Institute of Standards and Technology
Evan E. Eichler: University of Washington School of Medicine
David Haussler: University of California
Ting Wang: Washington University School of Medicine
Erich D. Jarvis: The Rockefeller University
Karen H. Miga: University of California
Erik Garrison: University of Tennessee Health Science Center
Tobias Marschall: Heinrich Heine University
Ira M. Hall: Yale University School of Medicine
Heng Li: Dana-Farber Cancer Institute
Benedict Paten: University of California

Nature, 2023, vol. 617, issue 7960, 312-324

Abstract: 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 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.

Date: 2023
References: Add references at CitEc
Citations: View citations in EconPapers (10)

Downloads: (external link)
https://www.nature.com/articles/s41586-023-05896-x Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:617:y:2023:i:7960:d:10.1038_s41586-023-05896-x

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-023-05896-x

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().