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A draft human pangenome reference

Author

Listed:
  • Wen-Wei Liao

    (Yale University School of Medicine
    Yale University School of Medicine
    Washington University School of Medicine)

  • Mobin Asri

    (University of California)

  • Jana Ebler

    (Heinrich Heine University
    Heinrich Heine University)

  • Daniel Doerr

    (Heinrich Heine University
    Heinrich Heine University)

  • Marina Haukness

    (University of California)

  • Glenn Hickey

    (University of California)

  • Shuangjia Lu

    (Yale University School of Medicine
    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
    Harvard Medical School)

  • Justin Chu

    (Dana-Farber Cancer Institute)

  • Vincenza Colonna

    (National Research Council
    University of Tennessee Health Science Center)

  • Jordan M. Eizenga

    (University of California)

  • Xiaowen Feng

    (Dana-Farber Cancer Institute
    Harvard Medical School)

  • Christian Fischer

    (University of Tennessee Health Science Center)

  • Robert S. Fulton

    (Washington University School of Medicine
    Washington University School of Medicine)

  • Shilpa Garg

    (Technical University of Denmark)

  • Cristian Groza

    (McGill University)

  • Andrea Guarracino

    (University of Tennessee Health Science Center
    Human Technopole)

  • William T. Harvey

    (University of Washington School of Medicine)

  • Simon Heumos

    (University of Tübingen
    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
    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
    Heinrich Heine University
    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
    University of California
    University of California)

  • Carlos Garcia Giron

    (Wellcome Genome Campus, Hinxton)

  • Richard E. Green

    (University of California
    Dovetail Genomics)

  • 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
    European Molecular Biology Laboratory)

  • 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
    Heinrich Heine University)

  • Santiago Marco-Sola

    (Barcelona Supercomputing Center
    Universitat Autònoma de Barcelona)

  • Pierre Marijon

    (Heinrich Heine University
    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
    Mohammed Bin Rashid University of Medicine and Health Sciences)

  • 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
    Johns Hopkins University)

  • Guillaume Bourque

    (McGill University
    McGill University
    Kyoto 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
    Howard Hughes Medical Institute)

  • David Haussler

    (University of California
    Howard Hughes Medical Institute)

  • Ting Wang

    (Washington University School of Medicine
    Washington University School of Medicine)

  • Erich D. Jarvis

    (The Rockefeller University
    Howard Hughes Medical Institute
    The Rockefeller University)

  • Karen H. Miga

    (University of California)

  • Erik Garrison

    (University of Tennessee Health Science Center)

  • Tobias Marschall

    (Heinrich Heine University
    Heinrich Heine University)

  • Ira M. Hall

    (Yale University School of Medicine
    Yale University School of Medicine)

  • Heng Li

    (Dana-Farber Cancer Institute
    Harvard Medical School)

  • Benedict Paten

    (University of California)

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.

Suggested Citation

  • 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 , 2023. "A draft human pangenome reference," Nature, Nature, vol. 617(7960), pages 312-324, May.
    • Handle: RePEc:nat:nature:v:617:y:2023:i:7960:d:10.1038_s41586-023-05896-x
    DOI: 10.1038/s41586-023-05896-x
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    Cited by:

    1. Sean A. Misek & Aaron Fultineer & Jeremie Kalfon & Javad Noorbakhsh & Isabella Boyle & Priyanka Roy & Joshua Dempster & Lia Petronio & Katherine Huang & Alham Saadat & Thomas Green & Adam Brown & John, 2024. "Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Tobias T. Schmidt & Carly Tyer & Preeyesh Rughani & Candy Haggblom & Jeffrey R. Jones & Xiaoguang Dai & Kelly A. Frazer & Fred H. Gage & Sissel Juul & Scott Hickey & Jan Karlseder, 2024. "High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Tuomas Hämälä & Christopher Moore & Laura Cowan & Matthew Carlile & David Gopaulchan & Marie K. Brandrud & Siri Birkeland & Matthew Loose & Filip Kolář & Marcus A. Koch & Levi Yant, 2024. "Impact of whole-genome duplications on structural variant evolution in Cochlearia," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Wolfram Höps & Tobias Rausch & Michael Jendrusch & Jan O. Korbel & Fritz J. Sedlazeck, 2024. "Impact and characterization of serial structural variations across humans and great apes," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    5. Cristian Groza & Carl Schwendinger-Schreck & Warren A. Cheung & Emily G. Farrow & Isabelle Thiffault & Juniper Lake & William B. Rizzo & Gilad Evrony & Tom Curran & Guillaume Bourque & Tomi Pastinen, 2024. "Pangenome graphs improve the analysis of structural variants in rare genetic diseases," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Can Luo & Yichen Henry Liu & Xin Maizie Zhou, 2024. "VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    7. Cristian Groza & Xun Chen & Travis J. Wheeler & Guillaume Bourque & Clément Goubert, 2024. "A unified framework to analyze transposable element insertion polymorphisms using graph genomes," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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