ArticlebioRxiv : the preprint server for biology2026
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.
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Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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215 authors.
Julian K LucasUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0001-9163-2756
Prajna HebbarUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.ORCID 0009-0008-9817-5330
Wen-Wei LiaoCenter for Genomic Health, Yale University School of Medicine, New Haven, CT 06510, USA.ORCID 0000-0001-8183-213X
Juan F Macias-VelascoMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.ORCID 0000-0003-2827-4647
Adam M NovakUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0001-5828-047X
Mobin AsriUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0002-7194-5138
Jennifer R BalaccoThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Andrew P BlairUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0002-3196-6233
Davide BologniniHuman Technopole, Milan, Italy.ORCID 0000-0002-8735-8093
Jana EblerCenter for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, NRW, DE.ORCID 0000-0002-0382-3702
Joshua M V GardnerUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Margarita GeletaDepartment of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA.ORCID 0000-0001-5823-9776
Cristian GrozaMontreal Heart Institute, Montréal, QC, Canada.
Andrea GuarracinoBioinnovation and Genome Sciences, The Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA.
Peter HeringerCenter for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, NRW, DE.
Glenn HickeyUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Sergey KorenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Shuangjia LuCenter for Genomic Health, Yale University School of Medicine, New Haven, CT 06510, USA.ORCID 0000-0001-8571-6902
Maximillian G MarinDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Christopher MarkovicMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Mira MastorasUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Capucine MayoudISEM, Univ Montpellier, CNRS, IRD, Montpellier, FR.
Brandy McNultyUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Julian M MenendezUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Anna MinkinaDivision of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.
Saswat K MohantyDepartment of Biology, Penn State University, University Park, PA 16802, USA.
Jean MonlongIRSD - Digestive Health Research Institute, University of Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, FR.ORCID 0000-0002-9737-5516
Katherine M MunsonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Keisuke K OshimaDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
David PorubskyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
T Rhyker Ranallo-BenavidezBioinnovation and Genome Sciences, The Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA.
Alessandro RaveaneHuman Technopole, Milan, Italy.
William E SeligmannDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA.
Ruhollah ShemiraniInstitute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Yoshihiko SuzukiDepartment of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.
Jack A S TierneyEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Ivo ViolichUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
DongAhn YooDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Xiaoyu ZhuoDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.ORCID 0000-0002-1400-5609
Derek AlbrachtMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Ivan A AlexandrovDepartment of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Jamie AllenEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Alawi A Alsheikh-AliCenter for Applied and Translational Genomics (CATG), Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
Casey AndrewsDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Dmitry AntipovGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Lucinda Antonacci-FultonMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Alexander ArguelloDivision of Genome Sciences, National Human Genome Research Institute, Bethesda, MD 20871 USA.
Marcelo AyllonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Edward A BelterMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Halle D BenderUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Katherine E BoniniInstitute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Silvia BuonaiutoDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
Shuo CaoDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
Ann M Mc CartneyInstitute of Clinical and Translational Sciences, University of California, Irvine, CA 92697, USA.ORCID 0000-0003-3191-3200
Pi-Chuan ChangGoogle LLC, Mountain View, CA 94043, USA.
Xian ChangUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Jitender CheemaEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Claudio CiofiDepartment of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy.
Hiram ClawsonUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Sarah CodyMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Vincenza ColonnaDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
Holland C ConwellDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA.
Mark DiekhansUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Maria Angela DiromaDepartment of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy.
Zheng DongDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Danilo DubocaninDepartment of Genetics, Stanford University, Palo Alto, CA 94304 USA.
Jordan M EizengaUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Parsa EskandarUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Eddie FerroDepartment of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.ORCID 0009-0002-9738-0216
Sarah M FordDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA.ORCID 0009-0002-8855-3576
Willard W FordDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.
Adam FrankishEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Mallory A FreebergEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Qichen FuDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.ORCID 0000-0003-3291-3157
Shenghan GaoDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Yan GaoDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Gage H GarciaDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Obed A GarciaDepartment of Anthropology, University of Kansas, Lawrence, KS 66045, USA.
John E GarzaMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Mohammadmersad GhorbaniMedical and Population Genomics Lab, Sidra Medicine, Doha, Qatar.
Tina A Graves-LindsayMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Bida GuQuantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
Leanne HaggertyEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Nancy F HansenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Yue HaoBioinnovation and Genome Sciences, The Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA.
Todd L HillakerUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
S Nakib HossainEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Neng HuangDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Sarah E HuntEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Toby HuntEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Nafiseh JafarzadehUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Nivesh JainThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Maryam JehangirBioinnovation and Genome Sciences, The Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA.
Juan JiangDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Juhyun KimGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Bonhwang KooThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Milinn KremitzkiMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Daofeng LiDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.ORCID 0000-0001-7492-3703
Ronghan LiDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Jiadong LinDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Tianjie LiuDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Ryan Lorig-RoachUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Hailey LoucksUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Jane E LovelandEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Jianguo LuSun Yat-sen University, Guangzhou, China.
Walfred MaQuantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.ORCID 0000-0001-8650-5541
Franco L MarsicoDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
Jack A MedicoThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.ORCID 0000-0003-1855-0855
Younes MokrabMedical and Population Genomics Lab, Sidra Medicine, Doha, Qatar.
Shabir MoosaMedical and Population Genomics Lab, Sidra Medicine, Doha, Qatar.
Avelina Moreno-OchandoMATCH biosystems, S.L., Elche, Spain.
Shinichi MorishitaDepartment of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.
Jonathan M MudgeEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Njagi MwanikiDepartment of Computer Science, University of Pisa, Pisa, Italy.
Nasna NassirCenter for Applied and Translational Genomics (CATG), Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
Chiara NataliDepartment of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy.
Shloka NegiUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0002-9839-4030
Lingbin NiDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Faith OkamotoUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Chie OwaDepartment of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.
Sadye PaezThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Clelia PeanoHuman Technopole, Milan, Italy.
Brandon D PickettGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0001-8235-4440
Laura PignataDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
Timofey ProdanovCenter for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, NRW, DE.ORCID 0000-0001-7469-6651
Anandi RadhakrishnanUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Brian J RaneyUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Andreas RechtsteinerDepartment of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
Luyao RenDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Fedor RyabovThe Center for Bio- and Medical Technologies, Moscow, RUS.
Samuel SaccoDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA.
Farnaz SalehiDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
Aarushi SehgalDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.
Mahsa ShabaniUniversity of Amsterdam, Amsterdam, Netherlands.
Shadi ShahatitISEM, Univ Montpellier, CNRS, IRD, Montpellier, FR.
Vikram S ShivakumarDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0002-1424-3711
Swati SinhaEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Linnéa SmedsDepartment of Biology, Penn State University, University Park, PA 16802, USA.
Steven J SolarGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Marco SollittoThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Nicole SoranzoHuman Technopole, Milan, Italy.
Marie-Marthe SunerEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Arda SöylevCenter for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, NRW, DE.
Chad TomlinsonMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Francesca Floriana TricomiEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Matteo Tommaso UngaroDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0002-1107-3307
Rahul VarkiDepartment of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.
Brian P WalenzGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Charles WangCenter for Genomics, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA.
Lisa E WangInstitute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Aaron M WengerPacBio, Menlo Park, CA 94025, USA.
Conor V WhelanThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Zilan XinDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Zheng XuDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Wenjin ZhangDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Ying ZhouDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Giulia ZuninoHuman Technopole, Milan, Italy.
Nicolas AltemoseDepartment of Genetics, Stanford University, Palo Alto, CA 94304 USA.ORCID 0000-0002-7231-6026
Floris P BarthelBioinnovation and Genome Sciences, The Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA.
Christina BoucherDepartment of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.ORCID 0000-0001-9509-9725
Guillaume BourqueCanadian Center for Computational Genomics, McGill University, Montréal, QC H3A 0G1, Canada.ORCID 0000-0002-3933-9656
Andrew CarrollGoogle LLC, Mountain View, CA 94043, USA.ORCID 0000-0002-4824-6689
Monika CechovaUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Mark J P ChaissonQuantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
Haoyu ChengDepartment of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT 06510, USA.
Robert Cook-DeeganArizona State University, Consortium for Science, Policy & Outcomes, Washington, DC 20006, USA.
Daniel DoerrCenter for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, NRW, DE.
Richard DurbinWellcome Sanger Institute, Genome Campus, Hinxton, CB10 1RQ, UK.
Anna-Sophie Fiston-LavierISEM, Univ Montpellier, CNRS, IRD, Montpellier, FR.ORCID 0000-0002-7306-6532
Giulio FormentiThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.ORCID 0000-0002-7554-5991
Stephanie M FullertonDepartment of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA 98195, USA.
Robert S FultonMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Shilpa GargSchool of Health Sciences, University of Manchester, Manchester M13 9PL, UK.
Nanibaa' A GarrisonTraditional, ancestral and unceded territory of the Gabrielino/Tongva peoples, Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Richard E GreenDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0003-0516-5827
Carol W GreiderDepartment of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
Melissa GymrekDepartment of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.ORCID 0000-0002-6086-3903
Maximilian HaeusslerUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Mohammad Amiruddin HashmiCenter for Applied and Translational Genomics (CATG), Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
David HausslerUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Alexander G IoannidisUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.
Charles H LangleyDepartment of Evolution and Ecology and the Center for Population Biology, University of California, One Shields, Davis, CA 95616, USA.
Ben LangmeadDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0003-2437-1976
Heather A LawsonDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Glennis A LogsdonDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Kateryna D MakovaDepartment of Biology and Center for Medical Genomics, Penn State University, University Park, PA 16802, USA.
Fergal J MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Matthew W MitchellThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Pilar N OssorioLaw School, University of Wisconsin-Madison, Madison, WI 53706, USA.
Nadia PisantiDepartment of Computer Science, University of Pisa, Pisa, Italy.
Pjotr PrinsDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
Mikko RautiainenInstitute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.ORCID 0000-0003-2971-267X
Arang RhieGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0002-9809-8127
Michael C SchatzDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Laura B ScheinfeldtCoriell Institute for Medical Research, Camden, NJ 08103, USA.ORCID 0000-0001-6529-6701
Kishwar ShafinGoogle LLC, Mountain View, CA 94043, USA.
Jouni SirénUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0001-5828-4139
Andrew B StergachisDivision of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0002-1299-3674
Ahmad Abou TayounCenter for Genomic Discovery, Mohammed Bin Rashid University, Dubai Health, UAE.
Mohammed UddinCenter for Applied and Translational Genomics (CATG), Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
Flavia VillaniDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
Mitchell R VollgerDepartment of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.ORCID 0000-0002-8651-1615
Kai YeThe first affiliated hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.ORCID 0000-0002-2851-6741
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0002-8246-4014
Erik GarrisonDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.ORCID 0000-0003-3821-631X
Ira M HallCenter for Genomic Health, Yale University School of Medicine, New Haven, CT 06510, USA.ORCID 0000-0003-4442-6655
Erich D JarvisThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.ORCID 0000-0001-8931-5049
Eimear E KennyInstitute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.ORCID 0000-0001-9198-759X
Heng LiDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA.ORCID 0000-0003-4874-2874
Jonathan LoTempioInstitute of Clinical and Translational Sciences, University of California, Irvine, CA 92697, USA.ORCID 0000-0001-6897-5419
Tobias MarschallCenter for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, NRW, DE.ORCID 0000-0002-9376-1030
Karen H MigaUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0001-9709-4565
Adam M PhillippyGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0003-2983-8934
Ting WangMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.ORCID 0000-0002-6800-242X
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0001-8863-3539
Funding
The AnVIL Data Ecosystem DACReS SupplementU24HG010262 · NHGRI · BROAD INSTITUTE, INC. · PI Robert J Carroll, Jonathan Lawson · 2018 to 2026
$40.5MThe WashU-UCSC-EBI Human Genome Reference Center."U41HG010972 · NHGRI · WASHINGTON UNIVERSITY · PI Ira M Hall, Heng Li · 2019 to 2026
$24.9MImplementing the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)U24HG010263 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI Enis Afgan, VINCENT JAMES CAREY · 2018 to 2026
$23.8MGENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MThe UCSC Genome BrowserU24HG002371 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Maximilian Haeussler · 2022 to 2026
$17.6MIdentifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human GenomesU24HG007497 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Evan Eichler, Jan Oliver Korbel · 2019 to 2026
$17.2MGENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1MCenter for Human Genome Reference DiversityUM1HG010971 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Robert Mullan Cook-Deegan, Evan Eichler · 2024 to 2026
$8.6MData Resource and Administrative Coordination Center for the Scalable and Systematic Neurobiology of Psychiatric and Neurodevelopmental Disorder Risk Genes ConsortiumU24MH132628 · NIMH · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI DAVID H HAUSSLER, Tomasz Nowakowski · 2023 to 2026
$7.9MDockstore: The Community Platform for Reproducible Biomedical Workflows and ApplicationsU24HG011853 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Jonathan Lawson, Benedict Paten · 2021 to 2026
$5.7MNHGRI Sample Repository for Human Genetic ResearchU24HG008736 · NHGRI · CORIELL INSTITUTE FOR MEDICAL RESEARCH · PI LAURA SCHEINFELDT · 2021 to 2026
$5.4MTelomere-to-telomere assemblies of human genomesR01HG011274 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Karen Hayden Miga · 2020 to 2026
$4.5MNCI NIH HHS U24 CA258407NCI NIH HHS U24 CA294203NHGRI NIH HHS R00 HG012798NHGRI NIH HHS R01 HG010040NHGRI NIH HHS R01 HG011274NHGRI NIH HHS R01 HG011392NHGRI NIH HHS R01 HG011649NHGRI NIH HHS R01 HG013017NHGRI NIH HHS R01 HG013618NHGRI NIH HHS R01 HG014175NHGRI NIH HHS R01 HG014490NHGRI NIH HHS R01 HG014872NHGRI NIH HHS U01 HG010961NHGRI NIH HHS U01 HG013744NHGRI NIH HHS U01 HG013748NHGRI NIH HHS U01 HG013755NHGRI NIH HHS U01 HG013760NHGRI NIH HHS U01 HG014892NHGRI NIH HHS U24 HG002371NHGRI NIH HHS U24 HG007234NHGRI NIH HHS U24 HG007497NHGRI NIH HHS U24 HG008736NHGRI NIH HHS U24 HG010262NHGRI NIH HHS U24 HG010263NHGRI NIH HHS U24 HG011853NHGRI NIH HHS U41 HG007234NHGRI NIH HHS U41 HG010972NHGRI NIH HHS UM1 HG010971NIDA NIH HHS U01 DA057530NIDA NIH HHS U01 DA058278NIGMS NIH HHS R00 GM147352NIGMS NIH HHS R00 GM155552NIGMS NIH HHS R01 GM152471NIGMS NIH HHS R35 GM151945NIGMS NIH HHS T32 GM141828NIH HHS DP5 OD029630NIH HHS OT2 OD026682NIMH NIH HHS U24 MH132628NINDS NIH HHS U24 NS146314Wellcome Trust
Abstract
A pangenome reference overcomes the inherent limitation of any individual reference genome by integrating the variation present in a population. We present the Human Pangenome Reference Consortium's (HPRC) Release 2 (HPRC2), an openly available, second phase pangenome that is an approximately fivefold expansion in genome number over HPRC Release 1 (HPRC1) and measurable improvement in genome completeness, contiguity, and accuracy. Selecting samples with a principled algorithm prioritising common variant coverage, HPRC2 contributes 460 haplotypes that together capture over 99% of common variation observed in the All of Us Research Program v8 cohort. Combining high-coverage long and ultra-long reads with modern assemblers and polishers, we produce thousands of telomere-to-telomere (T2T) chromosomes, and relative to HPRC1 halve the number of structurally unreliable regions as well as individual base errors per haplotype. We complement the assemblies with whole genome multiple alignments and gene annotations, and derive formal pangenome coordinate systems for addressing off-reference variation, demonstrating that individual human genomes contain more than one hundred thousand variants not succinctly described with respect to existing reference genomes. We also present the first matched long-read backed pantranscriptome and panepigenome at this scale, provide continuous local-ancestry estimates spanning every genome, and outline a host of new tools and applications that leverage the pangenome resource for improved genomics analysis.
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