ArticlebioRxiv : the preprint server for biology2024
Complex genetic variation in nearly complete human genomes.
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Article in bioRxiv : the preprint server for biology, 2024. 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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68 authors.
Glennis A LogsdonPerelman School of Medicine, University of Pennsylvania, Department of Genetics, Epigenetics Institute, Philadelphia, PA, USA.ORCID 0000-0003-2396-0656
Peter EbertCore Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0001-7441-532X
Peter A AudanoThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0002-5187-0415
Mark LoftusClemson University, Department of Genetics & Biochemistry, Clemson, SC, USA.ORCID 0000-0002-6279-6855
David PorubskyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0001-8414-8966
Jana EblerInstitute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0002-0382-3702
Feyza YilmazThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0001-8795-5800
Pille HallastThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0002-0588-3987
Timofey ProdanovInstitute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0001-7469-6651
DongAhn YooDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0003-0033-3721
Carolyn A PaisieThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0003-4306-4154
William T HarveyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0003-0646-7528
Xuefang ZhaoProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Gianni V MartinoClemson University, Department of Genetics & Biochemistry, Clemson, SC, USA.ORCID 0009-0005-4143-7465
Mir HenglinInstitute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0003-3604-4868
Katherine M MunsonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0001-8413-6498
Keon RabbaniDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.ORCID 0009-0004-1448-2167
Chen-Shan ChinFoundation of Biological Data Sciences, Belmont, CA, USA.ORCID 0000-0003-4394-2455
Bida GuDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.ORCID 0000-0001-8575-997X
Hufsah AshrafInstitute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0001-7760-0627
Olanrewaju Austine-OrimoloyeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.ORCID 0000-0002-4390-1437
Parithi BalachandranThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0003-3256-1403
Marc Jan BonderDepartment of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Oncode Institute, Utrecht, The Netherlands.ORCID 0000-0002-8431-3180
Haoyu ChengDepartment of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, USA.ORCID 0000-0002-9209-5793
Zechen ChongDepartment of Biomedical Informatics and Data Science, Heersink School of Medicine, University of Alabama, Birmingham, AL, USA.ORCID 0000-0001-5750-1808
Jonathan CrabtreeInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID 0000-0002-7286-5690
Mark GersteinDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID 0000-0002-9746-3719
Lisbeth A GuethleinDepartment of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA.ORCID 0000-0002-1301-8301
Patrick HasenfeldEuropean Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
Glenn HickeyUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID 0000-0002-2280-9404
Kendra HoekzemaDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0002-8058-0177
Sarah E HuntEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.ORCID 0000-0002-8350-1235
Matthew JensenDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID 0000-0002-5153-8543
Yunzhe JiangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID 0000-0001-8768-0050
Sergey KorenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-1472-8962
Youngjun KwonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Chong LiTemple University, Department of Computer and Information Sciences, College of Science and Technology, Philadelphia, PA, USA.ORCID 0000-0003-1949-4074
Heng LiDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0003-4874-2874
Jiaqi LiDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID 0000-0002-6796-335X
Paul J NormanDepartment of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.ORCID 0000-0001-8370-7703
Keisuke K OshimaPerelman School of Medicine, University of Pennsylvania, Department of Genetics, Epigenetics Institute, Philadelphia, PA, USA.ORCID 0009-0002-2229-8998
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID 0000-0001-8863-3539
Adam M PhillippyGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0003-2983-8934
Nicholas R PollockDepartment of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.ORCID 0000-0003-0114-528X
Tobias RauschEuropean Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.ORCID 0000-0001-5773-5620
Mikko RautiainenInstitute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.ORCID 0000-0003-2971-267X
Stephan ScholzInstitute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.ORCID 0009-0000-0268-1979
Yuwei SongDepartment of Biomedical Informatics and Data Science, Heersink School of Medicine, University of Alabama, Birmingham, AL, USA.ORCID 0000-0003-2537-4343
Arda SöylevInstitute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0003-2198-1920
Arvis SulovariDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Likhitha SurapaneniEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.ORCID 0000-0002-0575-7673
Vasiliki TsapalouEuropean Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.ORCID 0009-0002-3588-7003
Weichen ZhouDepartment of Computational Medicine & Bioinformatics, University of Michigan, MI, USA.ORCID 0000-0003-4755-1072
Ying ZhouDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-8107-3927
Qihui ZhuThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0003-2401-8443
Michael C ZodyNew York Genome Center, New York, NY, USA.
Ryan E MillsDepartment of Computational Medicine & Bioinformatics, University of Michigan, MI, USA.ORCID 0000-0003-3425-6998
Scott E DevineInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID 0000-0001-7629-8331
Xinghua ShiTemple University, Department of Computer and Information Sciences, College of Science and Technology, Philadelphia, PA, USA.ORCID 0000-0003-4662-3177
Mike E TalkowskiProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Mark J P ChaissonDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.ORCID 0000-0001-5395-1457
Alexander T DiltheyCenter for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0002-6394-4581
Miriam K KonkelClemson University, Department of Genetics & Biochemistry, Clemson, SC, USA.ORCID 0000-0002-3190-1667
Jan O KorbelEuropean Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.ORCID 0000-0002-2798-3794
Charles LeeThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0001-7317-6662
Christine R BeckThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0001-7821-8489
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0002-8246-4014
Tobias MarschallInstitute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.ORCID 0000-0002-9376-1030
Funding
Shared Resource ManagementP30CA034196 · NCI · JACKSON LABORATORY · PI Paul Robson · 1985 to 2026
$61.9MIdentifying 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
$17.2MInsights Into Immune-Related Diseases Born from Population GenomicsU01AI090905 · NIAID · UNIVERSITY OF COLORADO DENVER · PI Paul John Norman · 2010 to 2026
$10.9MStatistical Methods for Gene Regulatory Analysis From Single Cell Genomics DataP20GM139769 · NIGMS · CLEMSON UNIVERSITY · PI KONKEL, MIRIAM KRISTINE · 2021 to 2025
$10.8MRepetitive sequences drive genome variation and plasticityR35GM133600 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Christine R Beck · 2019 to 2026
$3.0MStructural variation analysis with and without a reference genomeR35GM138212 · NIGMS · UNIVERSITY OF VIRGINIA · PI Zechen Chong · 2020 to 2026
$2.6MDetection and genotyping complex human genetic variation using single-molecule sequencingR01HG011649 · NHGRI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI Mark Chaisson · 2021 to 2026
$2.5MMobile element mutagenesis as a driver of human cancersR01CA261934 · NCI · UNIVERSITY OF MARYLAND BALTIMORE · PI Scott E Devine · 2022 to 2026
$1.7MRobust and cost-effective computational methods for haplotype-resolved genome assembliesR00HG012798 · NHGRI · YALE UNIVERSITY · PI Haoyu Cheng · 2024 to 2026
$747kHuman centromere variation and functionR00GM147352 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI Glennis Amelia Logsdon · 2024 to 2026
$747kL1 element mutagenesis as a driver of epithelial cancers in African AmericansR21CA259309 · NCI · UNIVERSITY OF MARYLAND BALTIMORE · PI DEVINE, SCOTT E · 2022 to 2023
$394kRobust and cost-effective computational methods for haplotype-resolved genome assembliesK99HG012798 · NHGRI · DANA-FARBER CANCER INST · PI CHENG, HAOYU · 2023 to 2024
$165kNCI NIH HHS P30 CA034196NCI NIH HHS R01 CA261934NCI NIH HHS R21 CA259309NHGRI NIH HHS K99 HG012798NHGRI NIH HHS R00 HG012798NHGRI NIH HHS R01 HG011649NHGRI NIH HHS U24 HG007497NIAID NIH HHS U01 AI090905NIGMS NIH HHS K99 GM147352NIGMS NIH HHS P20 GM139769NIGMS NIH HHS R00 GM147352NIGMS NIH HHS R35 GM133600NIGMS NIH HHS R35 GM138212
Abstract
Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (130 Mbp median continuity), closing 92% of all previous assembly gaps
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.