The Human Pangenome Project: a global resource to map genomic diversity
Open accessAbstract
The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation. A high-quality reference with global representation of common variants, including single-nucleotide variants, structural variants and functional elements, is needed. The Human Pangenome Reference Consortium aims to create a more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity. Here we leverage innovations in technology, study design and global partnerships with the goal of constructing the highest-possible quality human pangenome reference. Our goal is to improve data representation and streamline analyses to enable routine assembly of complete diploid genomes. With attention to ethical frameworks, the human pangenome reference will contain a more accurate and diverse representation of global genomic variation, improve gene-disease association studies across populations, expand the scope of genomics research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine.
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The authors sequenced and assembled a set of diverse individual genomes and present a draft human pangenome, the first release from HPRC.
“Here we sequence and assemble a set of diverse individual genomes and present a draft human pangenome, the first release from the Human Pangenome Reference Consortium (HPRC)15.”
From A draft human pangenome reference. (2023) · cites this paper as [15]
In “Initial Data Generation and Release” (page not available), the paper reports assembling 47 genomes and releasing sequencing data from 47 participants as the first HPRC data release. It does not say that this release presented a draft human pangenome; “Goals and Strategies of the HPRC” describes construction of the pangenome reference as future work. (LLM, conf=0.86)
Experimental — accuracy not yet measuredPangenomic methods have rapidly progressed such that it is now practical to propose that common genomic analyses use a pangenome.
“Pangenomic methods have rapidly progressed over the past few years13–15 such that it is now practical to propose that common genomic analyses use a pangenome.”
From A draft human pangenome reference. (2023) · cites this paper as [15]
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Accelerating Sequence Alignment to Graphs
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Physicians' attitudes toward race, genetics, and clinical medicine
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Self-citationPangenome-based genome inferencePreprint
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DNA Returned to Tribe, Raising Questions About Consent
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SGTK: a toolkit for visualization and assessment of scaffold graphs
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The trouble with the Human Genome Diversity Project
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Assembly Graph Browser: interactive visualization of assembly graphs
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The “All of Us” Program and Indigenous Peoples
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Flagged first, then by citations
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Cited by
Sorted by citations
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · see citing works
“Here, we sequence and assemble a set of diverse individual genomes and present a draft human pangenome, the first release of the Human Pangenome Reference Consortium (HPRC) (Wang et al., 2022).”
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Self-citationSemi-automated assembly of high-quality diploid human reference genomes
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Self-citationLong-Read DNA Sequencing: Recent Advances and Remaining Challenges
Warburton, P. E., & Sebra, R. P. (2023) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-101722-103045 · Cited by 163 · see citing works
Single-cell genomics meets human genetics
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Next-generation data filtering in the genomics era
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Gaps and complex structurally variant loci in phased genome assemblies
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Self-citationGBZ file format for pangenome graphs
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Fragile sites, chromosomal lesions, tandem repeats, and disease
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Constructing a Draft Indian Cattle Pangenome Using Short-Read Sequencing
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- Authors
- Wang, T., Antonacci-Fulton, L., Howe, K., Lawson, H. A., Lucas, J. K., Phillippy, A. M., Popejoy, A. B., Asri, M., Carson, C., Chaisson, M. J. P., Chang, X., Cook-Deegan, R., Felsenfeld, A. L., Fulton, R. S., Garrison, E. P., Garrison, N. A., Graves-Lindsay, T. A., Ji, H., Kenny, E. E., Koenig, B. A., Li, D., Marschall, T., McMichael, J. F., Novak, A. M., Purushotham, D., Schneider, V. A., Schultz, B. I., Smith, M. W., Sofia, H. J., Weissman, T., Flicek, P., Li, H., Miga, K. H., Paten, B., Jarvis, E. D., Hall, I. M., Eichler, E. E., Haussler, D., & the Human Pangenome Reference Consortium
- Affiliations
- Washington University in St. Louis (US)
- Wellcome Sanger Institute (GB)
- University of California, Santa Cruz (US)
- National Human Genome Research Institute (US)
- University of California, Davis (US)
- University of Southern California (US)
- Washington Center (US)
- National Institutes of Health (US)
- University of Tennessee Health Science Center (US)
- University of California, Los Angeles (US)
- Stanford Medicine (US)
- Icahn School of Medicine at Mount Sinai (US)
- University of California, San Francisco (US)
- Heinrich Heine University Düsseldorf (DE)
- Stanford University (US)
- European Bioinformatics Institute (GB)
- Harvard University (US)
- Howard Hughes Medical Institute (US)
- Yale University (US)
- Corresponding author
- Wang, Ting
- Flicek, Paul
- Li, Heng
- Miga, Karen H.
- Paten, Benedict
- Jarvis, Erich D.
- Hall, Ira M.
- Eichler, Evan E.
- Haussler, David
- ORCID
- Wang, Ting
- Howe, Kerstin
- Lawson, Heather A.
- Lucas, Julian K.
- Phillippy, Adam M.
- Popejoy, Alice B.
- Asri, Mobin
- Carson, Caryn
- Chaisson, Mark J. P.
- Chang, Xian
- Cook-Deegan, Robert
- Fulton, Robert S.
- Garrison, Erik P.
- Garrison, Nanibaa’ A.
- Graves-Lindsay, Tina A.
- Ji, Hanlee
- Kenny, Eimear E.
- Koenig, Barbara A.
- Li, Daofeng
- Marschall, Tobias
- McMichael, Joshua F.
- Novak, Adam M.
- Purushotham, Deepak
- Smith, Michael W.
- Sofia, Heidi J.
- Weissman, Tsachy
- Flicek, Paul
- Li, Heng
- Miga, Karen H.
- Paten, Benedict
- Jarvis, Erich D.
- Hall, Ira M.
- Eichler, Evan E.
- Haussler, David
- Venue
- Nature
- Published
- 2022-04-20
- Volume
- 604
- Issue
- 7906
- Pages
- 437-446
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC9402379
- OpenAlex
- W4224278121
- Cited by
- 494
- References
- 102
- Citations by year
- 2026: 55 · 2025: 123 · 2024: 135 · 2023: 138 · 2022: 41 · 2012: 1
- FWCI
- 11.61
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, other-oa)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (U01HG010973, U01HG010963, U01HG010971, U01HG010961, U24HG007234, U41HG010972)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- human pangenome, reference genome, genomic diversity, Human Pangenome Reference Consortium, telomere-to-telomere genome assembly, diploid genome assembly, structural variants, single nucleotide variants, precision medicine
- MeSH terms
- Haplotypes, Humans, Genome, Human, Sequence Analysis, DNA, Genomics, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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