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Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
Open accessPublished version of a preprint
Abstract
The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.
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Metadata
- Authors
- Schneider, V. A., Graves-Lindsay, T., Howe, K., Bouk, N., Chen, H.-C., Kitts, P. A., Murphy, T. D., Pruitt, K. D., Thibaud-Nissen, F., Albracht, D., Fulton, R. S., Kremitzki, M., Magrini, V., Markovic, C., McGrath, S., Steinberg, K. M., Auger, K., Chow, W., Collins, J., Harden, G., Hubbard, T., Pelan, S., Simpson, J. T., Threadgold, G., Torrance, J., Wood, J. M., Clarke, L., Koren, S., Boitano, M., Peluso, P., Li, H., Chin, C.-S., Phillippy, A. M., Durbin, R., Wilson, R. K., Flicek, P., Eichler, E. E., & Church, D. M.
- Affiliations
- Washington University in St. Louis (US)
- Wellcome Sanger Institute (GB)
- National Institutes of Health (US)
- European Bioinformatics Institute (GB)
- Pacific Biosciences (United States) (US)
- Broad Institute (US)
- Howard Hughes Medical Institute (US)
- ORCID
- Graves-Lindsay, Tina
- Howe, Kerstin
- Murphy, Terence D.
- Pruitt, Kim D.
- Fulton, Robert S.
- Kremitzki, Milinn
- Magrini, Vincent
- McGrath, Sean
- Steinberg, Karyn Meltz
- Chow, William
- Collins, Joanna
- Pelan, Sarah
- Simpson, Jared T.
- Threadgold, Glen
- Torrance, James
- Wood, Jonathan M.
- Clarke, Laura
- Koren, Sergey
- Peluso, Paul
- Li, Heng
- Chin, Chen-Shan
- Phillippy, Adam M.
- Durbin, Richard
- Wilson, Richard K.
- Flicek, Paul
- Eichler, Evan E.
- Church, Deanna M.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2017-04-10
- Volume
- 27
- Issue
- 5
- Pages
- 849-864
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC5411779
- OpenAlex
- W2953263404
- Cited by
- 1,193
- References
- 76
- Citations by year
- 2026: 146 · 2025: 185 · 2024: 177 · 2023: 156 · 2022: 152 · 2021: 127 · 2020: 92 · 2019: 83 · 2018: 54 · 2017: 18
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health (5U54HG003079, 5U41HG007635, HG002385, HG007635)
- National Library of Medicine
- Wellcome Trust (WT095908, WT098051, WT104947/Z/14/Z)
- European Molecular Biology Laboratory
- National Human Genome Research Institute
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- GRCh38, long-read sequencing, centromere, population genetic variation, variant interpretation, read mapping, assembly quality evaluation
- MeSH terms
- Haploidy, Haplotypes, Humans, Polymorphism, Genetic, Reference Standards, Software, Genome, Human, Sequence Analysis, DNA, Contig Mapping, Genomics
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.
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