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Characterizing the Major Structural Variant Alleles of the Human Genome
Open accessAbstract
In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional 13,053 (6.9 Mbp) present in the majority, indicating minor alleles or errors in the reference. Genotyping in 440 additional genomes confirms the most common SVs in unique euchromatin are now sequence resolved. We report a ninefold SV bias toward the last 5 Mbp of human chromosomes with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity.
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“This provides a large set of fully phased human genome assemblies and outperforms earlier efforts on many levels of assembly quality5,16,60.”
From A draft human pangenome reference. (2023) · cites this paper as [60]
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“This is the largest set of fully phased genome assemblies currently available, outperforming earlier efforts on many levels of assembly quality (Audano et al., 2019; Ebert et al., 2021; Shafin et al., 2020).”
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Metadata
- Authors
- Audano, P. A., Sulovari, A., Graves-Lindsay, T. A., Cantsilieris, S., Sorensen, M., Welch, A. E., Dougherty, M. L., Nelson, B. J., Shah, A., Dutcher, S. K., Warren, W. C., Magrini, V., McGrath, S. D., Li, Y. I., Wilson, R. K., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- Washington University in St. Louis (US)
- University of Chicago (US)
- Nationwide Children's Hospital (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Eichler, Evan E.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2019-01
- Volume
- 176
- Issue
- 3
- Pages
- 663-675.e19
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6438697
- OpenAlex
- W2908721251
- Cited by
- 492
- References
- 73
- Citations by year
- 2026: 31 · 2025: 37 · 2024: 49 · 2023: 68 · 2022: 60 · 2021: 121 · 2020: 84 · 2019: 41
- FWCI
- 48.23
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. National Institutes of Health (HG002385, HG007635, HG009081, HG003079, HG009478, T32 HG000035-23)
- National Health and Medical Research Council
- NHMRC (1073726)
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- structural variants, human genome, insertion, deletion, inversion, long-read sequencing, variable number tandem repeats, euchromatin, regulatory loci, allelic diversity
- MeSH terms
- Alleles, Gene Frequency, Humans, Genome, Human, Sequence Analysis, DNA, Minisatellite Repeats, Euchromatin, Genomics, Genomic Structural Variation
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.
What counts as a claim ›How we measure confidence ›How we check this ›
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