Cited by 513Genomic variations and chromosomal abnormalitiesGenome Rearrangement AlgorithmsGenomics and Phylogenetic Studies

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Characterizing the Major Structural Variant Alleles of the Human Genome

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Audano, Peter A., Sulovari, Arvis, Graves-Lindsay, Tina A., Cantsilieris, Stuart, Sorensen, Melanie, Welch, AnneMarie E., Dougherty, Max L., Nelson, Bradley J., Shah, Ankeeta, Dutcher, Susan K., Warren, Wesley C., Magrini, Vincent, McGrath, Sean D., Li, Yang I., Wilson, Richard K., Eichler, Evan E.·2019·Cell

DOI 10.1016/j.cell.2018.12.019PMC PMC6438697

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Abstract

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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Additional file 5 of SVhound: detection of regions that harbor yet undetected structural variation
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Additional file 14 of Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression
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Additional file 7 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
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Additional file 15 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
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Additional file 4 of A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
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Additional file 27 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
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Additional file 4 of Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
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Additional file 1 of SVhound: detection of regions that harbor yet undetected structural variation
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Additional file 4 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812534
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Additional file 6 of SVhound: detection of regions that harbor yet undetected structural variation
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Additional file 2 of A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
Rice, E. S., Alberdi, A., Alfieri, J. M., Athrey, G., Balacco, J., Bardou, P., Blackmon, H., Charles, M., Cheng, H. H., Fedrigo, O. D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26643787
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Additional file 5 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
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Additional file 2 of SVFX: a machine learning framework to quantify the pathogenicity of structural variants
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Additional file 3 of Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
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Additional file 21 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812501
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Additional file 1 of Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
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Additional file 7 of Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
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Additional file 25 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812519
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Additional file 3 of A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
Rice, E. S., Alberdi, A., Alfieri, J. M., Athrey, G., Balacco, J., Bardou, P., Blackmon, H., Charles, M., Cheng, H. H., Fedrigo, O. D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26643790
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Self-citation
Additional file 1 of A benchmark of structural variation detection by long reads through a realistic simulated model
Dierckxsens, N., Li, T., Vermeesch, J. R., & Xie, Z. (2021) · Figshare · doi:10.6084/m9.figshare.17210245
Additional file 13 of Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
Höijer, I., Johansson, J., Gudmundsson, S., Chin, C.-S., Bunikis, I., Häggqvist, S., Emmanouilidou, A., Wilbe, M., den Hoed, M., Bondeson, M.-L., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13316827
Additional file 1 of Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly
Holley, G., Beyter, D., Ingimundardóttir, H., Møller, P. L., Kristmundsdóttir, S., Eggertsson, H. P., & Halldorsson, B. V. (2021) · Figshare · doi:10.6084/m9.figshare.13550011
Additional file 8 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812546
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Additional file 3 of A benchmark of structural variation detection by long reads through a realistic simulated model
Dierckxsens, N., Li, T., Vermeesch, J. R., & Xie, Z. (2021) · Figshare · doi:10.6084/m9.figshare.17210251
Additional file 1 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812495
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Additional file 2 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812528
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Additional file 10 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812459
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Additional file 12 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812465
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Additional file 22 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812507
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Additional file 11 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812462
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Additional file 17 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812483
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Additional file 26 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812522
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Additional file 13 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
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Additional file 20 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812498
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Additional file 18 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Wei, C., Wang, Z., Wang, J., Teng, J., Shen, S. S., Xiao, Q., Bao, S., Feng, Y., Zhang, Y., Li, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14812489
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Additional file 3 of SVhound: detection of regions that harbor yet undetected structural variation
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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: Audano, Peter A.
Sulovari, Arvis
Graves-Lindsay, Tina A.
Sorensen, Melanie
Welch, AnneMarie E.
Dougherty, Max L.
Nelson, Bradley J.
Shah, Ankeeta
Dutcher, Susan K.
Warren, Wesley C.
Magrini, Vincent
McGrath, Sean D.
Li, Yang I.
Wilson, Richard K.
Eichler, Evan E.
Venue: Cell
Publisher: Elsevier BV
Published: 2019-01
Volume: 176
Issue: 3
Pages: 663-675.e19
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2018.12.019
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: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 389 d)
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

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Characterizing the Major Structural Variant Alleles of the Human Genome

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