An integrated map of structural variation in 2,504 human genomes
Open accessAbstract
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association. The Structural Variation Analysis Group of The 1000 Genomes Project reports an integrated structural variation map based on discovery and genotyping of eight major structural variation classes in 2,504 unrelated individuals from across 26 populations; structural variation is compared within and between populations and its functional impact is quantified. The Structural Variation Analysis Group of The 1000 Genomes Project reports an integrated structural variation map based on discovery and genotyping of eight major structural variation classes in genomes for 2,504 unrelated individuals from across 26 populations. They characterize structural variation within and between populations and quantify its functional effect. The authors further create a phased reference panel that will be valuable for population genetic and disease association studies.
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Individual SVs are more likely to affect gene function than either individual SNPs or short insertions and deletions.
“despite individual SVs being more likely to affect gene function than either individual SNPs or short insertions and deletions (indels)9,10.”
From A draft human pangenome reference. (2023) · cites this paper as [10]
The Functional impact of SVs section reports that SV classes were enriched for expression-associated variants relative to the number tested, supporting a greater per-variant effect on gene expression. It uses eQTL associations as a surrogate for functional impact and groups SNPs with indels in the comparison; it does not establish the broader claim about gene function separately against each variant type. (LLM, conf=0.82)
Experimental — accuracy not yet measuredHuman genetic diversity ranges from single-nucleotide variation to large chromosomal events.
“However, the human genetic diversity ranges from the single-nucleotide variation to large chromosomal events [41, 42].”
From On the length, weight and GC content of the human genome (2019) · cites this paper as [42]
A subset of human retrotransposons are mobilization competent.
“a subset of human retrotransposons are mobilization competent”
From The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders (2024) · cites this paper as Sudmant et al. 2015
Most human retrotransposons and all human DNA transposons have lost transpositional ability due to their accumulation of truncations and mutations over the course of evolution.
“While most human retrotransposons and all human DNA transposons have lost transpositional ability due to their accumulation of truncations and mutations over the course of evolution”
From The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders (2024) · cites this paper as Sudmant et al. 2015
The Construction of our phase 3 SV release section reports mobile-element insertions, and the Discussion mentions retrotransposition, but neither addresses whether most human retrotransposons or all human DNA transposons have lost transpositional ability. Searches for truncations, mutations, and inactive transposons found no passage in our copy supporting the claimed evolutionary explanation. Page numbers were not available in the indexed passages. (LLM, conf=0.76)
Experimental — accuracy not yet measuredGenomic length of germline alterations tends to be shorter compared with somatic alterations observed in tumors due to negative selection against large SVs in the germline.
“Genomic length of the germline alterations tends to be shorter compared with somatic alterations observed in tumors due to negative selection against large SVs in the germline28.”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [28]
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“…short-read data and the human reference assembly (Chaisson et al., 2019; Wenger et al., 2019; Zhao et al., 2021), despite individual SVs being more likely to impact gene function than either individual SNPs or short insertions and deletions (indels) (Chiang et al., 2017; Sudmant et al., 2015).”
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- Authors
- Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., Konkel, M. K., Malhotra, A., Stütz, A. M., Shi, X., Paolo Casale, F., Chen, J., Hormozdiari, F., Dayama, G., Chen, K., Malig, M., Chaisson, M. J. P., Walter, K., Meiers, S., Kashin, S., Garrison, E., Auton, A., Lam, H. Y. K., Jasmine Mu, X., Alkan, C., Antaki, D., Bae, T., Cerveira, E., Chines, P., Chong, Z., Clarke, L., Dal, E., Ding, L., Emery, S., Fan, X., Gujral, M., Kahveci, F., Kidd, J. M., Kong, Y., Lameijer, E.-W., McCarthy, S., Flicek, P., Gibbs, R. A., Marth, G., Mason, C. E., Menelaou, A., Muzny, D. M., Nelson, B. J., Noor, A., Parrish, N. F., Pendleton, M., Quitadamo, A., Raeder, B., Schadt, E. E., Romanovitch, M., Schlattl, A., Sebra, R., Shabalin, A. A., Untergasser, A., Walker, J. A., Wang, M., Yu, F., Zhang, C., Zhang, J., Zheng-Bradley, X., Zhou, W., Zichner, T., Sebat, J., Batzer, M. A., McCarroll, S. A., The 1000 Genomes Project Consortium, Mills, R. E., Gerstein, M. B., Bashir, A., Stegle, O., Devine, S. E., Lee, C., Eichler, E. E., & Korbel, J. O.
- Affiliations
- University of Washington (US)
- European Molecular Biology Laboratory (DE)
- University of Maryland, Baltimore (US)
- Broad Institute (US)
- Mayo Clinic (US)
- Howard Hughes Medical Institute (US)
- Yale University (US)
- Washington University in St. Louis (US)
- University of Michigan (US)
- Louisiana State University (US)
- The Jackson Laboratory for Genomic Medicine (US)
- University of North Carolina at Charlotte (US)
- The University of Texas MD Anderson Cancer Center (US)
- Wellcome Sanger Institute (GB)
- Boston College (US)
- Albert Einstein College of Medicine (US)
- Bilkent University (TR)
- University of California San Diego (US)
- National Institutes of Health (US)
- European Bioinformatics Institute (GB)
- Leiden University Medical Center (NL)
- Baylor College of Medicine (US)
- Cornell University (US)
- University Medical Center Utrecht (NL)
- Icahn School of Medicine at Mount Sinai (US)
- Kyoto University (JP)
- Virginia Commonwealth University (US)
- Heidelberg University (DE)
- Ewha Womans University (KR)
- Corresponding author
- Eichler, Evan E.
- Korbel, Jan O.
- ORCID
- Sudmant, Peter H.
- Rausch, Tobias
- Gardner, Eugene J.
- Handsaker, Robert E.
- Abyzov, Alexej
- Huddleston, John
- Zhang, Yan
- Ye, Kai
- Jun, Goo
- Konkel, Miriam K.
- Malhotra, Ankit
- Stütz, Adrian M.
- Shi, Xinghua
- Chen, Jieming
- Hormozdiari, Fereydoun
- Dayama, Gargi
- Chen, Ken
- Malig, Maika
- Chaisson, Mark J. P.
- Walter, Klaudia
- Meiers, Sascha
- Kashin, Seva
- Garrison, Erik
- Auton, Adam
- Lam, Hugo Y. K.
- Alkan, Can
- Antaki, Danny
- Bae, Taejeong
- Cerveira, Eliza
- Chines, Peter
- Chong, Zechen
- Clarke, Laura
- Dal, Elif
- Ding, Li
- Gujral, Madhusudan
- Kahveci, Fatma
- Kidd, Jeffrey M.
- Kong, Yu
- Lameijer, Eric-Wubbo
- McCarthy, Shane
- Flicek, Paul
- Gibbs, Richard A.
- Mason, Christopher E.
- Muzny, Donna M.
- Nelson, Bradley J.
- Noor, Amina
- Parrish, Nicholas F.
- Pendleton, Matthew
- Quitadamo, Andrew
- Raeder, Benjamin
- Schadt, Eric E.
- Schlattl, Andreas
- Sebra, Robert
- Shabalin, Andrey A.
- Untergasser, Andreas
- Wang, Min
- Zhang, Chengsheng
- Zhang, Jing
- Zheng-Bradley, Xiangqun
- Zhou, Wanding
- Zichner, Thomas
- Sebat, Jonathan
- Batzer, Mark A.
- McCarroll, Steven A.
- Mills, Ryan E.
- Gerstein, Mark B.
- Bashir, Ali
- Stegle, Oliver
- Devine, Scott E.
- Lee, Charles
- Eichler, Evan E.
- Korbel, Jan O.
- Venue
- Nature
- Published
- 2015-09-30
- Volume
- 526
- Issue
- 7571
- Pages
- 75-81
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4617611
- OpenAlex
- W1912672559
- Cited by
- 2,354
- References
- 41
- Citations by year
- 2026: 126 · 2025: 162 · 2024: 195 · 2023: 180 · 2022: 252 · 2021: 283 · 2020: 287 · 2019: 284 · 2018: 230 · 2017: 223 · 2016: 117 · 2015: 10 · 2014: 1
- FWCI
- 132.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Civil War Book Review (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-sa)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Bilkent University Institutional Repository (Bilkent University) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Yale University
- Wellcome Trust (104947, 085532, RR19895, WT104947/Z/14/Z, WT085532/Z/08/Z)
- European Bioinformatics Institute
- European Molecular Biology Laboratory
- Deutsche Forschungsgemeinschaft
- Ewha Womans University
- Kunming University of Science and Technology
- National Institutes of Health (1s10rr019895-01)
- National Human Genome Research Institute (U41HG007497, P01HG007497, R01HG002898, R01HG007068, U24HG007497)
- National Cancer Institute (R01CA166661)
- National Institute of General Medical Sciences (R01GM059290, R01 GM59290)
- National Center for Research Resources (RR 19895, RR029676-01, S10_RR019895, S10RR029676)
- 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 › Genetics › Genetic Associations and Epidemiology
- Keywords
- structural variants, haplotype phasing, haplotype blocks, population stratification, genome-wide association study, expression quantitative trait loci, complex structural variants, 1000 Genomes Project, human populations
- MeSH terms
- Amino Acid Sequence, Genetics, Medical, Genetics, Population, Genotype, Haplotypes, Homozygote, Humans, Molecular Sequence Data, Genetic Variation, Genome, Human, Sequence Deletion, Sequence Analysis, DNA, Genetic Predisposition to Disease, Physical Chromosome Mapping, Polymorphism, Single Nucleotide, Genomics, Quantitative Trait Loci, Genome-Wide Association Study, Mutation Rate
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