Multi-platform discovery of haplotype-resolved structural variation in human genomes
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Abstract
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.
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Population-specific genes may provide insights into local adaptation, while structural variants may contribute to disease susceptibility or resistance in ways previously invisible to reference-based analyses.
“For example, population-specific genes may provide insights into local adaptation, while structural variants may contribute to disease susceptibility or resistance in ways that were previously invisible to reference-based analyses [112,113].”
From Origin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications (2025) · cites this paper as [112]
The Introduction (page unavailable) says reference-aligned short reads miss some structural variants and that cryptic variants may contribute to disease. The passages do not support the separate claim that population-specific genes illuminate local adaptation, or specifically address disease resistance. (LLM, conf=0.86)
Experimental — accuracy not yet measuredMore than two-thirds of SVs have been missed in studies that used short-read data and the human reference assembly.
“more than two-thirds of SVs have been missed in studies that used short-read data and the human reference assembly6–8”
From A draft human pangenome reference. (2023) · cites this paper as [6]
Short-read-based SV discovery relative to a linear reference genome misses a large proportion of SVs.
“This result confirms that short-read-based SV discovery relative to a linear reference genome misses a large proportion of SVs5,6,8.”
From A draft human pangenome reference. (2023) · cites this paper as [6]
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“…paralogs from the reference genome, over two-thirds of SVs have been missed in studies using 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…”
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- Authors
- Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., Fan, X., Wen, J., Handsaker, R. E., Fairley, S., Kronenberg, Z. N., Kong, X., Hormozdiari, F., Lee, D., Wenger, A. M., Hastie, A. R., Antaki, D., Anantharaman, T., Audano, P. A., Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X., Chin, C.-S., Chong, Z., Chuang, N. T., Lambert, C. C., Church, D. M., Clarke, L., Farrell, A., Flores, J., Galeev, T., Gorkin, D. U., Gujral, M., Guryev, V., Heaton, W. H., Korlach, J., Kumar, S., Kwon, J. Y., Lam, E. T., Lee, J. E., Lee, J., Lee, W.-P., Lee, S. P., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K. M., Navarro, F. C. P., Nelson, B. J., Nodzak, C., Noor, A., Kyriazopoulou-Panagiotopoulou, S., Pang, A. W. C., Qiu, Y., Rosanio, G., Ryan, M., Stütz, A., Spierings, D. C. J., Ward, A., Welch, A. E., Xiao, M., Xu, W., Zhang, C., Zhu, Q., Zheng-Bradley, X., Lowy, E., Yakneen, S., McCarroll, S., Jun, G., Ding, L., Koh, C. L., Ren, B., Flicek, P., Chen, K., Gerstein, M. B., Kwok, P.-Y., Lansdorp, P. M., Marth, G. T., Sebat, J., Shi, X., Bashir, A., Ye, K., Devine, S. E., Talkowski, M. E., Mills, R. E., Marschall, T., Korbel, J. O., Eichler, E. E., & Lee, C.
- Affiliations
- University of Southern California (US)
- European Molecular Biology Laboratory (DE)
- Harvard University (US)
- The Jackson Laboratory for Genomic Medicine (US)
- University of Maryland, Baltimore (US)
- Icahn School of Medicine at Mount Sinai (US)
- Xi'an Jiaotong University (CN)
- The University of Texas MD Anderson Cancer Center (US)
- University of North Carolina at Charlotte (US)
- Broad Institute (US)
- European Bioinformatics Institute (GB)
- University of Washington (US)
- Yale University (US)
- University of California, Davis (US)
- University of Utah (US)
- Pacific Biosciences (United States) (US)
- BioNano Genomics (United States) (US)
- University of California San Diego (US)
- 10X Genomics (United States) (US)
- Illumina (United States) (US)
- University Medical Center Groningen (NL)
- Ewha Womans University (KR)
- Drexel University (US)
- The University of Texas Health Science Center at Houston (US)
- Washington University in St. Louis (US)
- University of Malaya (MY)
- University of California, San Francisco (US)
- BC Cancer Agency (CA)
- First Affiliated Hospital of Xi'an Jiaotong University (CN)
- University of Michigan (US)
- Max Planck Institute for Informatics (DE)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Korbel, Jan O.
- Eichler, Evan E.
- Lee, Charles
- ORCID
- Chaisson, Mark J. P.
- Sanders, Ashley D.
- Zhao, Xuefang
- Malhotra, Ankit
- Rausch, Tobias
- Gardner, Eugene J.
- Rodriguez, Oscar L.
- Guo, Li
- Collins, Ryan L.
- Wen, Jia
- Handsaker, Robert E.
- Fairley, Susan
- Kronenberg, Zev N.
- Hormozdiari, Fereydoun
- Wenger, Aaron M.
- Hastie, Alex R.
- Antaki, Danny
- Audano, Peter A.
- Brand, Harrison
- Cao, Han
- Cerveira, Eliza
- Chen, Chong
- Chen, Xintong
- Chin, Chen-Shan
- Chong, Zechen
- Chuang, Nelson T.
- Church, Deanna M.
- Clarke, Laura
- Farrell, Andrew
- Galeev, Timur
- Gorkin, David U.
- Gujral, Madhusudan
- Guryev, Victor
- Korlach, Jonas
- Kumar, Sushant
- Kwon, Jee Young
- Lee, Joyce
- Li, Shantao
- Marks, Patrick
- Meiers, Sascha
- Munson, Katherine M.
- Navarro, Fabio C. P.
- Nelson, Bradley J.
- Noor, Amina
- Pang, Andy W. C.
- Qiu, Yunjiang
- Stütz, Adrian
- Spierings, Diana C. J.
- Welch, AnneMarie E.
- Xiao, Ming
- Xu, Wei
- Zhang, Chengsheng
- Zhu, Qihui
- Zheng-Bradley, Xiangqun
- Lowy, Ernesto
- Yakneen, Sergei
- McCarroll, Steven
- Jun, Goo
- Ding, Li
- Koh, Chong Lek
- Ren, Bing
- Flicek, Paul
- Chen, Ken
- Gerstein, Mark B.
- Kwok, Pui-Yan
- Lansdorp, Peter M.
- Sebat, Jonathan
- Shi, Xinghua
- Bashir, Ali
- Ye, Kai
- Devine, Scott E.
- Talkowski, Michael E.
- Mills, Ryan E.
- Marschall, Tobias
- Korbel, Jan O.
- Eichler, Evan E.
- Lee, Charles
- Venue
- Nature Communications
- Published
- 2019-04-16
- Volume
- 10
- Issue
- 1
- Pages
- 1784-1784
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6467913
- OpenAlex
- W2949062400
- Cited by
- 891
- References
- 68
- Citations by year
- 2026: 48 · 2025: 80 · 2024: 103 · 2023: 119 · 2022: 133 · 2021: 184 · 2020: 126 · 2019: 76 · 2018: 16 · 2017: 4 · 2016: 1 · 2014: 1
- FWCI
- 80.48
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- Funders
- Wellcome Trust (WT104947, WT104947/Z/14/Z, WT085532)
- European Molecular Biology Laboratory
- National Natural Science Foundation of China (2018YFC0910400, 31701739, 2017YFC0907500, 31671372)
- Ewha Womans University
- Universiti Malaya
- National Institutes of Health (1r15hg009565-01, HG005946, MH115957)
- Medical Research Council
- National Health and Medical Research Council (1073726)
- National Institute of Mental Health (R56MH115957, R01MH115957)
- National Human Genome Research Institute (R15 HG009565, U41HG007497, R01HG002898, U01HG006513, R01HG007068, F31HG009223, R01HG005946, R01HG008628, R01HG002385)
- National Cancer Institute (R01CA166661)
- National Institute of Allergy and Infectious Diseases (R21AI117407)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD081256)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- structural variants, indels, chromosomal inversions, microdeletion syndromes, microduplication syndromes, long-read sequencing, optical mapping, trios, human genetic variation
- MeSH terms
- Whole Genome Sequencing, Algorithms, Chromosome Mapping, Haplotypes, Humans, Genome, Human, Genomics, Databases, Genetic, INDEL Mutation, Genomic Structural Variation, 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.
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