The impact of structural variation on human gene expression
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Abstract
Structural variants (SVs) are an important source of human genetic diversity, but their contribution to traits, disease and gene regulation remains unclear. We mapped cis expression quantitative trait loci (eQTLs) in 13 tissues via joint analysis of SVs, single-nucleotide variants (SNVs) and short insertion/deletion (indel) variants from deep whole-genome sequencing (WGS). We estimated that SVs are causal at 3.5-6.8% of eQTLs-a substantially higher fraction than prior estimates-and that expression-altering SVs have larger effect sizes than do SNVs and indels. We identified 789 putative causal SVs predicted to directly alter gene expression: most (88.3%) were noncoding variants enriched at enhancers and other regulatory elements, and 52 were linked to genome-wide association study loci. We observed a notable abundance of rare high-impact SVs associated with aberrant expression of nearby genes. These results suggest that comprehensive WGS-based SV analyses will increase the power of common- and rare-variant 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 [9]
The Results (Fine-mapping causal variants) state that, per variant, an SV is 28–54 times more likely to modulate gene expression than an SNV or indel. That supports the comparison for gene expression, but the cited analysis does not establish the broader claim about gene function generally. (LLM, conf=0.86)
Experimental — accuracy not yet measured
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- Authors
- GTEx Consortium, Chiang, C., Scott, A. J., Davis, J. R., Tsang, E. K., Li, X., Kim, Y., Hadzic, T., Damani, F. N., Ganel, L., Montgomery, S. B., Battle, A., Conrad, D. F., & Hall, I. M.
- Affiliations
- Washington University in St. Louis (US)
- Stanford Medicine (US)
- Johns Hopkins University (US)
- Corresponding author
- Conrad, Donald F
- Hall, Ira M
- ORCID
- Venue
- Nature Genetics
- Published
- 2017-04-03
- Volume
- 49
- Issue
- 5
- Pages
- 692-699
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC5406250
- OpenAlex
- W2949884285
- Cited by
- 495
- References
- 59
- Citations by year
- 2026: 45 · 2025: 67 · 2024: 55 · 2023: 74 · 2022: 55 · 2021: 74 · 2020: 50 · 2019: 43 · 2018: 19 · 2017: 12
- FWCI
- 22.69
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Open Scholarship Institutional Repository (Washington University in St. Louis) (submittedVersion)
- Washington University in St. Louis Libraries
- Funders
- National Institutes of Health (HHSN261200800001C)
- National Heart, Lung, and Blood Institute (HHSN268201000029C)
- National Institute of Mental Health (R01MH101814, R01MH101822, R01MH090937, R01MH101810, R01MH101782, R01MH101819, R01MH101820, R01MH090948, R01MH101825, R01MH090941, R01MH090936, R01MH090951)
- National Institute on Drug Abuse (R01DA033684, R01DA006227)
- National Human Genome Research Institute (K22HG000044, R01HG008150, UM1HG008853, R01HG007178, T32HG000044)
- National Cancer Institute (HHSN261200800001E))
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD087011)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- structural variants, gene expression regulation, cis-expression quantitative trait loci, enhancers, rare variants, single nucleotide variants, insertion-deletion variants, tissue-specific gene expression, GTEx, human genetic variation
- MeSH terms
- Algorithms, Chromosome Mapping, Gene Expression Regulation, Humans, Genetic Variation, Genome, Human, Linear Models, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Quantitative Trait Loci, INDEL Mutation, Genome-Wide Association Study
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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