Cited by 519Genomic variations and chromosomal abnormalitiesGenetic Associations and EpidemiologyGenomics and Chromatin Dynamics

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The impact of structural variation on human gene expression

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GTEx Consortium, Chiang, Colby, Scott, Alexandra J, Davis, Joe R, Tsang, Emily K, Li, Xin, Kim, Yungil, Hadzic, Tarik, Damani, Farhan N, Ganel, Liron, Montgomery, Stephen B, Battle, Alexis, Conrad, Donald F, Hall, Ira M·2017·Nature Genetics

DOI 10.1038/ng.3834PMC PMC5406250

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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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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Self-citation
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247
Self-citation
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
The variant call format and VCFtools
Danecek, P., Auton, A., Abecasis, G. R., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G. A., Marth, G., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,450
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Analysis of protein-coding genetic variation in 60,706 humans
Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587
GCTA: a tool for genome-wide complex trait analysis
Yang, J., Lee, S. H., Goddard, M. E., & Visscher, P. M. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.11.011 · Cited by 8,279
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183

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Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997/ (2013). · arXiv
Ongen, H., Buil, A., Brown, A., Dermitzakis, E. & Delaneau, O. Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics http://dx.doi.org/10.1093/bioinformatics/btv722 (2016). · DOI

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HUMAN GENETIC VARIANTS AND THEIR ANALYSIS: CURRENT STATE AND FUTURE PERSPECTIVES
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Loegler, V., Friedrich, A., & Schacherer, J. (2026) · Science Advances · doi:10.1101/2025.08.26.672342
Multifocal Genomic Reconstruction Leading to Germline Structural Variants
Hattori, A., & Fukami, M. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4750-9_30
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Additional file 10 of InvertypeR: Bayesian inversion genotyping with Strand-seq data
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Additional file 2 of Mapping and functional characterization of structural variation in 1060 pig genomes
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Additional file 9 of InvertypeR: Bayesian inversion genotyping with Strand-seq data
Hanlon, V. C. T., Mattsson, C.-A., Spierings, D. C. J., Guryev, V., & Lansdorp, P. M. (2021) · Figshare · doi:10.6084/m9.figshare.15087458
Additional file 4 of InvertypeR: Bayesian inversion genotyping with Strand-seq data
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Additional file 3 of Mapping and functional characterization of structural variation in 1060 pig genomes
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Additional file 1 of InvertypeR: Bayesian inversion genotyping with Strand-seq data
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Additional file 2 of InvertypeR: Bayesian inversion genotyping with Strand-seq data
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Additional file 3 of InvertypeR: Bayesian inversion genotyping with Strand-seq data
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Additional file 1 of Mapping and functional characterization of structural variation in 1060 pig genomes
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Kulej, K., Steinberg, A. P., Zhang, J., Casalena, G., Havasov, E., Shah, S. P., McPherson, A., & Kentsis, A. (2026) · eLife · doi:10.7554/elife.108878
Structural variant detection across sequencing technologies
Li, G., Liu, Y., Zhang, A., Lin, X., Hu, Z., Liu, B., Qian, L., & Wang, Y. (2026) · Nature Biotechnology · doi:10.1038/s41587-026-03332-9
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Yue, D., Lu, Y., Chong, Y., Wu, J., Gao, Z., Ma, R., Li, K., Deng, W., & Wang, B. (2026) · Biology · doi:10.3390/biology15060465
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Hu, Y., Wang, W., Wang, H., Gao, Z., Zhu, X., Yang, Y., & Lü, J. (2026) · iScience · doi:10.1016/j.isci.2026.115539
Apport du séquençage d'exome pour le diagnostic et le traitement des maladies complexes
Jacob, A. (2020) · theses.fr (ABES) · doi:10.70675/867c4f59zac67z45c8z821ez3513ef63ba7c

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: Chiang, Colby
Scott, Alexandra J
Davis, Joe R
Tsang, Emily K
Li, Xin
Ganel, Liron
Montgomery, Stephen B
Battle, Alexis
Conrad, Donald F
Hall, Ira M
Venue: Nature Genetics
Publisher: Springer Science and Business Media LLC
Published: 2017-04-03
Volume: 49
Issue: 5
Pages: 692-699
ISSN: 1061-4036 (ISSN-L)
1546-1718
DOI: 10.1038/ng.3834
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

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