Cited by 305Genomic variations and chromosomal abnormalitiesGenome Rearrangement AlgorithmsChromosomal and Genetic Variations

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Sequence-based characterization of structural variation in the mouse genome

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Yalcin, Binnaz, Wong, Kim, Agam, Avigail, Goodson, Martin, Keane, Thomas M., Gan, Xiangchao, Nellåker, Christoffer, Goodstadt, Leo, Nicod, Jérôme, Bhomra, Amarjit, Hernandez-Pliego, Polinka, Whitley, Helen, Cleak, James, Dutton, Rebekah, Janowitz, Deborah, Mott, Richard, Adams, David J., Flint, Jonathan·2011·Nature

DOI 10.1038/nature10432PMC PMC3428933

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Abstract

Structural variation is widespread in mammalian genomes and is an important cause of disease, but just how abundant and important structural variants (SVs) are in shaping phenotypic variation remains unclear. Without knowing how many SVs there are, and how they arise, it is difficult to discover what they do. Combining experimental with automated analyses, we identified 711,920 SVs at 281,243 sites in the genomes of thirteen classical and four wild-derived inbred mouse strains. The majority of SVs are less than 1 kilobase in size and 98% are deletions or insertions. The breakpoints of 160,000 SVs were mapped to base pair resolution, allowing us to infer that insertion of retrotransposons causes more than half of SVs. Yet, despite their prevalence, SVs are less likely than other sequence variants to cause gene expression or quantitative phenotypic variation. We identified 24 SVs that disrupt coding exons, acting as rare variants of large effect on gene function. One-third of the genes so affected have immunological functions.

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Additional file 4 of Detection of allele-specific expression in spatial transcriptomics with spASE
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Additional file 5 of Detection of allele-specific expression in spatial transcriptomics with spASE
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Additional file 1 of Analysis of structural variation among inbred mouse strains
Arslan, A., Fang, Z., Wang, M., Tan, Y., Cheng, Z., Chen, X., Guan, Y., Pisani, L. J., Yoo, B., Bejerano, G., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22610008
Additional file 2 of Detection of allele-specific expression in spatial transcriptomics with spASE
Zou, L. S., Cable, D. M., Barrera, I., Zhao, T., Murray, E. M., Aryee, M. J., Chen, F., & Irizarry, R. A. (2024) · Figshare · doi:10.6084/m9.figshare.26745764
Additional file 1 of Detection of allele-specific expression in spatial transcriptomics with spASE
Zou, L. S., Cable, D. M., Barrera, I., Zhao, T., Murray, E. M., Aryee, M. J., Chen, F., & Irizarry, R. A. (2024) · Figshare · doi:10.6084/m9.figshare.26745761
Additional file 3 of Detection of allele-specific expression in spatial transcriptomics with spASE
Zou, L. S., Cable, D. M., Barrera, I., Zhao, T., Murray, E. M., Aryee, M. J., Chen, F., & Irizarry, R. A. (2024) · Figshare · doi:10.6084/m9.figshare.26745767

Authors: Yalcin, B., Wong, K., Agam, A., Goodson, M., Keane, T. M., Gan, X., Nellåker, C., Goodstadt, L., Nicod, J., Bhomra, A., Hernandez-Pliego, P., Whitley, H., Cleak, J., Dutton, R., Janowitz, D., Mott, R., Adams, D. J., & Flint, J.
Affiliations: Centre for Human Genetics (GB)
Wellcome Sanger Institute (GB)
University of Oxford (GB)
Corresponding author: Adams, David J.
ORCID: Yalcin, Binnaz
Wong, Kim
Keane, Thomas M.
Gan, Xiangchao
Nellåker, Christoffer
Nicod, Jérôme
Bhomra, Amarjit
Whitley, Helen
Dutton, Rebekah
Janowitz, Deborah
Mott, Richard
Adams, David J.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2011-09
Volume: 477
Issue: 7364
Pages: 326-329
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature10432
PMC: PMC3428933
OpenAlex: W1967973651
Cited by: 301
References: 31
Citations by year: 2026: 7 · 2025: 9 · 2024: 6 · 2023: 16 · 2022: 17 · 2021: 20 · 2020: 14 · 2019: 18 · 2018: 23 · 2017: 20 · 2016: 20 · 2015: 26 · 2014: 27 · 2013: 34 · 2012: 38
FWCI: 20.75
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
HAL (submittedVersion)
RePEc: Research Papers in Economics (submittedVersion)
UCL Discovery (University College London) (submittedVersion)
Funders: Wellcome Trust (079912, 082356, 090532, 098051)
Cancer Research UK (13031)
Medical Research Council (MC_EX_G0802457)
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 › Chromosomal and Genetic Variations
Keywords: structural variants, mouse genome, inbred mouse strains, wild-derived mouse strains, retrotransposon insertion, indels, breakpoint mapping, phenotypic variability, gene expression variation, functional variants
MeSH terms: Animals, Exons, Female, Genotype, Male, Mice, Inbred Strains, Phenotype, Genetic Variation, Gene Expression, Mutagenesis, Insertional, Genome, Sequence Deletion, Retroelements, Genomics, Quantitative Trait Loci, Mice, Rats, Chromosome Breakpoints

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