The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
Sequence-based characterization of structural variation in the mouse genome
Open accessAbstract
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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“These variants include over 5 million single nucleotide polymorphisms (SNPs; Onos et al., 2019), 116 novel genes not present in B6 (Lilue et al., 2018), and between 250 and 400 large structural variants (Yalcin et al., 2011).”
From Network analysis identifies strain-dependent response to tau and tau seeding-associated genes (2023) · cites this paper as Yalcin et al., 2011
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Ye, K., Schulz, M. H., Long, Q., Apweiler, R., & Ning, Z. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp394 · Cited by 2,029
Origins and functional impact of copy number variation in the human genome
The Wellcome Trust Case Control Consortium, Conrad, D. F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., Aerts, J., Andrews, T. D., Barnes, C., et al. (2010) · Nature · doi:10.1038/nature08516 · Cited by 1,970
Burnside, R. D. (2015) · Cytogenetic and Genome Research · doi:10.1159/000438708 · Cited by 1,964
Mouse genomic variation and its effect on phenotypes and gene regulation.
Keane, T. M., Goodstadt, L., Danecek, P., White, M. A., Wong, K., Yalcin, B., Heger, A., Agam, A., Slater, G., Goodson, M., et al. (2011) · Nature · doi:10.1038/nature10413 · Cited by 1,580
Self-citationBreakDancer: an algorithm for high-resolution mapping of genomic structural variation
Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., McGrath, S. D., Wendl, M. C., Zhang, Q., Locke, D. P., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1363 · Cited by 1,489
Copy number variation in human health, disease, and evolution
Zhang, F., Gu, W., Hurles, M. E., & Lupski, J. R. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164217 · Cited by 1,207
Structural Variation in the Human Genome and its Role in Disease
Stankiewicz, P., & Lupski, J. R. (2010) · Annual Review of Medicine · doi:10.1146/annurev-med-100708-204735 · Cited by 1,201
Population genomics of human gene expression
Stranger, B. E., Nica, A. C., Forrest, M. S., Dimas, A. S., Bird, C., Beazley, C., Ingle, C., Dunning, M., Flicek, P., Koller, D., et al. (2007) · Nature Genetics · doi:10.1038/ng2142 · Cited by 1,153
Mapping copy number variation by population-scale genome sequencing
1000 Genomes Project, Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., et al. (2011) · Nature · doi:10.1038/nature09708 · Cited by 1,140
An integrative genomics approach to infer causal associations between gene expression and disease
Schadt, E. E., Lamb, J., Yang, X., Zhu, J., Edwards, S., GuhaThakurta, D., Sieberts, S. K., Monks, S., Reitman, M., Zhang, C., et al. (2005) · Nature Genetics · doi:10.1038/ng1589 · Cited by 1,043
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Uddin, M. M. (2019) · theses.fr (ABES) · doi:10.70675/c0ea56dez00b3z4321zac70z35e800418885 · Cited by 1
Zohud, O., Midlej, K., & Iraqi, F. A. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27167254
Buzzi, B., Fernandez, G. M., Baldwin, A., Palamar, A., Cornes, B. K., Kumar, V., & Damaj, M. I. (2026) · Psychopharmacology · doi:10.1007/s00213-026-07154-0
Metadata
- 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
- Venue
- Nature
- Published
- 2011-09
- Volume
- 477
- Issue
- 7364
- Pages
- 326-329
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- 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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