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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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
Genome architecture, rearrangements and genomic disorders
Stankiewicz, P., & Lupski, J. R. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02592-1 · Cited by 944
Hastings, P. J., Ira, G., & Lupski, J. R. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000327 · Cited by 818
Genome-wide genetic association of complex traits in heterogeneous stock mice
Valdar, W. S. J., Solberg, L. C., Gauguier, D., Heyes, S. B., Klenerman, P., Cookson, W., Taylor, M. S., Rawlins, J. N. P., Mott, R., & Flint, J. (2006) · Nature Genetics · doi:10.1038/ng1840 · Cited by 560
Self-citationZhang, F., Khajavi, M., Connolly, A. M., Towne, C. F., Batish, S. D., & Lupski, J. R. (2009) · Nature Genetics · doi:10.1038/ng.399 · Cited by 548
Positional cloning of the mouse retrovirus restriction gene Fvl
Best, S., Tissier, P. L., Towers, G. J., & Stoye, J. P. (1996) · Nature · doi:10.1038/382826a0 · Cited by 499
Ma, N. J.-L., Kim, E. M., Haber, J. E., & Lee, S. E. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.23.8820-8828.2003 · Cited by 384
Segmental copy number variation shapes tissue transcriptomes
Hor, C. N., Vinckenbosch, N., Zöllner, S. K., Chaignat, E., Pradervand, S., Schütz, F., Rüedi, M., Kaessmann, H., & Reymond, A. (2009) · Nature Genetics · doi:10.1038/ng.345 · Cited by 317
Boyden, L. M., Lewis, J. M., Barbee, S. D., Bas, A., Girardi, M., Hayday, A., Tigelaar, R. E., & Lifton, R. P. (2008) · Nature Genetics · doi:10.1038/ng.108 · Cited by 299
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genomePreprint
Quinlan, A. R., Clark, R. A., Sokolova, S., Leibowitz, M. L., Zhang, Y., Hurles, M. E., Mell, J. C., & Hall, I. M. (2010) · Genome Research · doi:10.1101/gr.102970.109 · Cited by 288
Commercially Available Outbred Mice for Genome-Wide Association Studies
Yalcin, B., Nicod, J., Bhomra, A., Davidson, S. I., Cleak, J., Farinelli, L., Østerås, M., Whitley, A., Wei, Y., Gan, X., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001085 · Cited by 139
Self-citationCahan, P., Li, Y., Izumi, M., & Graubert, T. A. (2009) · Nature Genetics · doi:10.1038/ng.350 · Cited by 135
Using Progenitor Strain Information to Identify Quantitative Trait Nucleotides in Outbred Mice
Yalcin, B., Flint, J., & Mott, R. (2005) · Genetics · doi:10.1534/genetics.104.028902 · Cited by 115
Self-citationAn expanded clade of rodent Trim5 genes
Tareen, S. U., Sawyer, S. L., Malik, H. S., & Emerman, M. (2009) · Virology · doi:10.1016/j.virol.2008.12.018 · Cited by 73
High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissuesPreprint
Huang, G., Shifman, S., Valdar, W. S. J., Johannesson, M., Yalcin, B., Taylor, M. S., Taylor, J. M., Mott, R., & Flint, J. (2009) · Genome Research · doi:10.1101/gr.088120.108 · Cited by 73
Self-citationLookSeq: A browser-based viewer for deep sequencing dataPreprint
Manske, M., & Kwiatkowski, D. P. (2009) · Genome Research · doi:10.1101/gr.093443.109 · Cited by 63
Copy number variant detection in inbred strains from short read sequence data
Simpson, J. T., McIntyre, R. E., Adams, D. J., & Durbin, R. M. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp693 · Cited by 51
Self-citationNelson, T. M., Munger, S. D., & Boughter, J. D. (2005) · BMC Genetics · doi:10.1186/1471-2156-6-32 · Cited by 35
Elusive Copy Number Variation in the Mouse Genome
Agam, A., Yalcin, B., Bhomra, A., Cubin, M., Webber, C., Holmes, C. C., Flint, J., & Mott, R. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012839 · Cited by 28
Self-citationMutations in Sterol O-Acyltransferase 1 (Soat1) Result in Hair Interior Defects in AKR/J Mice
Wu, B., Potter, C. S., Silva, K. A., Liang, Y., Reinholdt, L. G., Alley, L. M., Rowe, L. B., Roopenian, D. C., Awgulewitsch, A., & Sundberg, J. P. (2010) · Journal of Investigative Dermatology · doi:10.1038/jid.2010.168 · Cited by 28
Taylor, K. J., Rolfe, M., Reynolds, N. L., Kilanowski, F. M., Pathania, U., Clarke, D. J., Yang, D., Oppenheim, J. J., Samuel, K., Howie, S., et al. (2009) · European Journal of Immunology · doi:10.1002/eji.200838566 · Cited by 23
Persson, K., Heby, O., & Berger, F. G. (1999) · Mammalian Genome · doi:10.1007/s003359901092 · Cited by 12
Cited by
Sorted by citations
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-citationEndogenous viruses: insights into viral evolution and impact on host biology
Feschotte, C., & Gilbert, C. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3199 · Cited by 918
Phenotypic impact of genomic structural variation: insights from and for human disease
Weischenfeldt, J., Symmons, O., Spitz, F., & Korbel, J. O. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3373 · Cited by 674
Dynamic landscape and regulation of RNA editing in mammals
Tan, M. H., Li, Q., Shanmugam, R., Piskol, R., Kohler, J. N., Young, A. N., Liu, K. I., Zhang, R., Ramaswami, G., Ariyoshi, K., et al. (2017) · Nature · doi:10.1038/nature24041 · Cited by 620
Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations
Zhang, Y., McCord, R. P., Ho, Y.-J., Lajoie, B. R., Hildebrand, D. G., Simon, A. C., Becker, M. S., Alt, F. W., & Dekker, J. (2012) · Cell · doi:10.1016/j.cell.2012.02.002 · Cited by 572
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
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 ›
Are you an author, or do you see a problem with this page? Request a review
