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

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 access

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

Open this paper in CoChat — free account

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.

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

Crossref · 10.1038/nature10432

Cites

31 of 31 references verified0 citation errors · 0 not checkable

Statistics

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
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
22q11.21 Deletion Syndromes: A Review of Proximal, Central, and Distal Deletions and Their Associated Features
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-citation
BreakDancer: 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

Flagged first, then by citations

Show all 31 references

Sorted by citations

Items 101–200 of 305

Association studies in outbred mice in a new era of full-genome sequencing
Yalcin, B., & Flint, J. (2012) · Mammalian Genome · doi:10.1007/s00335-012-9409-z · Cited by 33
Self-citation
Dissecting Quantitative Traits in Mice
Mott, R., & Flint, J. (2013) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091212-153419 · Cited by 34
Self-citation
Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs
Zhao, P., Li, J., Kang, H., Wang, H., Fan, Z., Yin, Z., Wang, J., Zhang, Q., Wang, Z., & Liu, J. (2016) · Scientific Reports · doi:10.1038/srep18501 · Cited by 32
Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer
Perelli, L., Carbone, F., Zhang, L., Huang, J. K.-L., Le, C. N., Khan, H., Citron, F., Poggetto, E. D., Gutschner, T., Tomihara, H., et al. (2023) · Nature Cancer · doi:10.1038/s43018-023-00584-1 · Cited by 33
After GWAS: mice to the rescue?
Ermann, J., & Glimcher, L. H. (2012) · Current Opinion in Immunology · doi:10.1016/j.coi.2012.09.005 · Cited by 37
Association study and expression analysis of CYP4A11 gene copy number variation in Chinese cattle
Yang, M., Jing-qiao, L., Zhang, L., Li, M., Zhou, Y., Lan, X., Lei, C., & Chen, H. (2017) · Scientific Reports · doi:10.1038/srep46599 · Cited by 32
Chromosome substitution strains: gene discovery, functional analysis, and systems studies
Nadeau, J. H., Forejt, J., Takada, T., & Shiroishi, T. (2012) · Mammalian Genome · doi:10.1007/s00335-012-9426-y · Cited by 33
C57BL/6 substrain differences in inflammatory and neuropathic nociception and genetic mapping of a major quantitative trait locus underlying acute thermal nociception
Bryant, C. D., Bağdaş, D., Goldberg, L. R., Khalefa, T., Reed, E. R., Kirkpatrick, S. L., Kelliher, J. C., Chen, M. M., Johnson, W. E., Mulligan, M. K., et al. (2019) · Molecular Pain · doi:10.1177/1744806918825046 · Cited by 30
Severe ocular phenotypes in Rbp4-deficient mice in the C57BL/6 genetic background
Shen, J., Shi, D., Suzuki, T., Xia, Z., Zhang, H., Araki, K., Wakana, S., Takeda, N., Yamamura, K., Jin, S., et al. (2016) · Laboratory Investigation · doi:10.1038/labinvest.2016.39 · Cited by 31
PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice
Maclary, E. T., Hinten, M., Harris, C. E., Sethuraman, S., Gayen, S., & Kalantry, S. (2017) · Genome biology · doi:10.1186/s13059-017-1211-5 · Cited by 29
Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides
Nikolskiy, I., Conrad, D. F., Chun, S., Fay, J. C., Cheverud, J. M., & Lawson, H. A. (2015) · BMC Genomics · doi:10.1186/s12864-015-1592-3 · Cited by 27
SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains
Mortazavi, M., Ren, Y., Saini, S., Antaki, D., Pierre, C. L. S., Williams, A. E., Sohni, A., Wilkinson, M., Gymrek, M., Sebat, J. L., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100102 · Cited by 28
Genome‐ w ide patterns of large‐ s ize presence/ a bsence variants in sorghum
Zhang, L., Luo, H., Liu, Z., Zhao, Y., Luo, J., Hao, D., & Jing, H. (2013) · Journal of Integrative Plant Biology · doi:10.1111/jipb.12121 · Cited by 29
Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle
Uddin, M. M., Guldbrandtsen, B., Iso‐Touru, T., Vilkki, J., de Koning, D., Boichard, D., Lund, M. S., & Sahana, G. (2017) · DNA Research · doi:10.1093/dnares/dsx037 · Cited by 32
Diversity Outbred: A New Generation of Mouse Model
Schmidt, C. W. (2015) · Environmental Health Perspectives · doi:10.1289/ehp.123-a64 · Cited by 28
Natural Genetic Variation of Integrin Alpha L (Itgal) Modulates Ischemic Brain Injury in Stroke
Keum, S., Lee, H. K., Chu, P., Kan, M. J., Huang, M.-N., Gallione, C. J., Gunn, M. D., Lo, D. C., & Marchuk, D. A. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003807 · Cited by 26
Analysis of Structural Variants Reveal Novel Selective Regions in the Genome of Meishan Pigs by Whole Genome Sequencing
Du, H., Zheng, X., Zhao, Q., Hu, Z., Wang, H., Zhou, L., & Liu, J. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.550676 · Cited by 26
Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas
Griffith, O. L., Chan, S. R., Griffith, M., Krysiak, K., Skidmore, Z. L., Hundal, J., Allen, J. A., Arthur, C. D., Runci, D., Bugatti, M., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.08.076 · Cited by 27
An improved approach to mate-paired library preparation for Illumina sequencing
Park, N., Shirley, L. M., Gu, Y., Keane, T., Swerdlow, H., & Quail, M. (2013) · Methods in Next Generation Sequencing · doi:10.2478/mngs-2013-0001 · Cited by 25
Self-citation
A comprehensive benchmarking of WGS-based deletion structural variant callers
Sarwal, V., Niehus, S., Ayyala, R., Kim, M., Sarkar, A. P., Chang, S., Lu, A., Rajkumar, N., Darci-Maher, N., Littman, R., et al. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac221 · Cited by 28
Adaptive potential of genomic structural variation in human and mammalian evolution
Radke, D. W., & Lee, C. (2015) · Briefings in Functional Genomics · doi:10.1093/bfgp/elv019 · Cited by 23
Reduced Complexity Cross Design for Behavioral Genetics
Bryant, C. D., Ferris, M. T., De Villena, F. P. M., Damaj, M. I., Kumar, V., & Mulligan, M. K. (2018) · Molecular-Genetic and Statistical Techniques for Behavioral and Neural Research · doi:10.1016/b978-0-12-804078-2.00008-8 · Cited by 24
C57BL/6 Substrain Differences in Pharmacological Effects after Acute and Repeated Nicotine Administration
Akinola, L. S., Mckiver, B. D., Toma, W. B., Zhu, A. Z. X., Tyndale, R. F., Kumar, V., & Damaj, M. I. (2019) · Brain Sciences · doi:10.3390/brainsci9100244 · Cited by 23
Permissive and restricted virus infection of murine embryonic stem cells
Wash, R., Calabressi, S., Franz, S., Griffiths, S. J., Goulding, D., Tan, E., Wise, H. M., Digard, P., Haas, J., Efstathiou, S., et al. (2012) · Journal of General Virology · doi:10.1099/vir.0.043406-0 · Cited by 24
Identification of structural variation in mouse genomes
Keane, T., Wong, K., Adams, D. J., Flint, J., Reymond, A., & Yalcin, B. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00192 · Cited by 24
Self-citation
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) · BMC Genomics · doi:10.1186/s12864-023-09197-5 · Cited by 23
Identification of microRNAs associated with allergic airway disease using a genetically diverse mouse population
Rutledge, H. R., Baran‐Gale, J., de Villena, F. P., Chesler, E. J., Churchill, G. A., Sethupathy, P., & Kelada, S. N. P. (2015) · BMC Genomics · doi:10.1186/s12864-015-1732-9 · Cited by 23
QTL Analysis of Dietary Obesity in C57BL/6byj X 129P3/J F2 Mice: Diet- and Sex-Dependent Effects
Lin, C., Theodorides, M. L., McDaniel, A. H., Tordoff, M. G., Zhang, Q., Li, X., Bosak, N. P., Bachmanov, A. A., & Reed, D. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068776 · Cited by 23
Identification of a QTL inMus musculusfor Alcohol Preference, Withdrawal, andAp3m2Expression Using Integrative Functional Genomics and Precision Genetics
Bubier, J. A., Jay, J. J., Baker, C. L., Bergeson, S. E., Ohno, H., Metten, P., Crabbe, J. C., & Chesler, E. J. (2014) · Genetics · doi:10.1534/genetics.114.166165 · Cited by 22
Genetic Architectures of Quantitative Variation in RNA Editing Pathways
Gu, T., Gatti, D. M., Srivastava, A., Snyder, E. M., Raghupathy, N., Šimeček, P., Svenson, K. L., Dotú, I., Chuang, J. H., Keller, M. P., et al. (2015) · Genetics · doi:10.1534/genetics.115.179481 · Cited by 24
Evidence for Local Regulatory Control of Escape from Imprinted X Chromosome Inactivation
Mugford, J. W., Starmer, J., Williams, R. L., Calabrese, J. M., Mieczkowski, P. A., Yee, D., & Magnuson, T. (2014) · Genetics · doi:10.1534/genetics.114.162800 · Cited by 22
Selective Inhibition of PDE4B Reduces Binge Drinking in Two C57BL/6 Substrains
Chavez, C. L. J., Bryant, C. D., Munn‐Chernoff, M. A., & Szumlinski, K. K. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115443 · Cited by 22
Long-read-based single sperm genome sequencing for chromosome-wide haplotype phasing of both SNPs and SVs
Xie, H., Li, W., Guo, Y., Su, X., Chen, K., Wen, L., & Tang, F. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad532 · Cited by 21
A collective diabetes cross in combination with a computational framework to dissect the genetics of human obesity and Type 2 diabetes
Vogel, H., Kamitz, A., Hallahan, N., Lebek, S., Schallschmidt, T., Jonas, W., Jähnert, M., Gottmann, P., Zellner, L., Kanzleiter, T., et al. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy217 · Cited by 21
Identification of fibronectin 1 as a candidate genetic modifier in a Col4a1 mutant mouse model of Gould syndrome
Mao, M., Popli, T. A., Jeanne, M., Hoff, K., Sen, Ś., & Gould, D. B. (2021) · Disease Models & Mechanisms · doi:10.1242/dmm.048231 · Cited by 20
PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction
Shen, X., Liu, Z., Mocoeur, A., Xia, Y., & Jing, H. (2015) · Theoretical and Applied Genetics · doi:10.1007/s00122-015-2458-4 · Cited by 21
CNV instability associated with DNA replication dynamics: evidence for replicative mechanisms in CNV mutagenesis
Chen, L., Zhou, W., Zhang, C., Lupski, J. R., Li, J., & Zhang, F. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu572 · Cited by 19
Heritable L1 Retrotransposition Events During Development: Understanding Their Origins
Richardson, S. R., & Faulkner, G. J. (2018) · BioEssays · doi:10.1002/bies.201700189 · Cited by 20
Alcohol Sensitivity as an Endophenotype of Alcohol Use Disorder: Exploring Its Translational Utility between Rodents and Humans
Parker, C. C., Lusk, R., & Saba, L. M. (2020) · Brain Sciences · doi:10.3390/brainsci10100725 · Cited by 20
Copy number variation underlies complex phenotypes in domestic dog breeds and other canidsPreprint
Armero, A. S., Davis, B. W., Povolotskaya, I., Morcillo-Suárez, C., Plassais, J., Juan, D., Ostrander, E. A., & Marquès‐Bonet, T. (2021) · Genome Research · doi:10.1101/gr.266049.120 · Cited by 21
Recovery of novel association loci in Arabidopsis thaliana and Drosophila melanogaster through leveraging INDELs association and integrated burden test
Song, B., Mott, R., & Gan, X. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007699 · Cited by 22
Self-citation
Mouse protein coding diversity: What’s left to discover?
Lilue, J., Shivalikanjli, A., Adams, D. J., & Keane, T. M. (2019) · PLOS Genetics · doi:10.1371/journal.pgen.1008446 · Cited by 19
Self-citation
Phenotypic instability between the near isogenic substrains BALB/cJ and BALB/cByJ
Sittig, L. J., Jeong, C., Tixier, E. N., Davis, J. R., Barrios-Camacho, C. M., & Palmer, A. A. (2014) · Mammalian Genome · doi:10.1007/s00335-014-9531-1 · Cited by 19
Causes and Consequences of Chromatin Variation between Inbred Mice
Hosseini, M., Goodstadt, L., Hughes, J. R., Kowalczyk, M. S., Gobbi, M. D., Otto, G., Copley, R. R., Mott, R., Higgs, D. R., & Flint, J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003570 · Cited by 19
Self-citation
Functional Genomic Assessment of Phosgene-Induced Acute Lung Injury in Mice
Leikauf, G. D., Concel, V. J., Bein, K., Liu, P., Berndt, A., Martin, T. M., Ganguly, K., Jang, A., Brant, K. A., Dopico, R. A., et al. (2013) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2012-0337oc · Cited by 19
Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits
Imprialou, M., Kahles, A., Steffen, J. G., Osborne, E. J., Gan, X., Lempe, J., Bhomra, A., Belfield, E. J., Visscher, A. M., Greenhalgh, R., et al. (2017) · Genetics · doi:10.1534/genetics.116.192823 · Cited by 18
Self-citation
Tissue-Specific Trans Regulation of the Mouse Epigenome
Baker, C. L., Walker, M., Arat, S., Ananda, G., Petkova, P., Powers, N. R., Tian, H., Spruce, C. A., Ji, B., Rausch, D. M., et al. (2018) · Genetics · doi:10.1534/genetics.118.301697 · Cited by 17
Generating CRISPR/Cas9 Mediated Monoallelic Deletions to Study Enhancer Function in Mouse Embryonic Stem Cells
Moorthy, S. D., & Mitchell, J. A. (2016) · Journal of Visualized Experiments · doi:10.3791/53552 · Cited by 24
Whole-Genome Sequences of DA and F344 Rats with Different Susceptibilities to Arthritis, Autoimmunity, Inflammation and Cancer
Guo, X., Brenner, M., Zhang, X., Laragione, T., Tai, S., Li, Y., Bu, J., Yin, Y., Shah, A. A., Kwan, K., et al. (2013) · Genetics · doi:10.1534/genetics.113.153049 · Cited by 19
Genome-wide copy number profiling using high-density SNP array in chickens
Yi, G., Qu, L., Chen, S., Xu, G., & Yang, N. (2015) · Animal Genetics · doi:10.1111/age.12267 · Cited by 18
Identifying genes for neurobehavioural traits in rodents: progress and pitfalls
Baud, A., & Flint, J. (2017) · Disease Models & Mechanisms · doi:10.1242/dmm.027789 · Cited by 18
Genetic‐Genomic Replication to Identify Candidate Mouse Atherosclerosis Modifier Genes
Hsu, J., & Smith, J. D. (2013) · Journal of the American Heart Association · doi:10.1161/jaha.112.005421 · Cited by 19
Passenger mutations and aberrant gene expression in congenic tissue plasminogen activator‐deficient mouse strains
Szabo, R., Samson, A. L., Lawrence, D. A., Medcalf, R. L., & Bugge, T. H. (2016) · Journal of Thrombosis and Haemostasis · doi:10.1111/jth.13338 · Cited by 18
Genetic Control of Lyme Arthritis by Borrelia burgdorferi Arthritis–Associated Locus 1 Is Dependent on Localized Differential Production of IFN-β and Requires Upregulation of Myostatin
Paquette, J. K., Ma, Y., Fisher, C., Li, J., Lee, S. B., Zachary, J. F., Kim, Y. S., Teuscher, C., & Weis, J. J. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1701011 · Cited by 16
Allele-specific copy-number discovery from whole-genome and whole-exome sequencing
Wang, W., Wang, W. W., Sun, W., Crowley, J. J., & Szatkiewicz, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv319 · Cited by 17
Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC
Wu, H., Li, X., Jian, F., Yisimayi, A., Zheng, Y., Tan, L., Xing, D., & Xie, X. S. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2206450119 · Cited by 14
Isometric skeletal muscle contractile properties in common strains of male laboratory mice
Minchew, E. C., Williamson, N. C., Readyoff, A. T., McClung, J. M., & Spangenburg, E. E. (2022) · Frontiers in Physiology · doi:10.3389/fphys.2022.937132 · Cited by 16
Two Novel Candidate Genes for Insulin Secretion Identified by Comparative Genomics of Multiple Backcross Mouse Populations
Schallschmidt, T., Lebek, S., Altenhofen, D., Damen, M., Schulte, Y., Knebel, B., Herwig, R., Rasche, A., Stermann, T., Kamitz, A., et al. (2018) · Genetics · doi:10.1534/genetics.118.301578 · Cited by 16
The abiding relevance of mouse models of rare mutations to psychiatric neuroscience and therapeutics
Gogos, J. A., Crabtree, G. W., & Diamantopoulou, A. (2019) · Schizophrenia Research · doi:10.1016/j.schres.2019.03.018 · Cited by 15
Genetic Evidence for Differential Regulation of Corneal Epithelial and Stromal Thickness
Koehn, D., Meyer, K. J., & Anderson, M. G. (2015) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.15-17179 · Cited by 15
Inosine RNA modifications are enriched at the codon wobble position in mouse oocytes and eggs†
Brachova, P., Alvarez, N. S., Hong, X., Gunewardena, S., Vincent, K. A., Latham, K. E., & Christenson, L. K. (2019) · Biology of Reproduction · doi:10.1093/biolre/ioz130 · Cited by 18
Genetic control of the pluripotency epigenome determines differentiation bias in mouse embryonic stem cells
Byers, C., Spruce, C. A., Fortin, H. J., Hartig, E. I., Czechanski, A., Munger, S. C., Reinholdt, L. G., Skelly, D. A., & Baker, C. L. (2021) · The EMBO Journal · doi:10.15252/embj.2021109445 · Cited by 13
Complex Trait Analyses of the Collaborative Cross: Tools and Databases
Ram, R., & Morahan, G. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6427-7_5 · Cited by 15
Fc-Linked IgG N-Glycosylation in FcγR Knock-Out Mice
Zaytseva, O. O., Seeling, M., Krištić, J., Lauc, G., Pezer, M., & Nimmerjahn, F. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00067 · Cited by 14
Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicasePreprint
Yamanishi, A., Yusa, K., Horie, K., Tokunaga, M., Kusano, K., Kokubu, C., & Takeda, J. (2013) · Genome Research · doi:10.1101/gr.152744.112 · Cited by 14
Selection shapes the landscape of functional variation in wild house mice
Lawal, R. A., Arora, U. P., & Dumont, B. L. (2021) · BMC Biology · doi:10.1186/s12915-021-01165-3 · Cited by 18
Spontaneous 8bp Deletion in Nbeal2 Recapitulates the Gray Platelet Syndrome in Mice
Tomberg, K., Khoriaty, R. N., Westrick, R. J., Fairfield, H. E., Reinholdt, L. G., Brodsky, G. L., Davizon‐Castillo, P., Ginsburg, D., & Paola, J. D. (2016) · PLoS ONE · doi:10.1371/journal.pone.0150852 · Cited by 13
The role of Sp140 revealed in IgE and mast cell responses in Collaborative Cross mice
Matsushita, K., Li, X., Nakamura, Y., Dong, D., Mukai, K., Tsai, M. M., Montgomery, S. B., & Galli, S. J. (2021) · JCI Insight · doi:10.1172/jci.insight.146572 · Cited by 13
Mild inborn errors of metabolism in commonly used inbred mouse strains
Leandro, J., Violante, S. N., Argmann, C., Hagen, J., Dodatko, T., Bender, A. S., Zhang, W., Williams, E. G., Bachmann, A., Auwerx, J. H., et al. (2019) · Molecular Genetics and Metabolism · doi:10.1016/j.ymgme.2019.01.021 · Cited by 14
High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration
Hong, R., Lin, B., Lu, X., Lai, L.-T., Chen, X., Sanyal, A., Ng, H., Zhang, K., & Zhang, L. (2017) · Scientific Reports · doi:10.1038/srep45460 · Cited by 11
Genetic determinants of ammonia-induced acute lung injury in mice
Bein, K., Ganguly, K., Martin, T. M., Concel, V. J., Brant, K. A., Di, Y. P., Upadhyay, S., Fabisiak, J. P., Vuga, L. J., Kaminski, N., et al. (2020) · American Journal of Physiology-Lung Cellular and Molecular Physiology · doi:10.1152/ajplung.00276.2020 · Cited by 12
Loss of Cnot6l Impairs Inosine RNA Modifications in Mouse Oocytes
Brachova, P., Alvarez, N. S., & Christenson, L. K. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22031191 · Cited by 12
A large QTL for fear and anxiety mapped using an F2 cross can be dissected into multiple smaller QTLs
Parker, C. C., Sokoloff, G., Leung, E., Kirkpatrick, S. L., & Palmer, A. A. (2013) · Genes Brain & Behavior · doi:10.1111/gbb.12064 · Cited by 12
Ectopic expression of the Stabilin2 gene triggered by an intracisternal A particle (IAP) element in DBA/2J strain of mice
Maeda-Smithies, N., Hiller, S., Dong, S., Kim, H., Bennett, B. J., & Kayashima, Y. (2020) · Mammalian Genome · doi:10.1007/s00335-019-09824-1 · Cited by 12
Detecting differential copy number variation between groups of samplesPreprint
Lowe, C. B., Sanchez‐Luege, N., Howes, T. R., Brady, S. D., Daugherty, R. R., Jones, F. C., Bell, M. A., & Kingsley, D. M. (2017) · Genome Research · doi:10.1101/gr.206938.116 · Cited by 12
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) · Genome biology · doi:10.1186/s13059-024-03317-4 · Cited by 10
Structural evolution of CatSper1 in rodents is influenced by sperm competition, with effects on sperm swimming velocity
Vicens, A., Tourmente, M., & Roldán, E. R. S. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-106 · Cited by 11
Plethysmography Phenotype QTL in Mice Before and After Allergen Sensitization and Challenge
Kelada, S. N. P. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.032912 · Cited by 11
Evidence for dispensability of protein kinase R in host control of tuberculosis
Mundhra, S., Bryk, R., Hawryluk, N. A., Zhang, T., Jiang, X., & Nathan, C. (2018) · European Journal of Immunology · doi:10.1002/eji.201747180 · Cited by 11
Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states
Dirks, R. A. M., van Mierlo, G., Kerstens, H. H. D., Bernardo, A. S., Kobolák, J., Bock, I., Maruotti, J., Pedersen, R. A., Dinnyés, A., Huynen, M. A., et al. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0259-8 · Cited by 12
Multi-hazard susceptibility mapping in the Salt Lake watershed
Pourhashemi, S., Asadi, M. A. Z., & Boroughani, M. (2024) · Environmental Challenges · doi:10.1016/j.envc.2024.101079 · Cited by 10
Fine Mapping and Candidate Gene Search of Quantitative Trait Loci for Growth and Obesity Using Mouse Intersubspecific Subcongenic Intercrosses and Exome Sequencing
Ishikawa, A., & Okuno, S.-I. (2014) · PLoS ONE · doi:10.1371/journal.pone.0113233 · Cited by 10
Whole Genome Sequencing of the Mutamouse Model Reveals Strain- and Colony-Level Variation, and Genomic Features of the Transgene Integration Site
Meier, M. J., Beal, M. A., Schoenrock, A., Yauk, C. L., & Marchetti, F. (2019) · Scientific Reports · doi:10.1038/s41598-019-50302-0 · Cited by 10
Chromosome-Level Genome Assembly of a Fragrant Japonica Rice Cultivar ‘Changxianggeng 1813’ Provides Insights into Genomic Variations between Fragrant and Non-Fragrant Japonica Rice
Lu, R., Liu, J., Wang, X., Song, Z., Xiangdong, J., Li, N., Ma, G., & Sun, X. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23179705 · Cited by 11
Copy number variants and selective sweeps in natural populations of the house mouse (Mus musculus domesticus)
Bryk, J., & Tautz, D. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00153 · Cited by 11
Dissecting the Genetic Architecture of Cystatin C in Diversity Outbred Mice
Huda, M. N., VerHague, M., Albright, J., Smallwood, T., Bell, T. A., Que, E., Miller, D. R., Roshanravan, B., Allayee, H., Manuel de Villena, F. P., et al. (2020) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.120.401275 · Cited by 10
Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional lociPreprint
Lilue, J., Doran, A., Fiddes, I. T., Abrudan, M. I., Armstrong, J. C., Bennett, R., Chow, W., Collins, J., Collins, S. C., Czechanski, A., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/235838 · Cited by 10
Self-citation
Modulation of Sox10, HIF-1α, Survivin, and YAP by Minocycline in the Treatment of Neurodevelopmental Handicaps following Hypoxic Insult
Li, Q., Tsuneki, M., Krauthammer, M. O., Couture, R., Schwartz, M. L., & Madri, J. A. (2015) · American Journal Of Pathology · doi:10.1016/j.ajpath.2015.05.016 · Cited by 9
Modeling the Neurovascular Niche: Unbiased Transcriptome Analysis of the Murine Subventricular Zone in Response to Hypoxic Insult
Li, Q., Canosa, S., Flynn, K. M., Michaud, M., Krauthammer, M. O., & Madri, J. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0076265 · Cited by 9
An Interval of the Obesity QTL Nob3.38 within a QTL Hotspot on Chromosome 1 Modulates Behavioral Phenotypes
Vogel, H., Montag, D., Kanzleiter, T., Jonas, W., Matzke, D., Scherneck, S., Chadt, A., Töle, J., Kluge, R., Joost, H., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053025 · Cited by 9
Animal Models in Pharmacogenomics
Olson, E. D., & Graham, D. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-386882-4.00005-0 · Cited by 9
Genetic basis of thermal nociceptive sensitivity and brain weight in a BALB/c reduced complexity cross
Beierle, J. A., Yao, E. J., Goldstein, S. I., Scotellaro, J. L., Sena, K. D., Linnertz, C. A., Willits, A., Kader, L., Young, E. E., Peltz, G., et al. (2022) · Molecular Pain · doi:10.1177/17448069221079540 · Cited by 10
Cell numbers, cell ratios, and developmental plasticity in the rod pathway of the mouse retina
Keeley, P. W., Patel, S. S., & Reese, B. E. (2022) · Journal of Anatomy · doi:10.1111/joa.13653 · Cited by 8
Cancer gene discovery in the mouse
McIntyre, R. E., van der Weyden, L., & Adams, D. J. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.12.003 · Cited by 9
Self-citation
Nxf1 Natural Variant E610G Is a Semi-dominant Suppressor of IAP-Induced RNA Processing Defects
Concepcion, D., Ross, K. D., Hutt, K. R., Yeo, G. W.-M., & Hamilton, B. A. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005123 · Cited by 9
Mapping DNA methylation to cardiac pathologies induced by beta-adrenergic stimulation in a large panel of mice
Lahue, C., Wong, E., Dalal, A., Tan, W. L. W., Ren, S. V., Foo, R., Wang, Y., & Rau, C. D. (2025) · Epigenetics · doi:10.1080/15592294.2025.2524411 · Cited by 8
Gv1, a Zinc Finger Gene Controlling Endogenous MLV Expression
Young, G. R., Ferron, A., Panova, V., Eksmond, U., Oliver, P. L., Kassiotis, G., & Stoye, J. P. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab039 · Cited by 8
SNP Formation Bias in the Murine Genome Provides Evidence for Parallel Evolution
Plyler, Z. E., Hill, A. E., McAtee, C. W., Cui, X., Moseley, L. A., & Sorscher, E. J. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv150 · Cited by 8
Characterizing Serpinb2 as a Modulator of TCDD-Induced Suppression of the B Cell
Dornbos, P., Warren, M., Crawford, R. B., Kaminski, N. E., Threadgill, D. W., & LaPres, J. J. (2018) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.8b00225 · Cited by 8
Exploring the Role of Chemokine Receptor 6 (Ccr6) in the BXD Mouse Model of Gulf War Illness
Gao, J. L., Xu, F., Starlard‐Davenport, A., Miller, D. B., O'Callaghan, J. P., Jones, B. C., & Lu, L. (2020) · Frontiers in Neuroscience · doi:10.3389/fnins.2020.00818 · Cited by 8

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

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

Sequence-based characterization of structural variation in the mouse genome

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks