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Research: Clonal copy-number mosaicism in autoreactive T lymphocytes in diabetic NOD mice
- Maha Alriyami,
- Luc Marchand,
- Quan Li,
- Xiaoyu Du,
- Martin Olivier,
- and Constantin Polychronakos
Genome Res. December 2019 29: 1951-1961; Published in Advance November 6, 2019, doi:10.1101/gr.247882.118
...at the indicated percentages against 100% C57BL6/J as a reference. A known germline CNV between the two strains at Chr 11: 70,989,862–71,107,103 (region represented by colored lines below the charts) is significant even at 25%. (B) The intensity ratio of NOD copy losses is significantly lower than the baseline...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
..., followed by Tukey's HSD. Only significant P values (P-adj < 0.05) are shown.DiscussionSubstantial copy number variation in inbred mouse strains has been noted previously (Cutler et al. 2007; Egan et al. 2007; Graubert et al. 2007; Keane et al. 2014). Structural variations are known to accumulate during...
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Research: Copy number variation modifies expression time courses
- Evelyne Chaignat,
- Emilie Aït Yahya-Graison,
- Charlotte N. Henrichsen,
- Jacqueline Chrast,
- Frédéric Schütz,
- Sylvain Pradervand,
- and Alexandre Reymond
Genome Res. January 2011 21: 106-113; Published in Advance November 17, 2010, doi:10.1101/gr.112748.110
...expressed genes by their temporal patterns of expression and identified three clusters with strong support in each of the tissues (Supplemental Fig. S2). We then investigated whether the time courses registered for a given transcript in the three different mouse inbred strains (C57BL/6J, DBA/2J, and 129S2...
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LETTER: Significant gene content variation characterizes the genomes of inbred mouse strains
- Gene Cutler,
- Lisa A. Marshall,
- Ni Chin,
- Helene Baribault,
- and Paul D. Kassner
Genome Res. December 2007 17: 1743-1754; Published in Advance November 7, 2007, doi:10.1101/gr.6754607
...) Segmental duplications: An 'expanding' role in genomic instability and disease . Nat. Rev. Genet. 2 : 791 – 800 . ↵ Festing, M.F. ( 1998 ) Inbred strains of mice: C57BL ( Jackson Laboratories , Leicester, UK ) Mouse Genome Informatics . ↵ Feuk, L. , Carson, A.R. , Scherer, S.W. ( 2006 ) Structural variation...
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LETTER: Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
- Keiko Akagi,
- Jingfeng Li,
- Robert M. Stephens,
- Natalia Volfovsky,
- and David E. Symer
Genome Res. June 2008 18: 869-880; Published in Advance April 1, 2008, doi:10.1101/gr.075770.107
...are mostly unknown. Several mammalian s have been assembled, providing a framework for identifying structural variations. To identify variants between inbred mouse strains at a single nucleotide resolution, we aligned 26 million individual sequence traces from four laboratory mouse strains to the C57BL/6J...
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Resource: The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains
- Toyoyuki Takada,
- Toshinobu Ebata,
- Hideki Noguchi,
- Thomas M. Keane,
- David J. Adams,
- Takanori Narita,
- Tadasu Shin-I,
- Hironori Fujisawa,
- Atsushi Toyoda,
- Kuniya Abe,
- Yuichi Obata,
- Yoshiyuki Sakaki,
- Kazuo Moriwaki,
- Asao Fujiyama,
- Yuji Kohara,
- and Toshihiko Shiroishi
Genome Res. August 2013 23: 1329-1338; Published in Advance April 19, 2013, doi:10.1101/gr.156497.113
...the genomes of two M. m. molossinus –derived inbred strains, MSM/Ms and JF1/Ms. MSM/Ms originated from Japanese wild mice, and the ancestry of JF1/Ms was originally found in Europe and then transferred to Japan. We compared the characteristics of these sequences to those of the C57BL/6J reference sequence...
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REVIEW: Copy number variation: New insights in genome diversity
- Jennifer L. Freeman,
- George H. Perry,
- Lars Feuk,
- Richard Redon,
- Steven A. McCarroll,
- David M. Altshuler,
- Hiroyuki Aburatani,
- Keith W. Jones,
- Chris Tyler-Smith,
- Matthew E. Hurles,
- Nigel P. Carter,
- Stephen W. Scherer,
- and Charles Lee
Genome Res. August 2006 16: 949-961; Published in Advance June 29, 2006, doi:10.1101/gr.3677206
...). Li et al. (2004) used a minimal-tiled, whole- array platform containing ∼19,000 mouse BAC clones from the RPCI-23 library (derived from a C57BL/6J strain mouse) to interrogate the s of 15 commonly used inbred mouse strains. In total, the investigators identified 346 BAC clones that showed copy number...
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Resource: Analysis of copy number variations among diverse cattle breeds
- George E. Liu,
- Yali Hou,
- Bin Zhu,
- Maria Francesca Cardone,
- Lu Jiang,
- Angelo Cellamare,
- Apratim Mitra,
- Leeson J. Alexander,
- Luiz L. Coutinho,
- Maria Elena Dell'Aquila,
- Lou C. Gasbarre,
- Gianni Lacalandra,
- Robert W. Li,
- Lakshmi K. Matukumalli,
- Dan Nonneman,
- Luciana C. de A. Regitano,
- Tim P.L. Smith,
- Jiuzhou Song,
- Tad S. Sonstegard,
- Curt P. Van Tassell,
- Mario Ventura,
- Evan E. Eichler,
- Tara G. McDaneld,
- and John W. Keele
Genome Res. May 2010 20: 693-703; Published in Advance March 8, 2010, doi:10.1101/gr.105403.110
...Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR...
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RESOURCE: A Whole-Genome Mouse BAC Microarray With 1-Mb Resolution for Analysis of DNA Copy Number Changes by Array Comparative Genomic Hybridization
- Yeun-Jun Chung,
- Jos Jonkers,
- Hannah Kitson,
- Heike Fiegler,
- Sean Humphray,
- Carol Scott,
- Sarah Hunt,
- Yuejin Yu,
- Ichiko Nishijima,
- Arno Velds,
- Henne Holstege,
- Nigel Carter,
- and Allan Bradley
Genome Res. January 2004 14: 188-196; doi:10.1101/gr.1878804
...: In this window In a new window Figure 2 Detection of single-copy differences. ( A ) Normal vs. normal hybridization of spleen DNA from a C57BL/6J female. ( B ) Comparative genomic hybridization of normal C57BL/6J female DNA vs. normal C57BL/6J male DNA. Plotted are log2-transformed hybridization ratios against...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...the effect of ART on mutation accumulation in a single genetic background (C57BL/6J). Additional studies are needed to evaluate whether our findings are generalizable across mouse strains, including mouse models of reduced fertility or infertility. Finally, although our reliance on inbred mice from a single...

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