A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains.

Michelle M Simon, Simon Greenaway, Jacqueline K White, Helmut Fuchs, Valérie Gailus-Durner, Tania Sorg, Kim Wong, Elodie Bedu, Elizabeth Cartwright, Romain Dacquin, Sophia Djebali, Jeanne Estabel, Jochen Graw, Neil J Ingham, Ian J Jackson, Andreas Lengeling, Silvia Mandillo, Jacqueline Marvel, Hamid Meziane, Frédéric PreitnerOliver Puk, Michel Roux, David J Adams, Sarah Atkins, Abdel Ayadi, Lore Becker, Andrew Blake, Debra Brooker, Heather Cater, Marie-France Champy, Roy Combe, Petr Danecek, Armida di Fenza, Hilary Gates, Anna-Karin Gerdin, Elisabetta Golini, John M Hancock, Wolfgang Hans, Sabine M Hölter, Tertius Hough, Pierre Jurdic, Thomas M Keane, Hugh Morgan, Werner Muller, Frauke Neff, George Nicholson, Bastian Pasche, Laura-Anne Roberson, Jan Rozman, Mark Sanderson, Luis Santos, Mohammed Selloum, Carl Shannon, Anne Southwell, Glauco P Tocchini-Valentini, Valerie E Vancollie, Sara Wells, Henrik Westerberg, Wolfgang Wurst, Min Zi, Binnaz Yalcin, Ramiro Ramirez-Solis, Karen P Steel, Ann-Marie Mallon, Martin Hrab 283 de Angelis, Yann Herault, Steve Dm Brown

Research output: Contribution to journalArticlepeer-review


BACKGROUND: The mouse inbred line C57BL/6J is widely used in mouse genetics and its genome has been incorporated into many genetic reference populations. More recently large initiatives such as The International Knockout Mouse Consortium (IKMC) are using the C57BL/6N mouse strain to generate null alleles for all mouse genes. Hence both strains are now widely used in mouse genetics studies. Here we perform a comprehensive genomic and phenotypic analysis of the two strains to identify differences that may influence their underlying genetic mechanisms. RESULTS: We undertake genome sequence comparisons of C57BL/6J and C57BL/6N to identify SNPs, indels and structural variants, with a focus on identifying all coding variants. We annotate 34 SNPs and 2 indels that distinguish C57BL/6J and C57BL/6N coding sequences, as well as 15 structural variants that overlap a gene. In parallel we assess the comparative phenotypes of the two inbred lines utilizing the EMPReSSslim phenotyping pipeline, a broad based assessment encompassing diverse biological systems. We perform additional secondary phenotyping assessments to explore other phenotype domains and to elaborate phenotype differences identified in the primary assessment. We uncover significant phenotypic differences between the two lines, replicated across multiple centers, in a number of physiological, biochemical and behavioral systems. CONCLUSIONS: Comparison of C57BL/6J and C57BL/6N demonstrates a range of phenotypic differences that have the potential to impact upon penetrance and expressivity of mutational effects in these strains. Moreover, the sequence variants we identify provide a set of candidate genes for the phenotypic differences observed between the two strains.
Original languageEnglish
JournalGenome biology
Issue number7
Publication statusPublished - 31 Jul 2013


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