2.50
Hdl Handle:
http://hdl.handle.net/10033/620694
Title:
A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains
Authors:
Simon, Michelle M; Greenaway, Simon; White, Jacqueline K; Fuchs, Helmut; Gailus-Durner, Valérie; Wells, Sara; Sorg, Tania; Wong, Kim; Bedu, Elodie; Cartwright, Elizabeth J; Dacquin, Romain; Djebali, Sophia; Estabel, Jeanne; Graw, Jochen; Ingham, Neil J; Jackson, Ian J; Lengeling, Andreas; Mandillo, Silvia; Marvel, Jacqueline; Meziane, Hamid; Preitner, Frédéric; Puk, Oliver; Roux, Michel; Adams, David J; Atkins, Sarah; Ayadi, Abdel; Becker, Lore; Blake, Andrew; Brooker, Debra; Cater, Heather; Champy, Marie-France; Combe, Roy; Danecek, Petr; di Fenza, Armida; Gates, Hilary; Gerdin, Anna-Karin; Golini, Elisabetta; Hancock, John M; Hans, Wolfgang; Hölter, Sabine M; Hough, Tertius; Jurdic, Pierre; Keane, Thomas M; Morgan, Hugh; Müller, Werner; Neff, Frauke; Nicholson, George; Pasche, Bastian; Roberson, Laura-Anne; Rozman, Jan; Sanderson, Mark; Santos, Luis; Selloum, Mohammed; Shannon, Carl; Southwell, Anne; Tocchini-Valentini, Glauco P; Vancollie, Valerie E; Westerberg, Henrik; Wurst, Wolfgang; Zi, Min; Yalcin, Binnaz; Ramirez-Solis, Ramiro; Steel, Karen P; Mallon, Ann-Marie; Hrabě de Angelis, Martin; Herault, Yann; Brown, Steve D
Abstract:
Abstract 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.
Citation:
Genome Biology. 2013 Jul 31;14(7):R82
Issue Date:
31-Jul-2013
URI:
http://dx.doi.org/10.1186/gb-2013-14-7-r82; http://hdl.handle.net/10033/620694
Type:
Journal Article
Appears in Collections:
publications of the department infection genetics (INFG)

Full metadata record

DC FieldValue Language
dc.contributor.authorSimon, Michelle Men
dc.contributor.authorGreenaway, Simonen
dc.contributor.authorWhite, Jacqueline Ken
dc.contributor.authorFuchs, Helmuten
dc.contributor.authorGailus-Durner, Valérieen
dc.contributor.authorWells, Saraen
dc.contributor.authorSorg, Taniaen
dc.contributor.authorWong, Kimen
dc.contributor.authorBedu, Elodieen
dc.contributor.authorCartwright, Elizabeth Jen
dc.contributor.authorDacquin, Romainen
dc.contributor.authorDjebali, Sophiaen
dc.contributor.authorEstabel, Jeanneen
dc.contributor.authorGraw, Jochenen
dc.contributor.authorIngham, Neil Jen
dc.contributor.authorJackson, Ian Jen
dc.contributor.authorLengeling, Andreasen
dc.contributor.authorMandillo, Silviaen
dc.contributor.authorMarvel, Jacquelineen
dc.contributor.authorMeziane, Hamiden
dc.contributor.authorPreitner, Frédéricen
dc.contributor.authorPuk, Oliveren
dc.contributor.authorRoux, Michelen
dc.contributor.authorAdams, David Jen
dc.contributor.authorAtkins, Sarahen
dc.contributor.authorAyadi, Abdelen
dc.contributor.authorBecker, Loreen
dc.contributor.authorBlake, Andrewen
dc.contributor.authorBrooker, Debraen
dc.contributor.authorCater, Heatheren
dc.contributor.authorChampy, Marie-Franceen
dc.contributor.authorCombe, Royen
dc.contributor.authorDanecek, Petren
dc.contributor.authordi Fenza, Armidaen
dc.contributor.authorGates, Hilaryen
dc.contributor.authorGerdin, Anna-Karinen
dc.contributor.authorGolini, Elisabettaen
dc.contributor.authorHancock, John Men
dc.contributor.authorHans, Wolfgangen
dc.contributor.authorHölter, Sabine Men
dc.contributor.authorHough, Tertiusen
dc.contributor.authorJurdic, Pierreen
dc.contributor.authorKeane, Thomas Men
dc.contributor.authorMorgan, Hughen
dc.contributor.authorMüller, Werneren
dc.contributor.authorNeff, Fraukeen
dc.contributor.authorNicholson, Georgeen
dc.contributor.authorPasche, Bastianen
dc.contributor.authorRoberson, Laura-Anneen
dc.contributor.authorRozman, Janen
dc.contributor.authorSanderson, Marken
dc.contributor.authorSantos, Luisen
dc.contributor.authorSelloum, Mohammeden
dc.contributor.authorShannon, Carlen
dc.contributor.authorSouthwell, Anneen
dc.contributor.authorTocchini-Valentini, Glauco Pen
dc.contributor.authorVancollie, Valerie Een
dc.contributor.authorWesterberg, Henriken
dc.contributor.authorWurst, Wolfgangen
dc.contributor.authorZi, Minen
dc.contributor.authorYalcin, Binnazen
dc.contributor.authorRamirez-Solis, Ramiroen
dc.contributor.authorSteel, Karen Pen
dc.contributor.authorMallon, Ann-Marieen
dc.contributor.authorHrabě de Angelis, Martinen
dc.contributor.authorHerault, Yannen
dc.contributor.authorBrown, Steve Den
dc.date.accessioned2017-01-13T09:46:41Z-
dc.date.available2017-01-13T09:46:41Z-
dc.date.issued2013-07-31en
dc.identifier.citationGenome Biology. 2013 Jul 31;14(7):R82en
dc.identifier.urihttp://dx.doi.org/10.1186/gb-2013-14-7-r82en
dc.identifier.urihttp://hdl.handle.net/10033/620694-
dc.description.abstractAbstract 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.en
dc.titleA comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strainsen
dc.typeJournal Articleen
dc.language.rfc3066enen
dc.rights.holderSimon et al.; licensee BioMed Central Ltd.en
dc.date.updated2015-09-04T08:31:22Zen
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