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

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• 作者：Michelle M Simon (1)
  Simon Greenaway (1)
  Jacqueline K White (2)
  Helmut Fuchs (3)
  Valérie Gailus-Durner (3)
  Sara Wells (1)
  Tania Sorg (6)
  Kim Wong (2)
  Elodie Bedu (6)
  Elizabeth J Cartwright (7)
  Romain Dacquin (9)
  Sophia Djebali (9)
  Jeanne Estabel (2)
  Jochen Graw (4)
  Neil J Ingham (2)
  Ian J Jackson (10)
  Andreas Lengeling (11)
  Silvia Mandillo (12)
  Jacqueline Marvel (9)
  Hamid Meziane (6)
  Frédéric Preitner (13)
  Oliver Puk (4)
  Michel Roux (6)
  David J Adams (2)
  Sarah Atkins (1)
  Abdel Ayadi (6)
  Lore Becker (3)
  Andrew Blake (1)
  Debra Brooker (1)
  Heather Cater (1)
  Marie-France Champy (6)
  Roy Combe (6)
  Petr Danecek (2)
  Armida di Fenza (1)
  Hilary Gates (1)
  Anna-Karin Gerdin (2)
  Elisabetta Golini (12)
  John M Hancock (1)
  Wolfgang Hans (3)
  Sabine M H?lter (3)
  Tertius Hough (1)
  Pierre Jurdic (9)
  Thomas M Keane (2)
  Hugh Morgan (1)
  Werner Müller (8)
  Frauke Neff (5)
  George Nicholson (1)
  Bastian Pasche (14)
  Laura-Anne Roberson (2)
  Jan Rozman (3)
  Mark Sanderson (2)
  Luis Santos (1)
  Mohammed Selloum (6)
  Carl Shannon (2)
  Anne Southwell (1)
  Glauco P Tocchini-Valentini (12)
  Valerie E Vancollie (2)
  Henrik Westerberg (1)
  Wolfgang Wurst (16) (17) (18) (4)
  Min Zi (7)
  Binnaz Yalcin (15) (6)
  Ramiro Ramirez-Solis (2)
  Karen P Steel (2)
  Ann-Marie Mallon (1)
  Martin Hrabě de Angelis (3)
  Yann Herault (6)
  Steve DM Brown (1)
  
• 关键词：Mouse inbred lines ; sequence variation ; mouse phenotyping ; gene knockout ; C57BL/6
• 刊名：Genome Biology
• 出版年：2013
• 出版时间：July 2013
• 年：2013
• 卷：14
• 期：7
• 全文大小：1,267 KB
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• 作者单位：Michelle M Simon (1)
  Simon Greenaway (1)
  Jacqueline K White (2)
  Helmut Fuchs (3)
  Valérie Gailus-Durner (3)
  Sara Wells (1)
  Tania Sorg (6)
  Kim Wong (2)
  Elodie Bedu (6)
  Elizabeth J Cartwright (7)
  Romain Dacquin (9)
  Sophia Djebali (9)
  Jeanne Estabel (2)
  Jochen Graw (4)
  Neil J Ingham (2)
  Ian J Jackson (10)
  Andreas Lengeling (11)
  Silvia Mandillo (12)
  Jacqueline Marvel (9)
  Hamid Meziane (6)
  Frédéric Preitner (13)
  Oliver Puk (4)
  Michel Roux (6)
  David J Adams (2)
  Sarah Atkins (1)
  Abdel Ayadi (6)
  Lore Becker (3)
  Andrew Blake (1)
  Debra Brooker (1)
  Heather Cater (1)
  Marie-France Champy (6)
  Roy Combe (6)
  Petr Danecek (2)
  Armida di Fenza (1)
  Hilary Gates (1)
  Anna-Karin Gerdin (2)
  Elisabetta Golini (12)
  John M Hancock (1)
  Wolfgang Hans (3)
  Sabine M H?lter (3)
  Tertius Hough (1)
  Pierre Jurdic (9)
  Thomas M Keane (2)
  Hugh Morgan (1)
  Werner Müller (8)
  Frauke Neff (5)
  George Nicholson (1)
  Bastian Pasche (14)
  Laura-Anne Roberson (2)
  Jan Rozman (3)
  Mark Sanderson (2)
  Luis Santos (1)
  Mohammed Selloum (6)
  Carl Shannon (2)
  Anne Southwell (1)
  Glauco P Tocchini-Valentini (12)
  Valerie E Vancollie (2)
  Henrik Westerberg (1)
  Wolfgang Wurst (16) (17) (18) (4)
  Min Zi (7)
  Binnaz Yalcin (15) (6)
  Ramiro Ramirez-Solis (2)
  Karen P Steel (2)
  Ann-Marie Mallon (1)
  Martin Hrabě de Angelis (3)
  Yann Herault (6)
  Steve DM Brown (1)
  
  1. Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Science Campus, OX11 0RD, Kragujevac, UK
  2. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
  3. Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Ingolst?dter Landstra?e 1, Neuherberg, D-85764, Germany
  6. Institut Clinique de la Souris, ICS/MCI, PHENOMIN, GIE CERBM, IGBMC, CNRS, INSERM, 1 Rue Laurent Fries, 67404, Illkirch-Graffenstaden Cedex, France
  7. Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, MN13 9PT, UK
  9. AniRA ImmOs phenotyping facility- SFR Biosciences Lyon Gerland- UMS3444/US8, 21 avenue Tony Garnier, F-69007, Lyon, France
  4. Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Developmental Genetics, Ingolst?dter Landstra?e 1, Neuherberg, D-85764, Germany
  10. Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
  11. Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Veterinary Campus, Midlothian, EH25 9RG, UK
  12. Consiglio Nazionale delle Ricerche- Cell Biology and Neurobiology Institute, Via E.Ramarini 32, 00015, Monterotondo Scala, Italy
  13. Department of Infection Genetics, Helmholtz Centre for Infection Research, Inhoffenstra?e 7, Braunschweig, 38124, Germany
  8. Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, MN13 9PT, UK
  5. Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Pathology, Ingolst?dter Landstra?e 1, Neuherberg, D-85764, Germany
  14. Mouse Metabolic Facility of the Cardiomet Center, University Hospital, and Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
  16. Chair for Developmental Genetics, Technische Universit?t München, Arcisstr. 21, Munich, 80333, Germany
  17. Max Planck Institute of Psychiatry, Kraepelinstrasse 2, Munich, 80804, Germany
  18. Deutsches Zentrum für Neurodegenerative Erkrankungen, Schillerstrasse 44, Munich, 80336, Germany
  15. Center for Integrative Genomics, University of Lausanne, Lausanne, CH-1015, Switzerland
  
• ISSN：1465-6906

文摘

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.