Mouse genetic and phenotypic resources for human genetics

The use of model organisms to provide information on gene function has proved to be a powerful approach to our understanding of both human disease and fundamental mammalian biology. Large‐scale community projects using mice, based on forward and reverse genetics, and now the pan‐genomic phenotyping efforts of the International Mouse Phenotyping Consortium, are generating resources on an unprecedented scale, which will be extremely valuable to human genetics and medicine. We discuss the nature and availability of data, mice and embryonic stem cells from these large‐scale programmes, the use of these resources to help prioritize and validate candidate genes in human genetic association studies, and how they can improve our understanding of the underlying pathobiology of human disease. Hum Mutat 33:826–836, 2012. © 2012 Wiley Periodicals, Inc.

[1]  The Mouse Phenotype Database Integration Consortium,et al.  The European dimension for the mouse genome mutagenesis program , 2004, Nature Genetics.

[2]  Robert W. Williams,et al.  Identifying Human Disease Genes through Cross-Species Gene Mapping of Evolutionary Conserved Processes , 2011, PloS one.

[3]  H. Parkinson,et al.  Large scale comparison of global gene expression patterns in human and mouse , 2010, Genome Biology.

[4]  M. Cornel,et al.  [Orphanet: a European database for rare diseases]. , 2008, Nederlands tijdschrift voor geneeskunde.

[5]  A. F. Stewart,et al.  High-throughput engineering of the mouse genome coupled with high-resolution expression analysis , 2003, Nature Biotechnology.

[6]  Songyan Liu,et al.  The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium , 2010, Nucleic Acids Res..

[7]  R. Cox,et al.  Mouse models and the interpretation of human GWAS in type 2 diabetes and obesity , 2011, Disease Models & Mechanisms.

[8]  K. Lange,et al.  Prioritizing GWAS results: A review of statistical methods and recommendations for their application. , 2010, American journal of human genetics.

[9]  F. Collins,et al.  Genomic medicine--an updated primer. , 2010, The New England journal of medicine.

[10]  H. Fuchs,et al.  The German Mouse Clinic: a platform for systemic phenotype analysis of mouse models. , 2009, Current pharmaceutical biotechnology.

[11]  Christopher P Austin,et al.  The Knockout Mouse Project , 2004, Nature Genetics.

[12]  Michael Zouberakis,et al.  Mouse Resource Browser—a database of mouse databases , 2010, Database J. Biol. Databases Curation.

[13]  M. Justice Removing the cloak of invisibility: phenotyping the mouse , 2008, Disease Models & Mechanisms.

[14]  Steve D. M. Brown,et al.  The mouse ascending: perspectives for human-disease models , 2007, Nature Cell Biology.

[15]  C. Bult From information to understanding: the role of model organism databases in comparative and functional genomics. , 2006, Animal genetics.

[16]  S. S. Weinreich,et al.  Orphanet : een Europese database over zeldzame ziekten , 2008 .

[17]  J. Ioannidis,et al.  Laboratory Mouse Models for the Human Genome-Wide Associations , 2010, PloS one.

[18]  Bonnie Berger,et al.  An integrative approach to ortholog prediction for disease-focused and other functional studies , 2011, BMC Bioinformatics.

[19]  Lisa E. Gralinski,et al.  The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population , 2012, Genetics.

[20]  Monte Westerfield,et al.  Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation , 2009, PLoS biology.

[21]  R. Mott,et al.  Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection. , 2011, Genome research.

[22]  Alison Abbott,et al.  Mouse project to find each gene's role , 2010, Nature.

[23]  D. Smedley,et al.  Cre recombinase resources for conditional mouse mutagenesis. , 2011, Methods.

[24]  Joseph K. Pickrell,et al.  A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes , 2012, Science.

[25]  John M. Hancock,et al.  EuroPhenome and EMPReSS: online mouse phenotyping resource , 2008 .

[26]  Ken Chen,et al.  Consortium, G.P A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 , 2010 .

[27]  Caleb Webber,et al.  Accurate Distinction of Pathogenic from Benign CNVs in Mental Retardation , 2010, PLoS Comput. Biol..

[28]  David W Threadgill,et al.  The collaborative cross: a recombinant inbred mouse population for the systems genetic era. , 2011, ILAR journal.

[29]  Steve D. M. Brown,et al.  Reliability, robustness, and reproducibility in mouse behavioral phenotyping: a cross-laboratory study. , 2008, Physiological genomics.

[30]  P. Robinson,et al.  Strategies for exome and genome sequence data analysis in disease‐gene discovery projects , 2011, Clinical genetics.

[31]  Michel Dumontier,et al.  Interoperability between Biomedical Ontologies through Relation Expansion, Upper-Level Ontologies and Automatic Reasoning , 2011, PloS one.

[32]  Leonard McMillan,et al.  High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population , 2012, Genetics.

[33]  Steve D. M. Brown,et al.  The European dimension for the mouse genome mutagenesis program , 2004 .

[34]  J. Sundberg,et al.  The mouse as a model for understanding chronic diseases of aging: the histopathologic basis of aging in inbred mice , 2011, Pathobiology of aging & age related diseases.

[35]  Elizabeth T. Cirulli,et al.  The Characterization of Twenty Sequenced Human Genomes , 2010, PLoS genetics.

[36]  H. von Melchner,et al.  High throughput gene trapping and postinsertional modifications of gene trap alleles. , 2011, Methods.

[37]  Damian Smedley,et al.  MouseFinder: Candidate disease genes from mouse phenotype data , 2012, Human mutation.

[38]  Janan T Eppig,et al.  The mammalian phenotype ontology: enabling robust annotation and comparative analysis , 2009, Wiley interdisciplinary reviews. Systems biology and medicine.

[39]  M. H. Angelis,et al.  EUMORPHIA and the European Mouse Phenotyping Resource for Standardized Screens (EMPReSS) , 2006 .

[40]  Wolfgang Wurst,et al.  A New Partner for the International Knockout Mouse Consortium , 2007, Cell.

[41]  Jianzhi Zhang,et al.  Null mutations in human and mouse orthologs frequently result in different phenotypes , 2008, Proceedings of the National Academy of Sciences.

[42]  N. Campbell Genetic association database , 2004, Nature Reviews Genetics.

[43]  Damian Smedley,et al.  EMMA—mouse mutant resources for the international scientific community , 2009, Nucleic Acids Res..

[44]  John M. Hancock,et al.  A Gene-Phenotype Network for the Laboratory Mouse and Its Implications for Systematic Phenotyping , 2011, PloS one.

[45]  P. Robinson,et al.  The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. , 2008, American journal of human genetics.

[46]  J. Guénet the mouse genome , 2005, Nature.

[47]  Brynn H Voy,et al.  Genetic analysis in the Collaborative Cross breeding population. , 2011, Genome research.

[48]  Teri A Manolio,et al.  Genomewide association studies and assessment of the risk of disease. , 2010, The New England journal of medicine.

[49]  Janan T. Eppig,et al.  The mouse Gene Expression Database (GXD): 2011 update , 2010, Nucleic Acids Res..

[50]  Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[51]  M. Davisson,et al.  FIMRe: Federation of International Mouse Resources: Global Networking of Resource Centers , 2006, Mammalian Genome.

[52]  Kriston L. McGary,et al.  Systematic discovery of nonobvious human disease models through orthologous phenotypes , 2010, Proceedings of the National Academy of Sciences.

[53]  Supriyo De,et al.  Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information , 2010, BMC Medical Genomics.

[54]  T. Pihlajaniemi,et al.  Mouse as a Model Organism , 2011 .

[55]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics , 2010, Nucleic Acids Res..

[56]  C. Haldeman-Englert,et al.  Genes and biological processes commonly disrupted in rare and heterogeneous developmental delay syndromes. , 2011, Human molecular genetics.

[57]  B. Rosen,et al.  Dual RMCE for efficient re-engineering of mouse mutant alleles , 2010, Nature Methods.

[58]  Carol J. Bult,et al.  The mouse as a model for human biology: a resource guide for complex trait analysis , 2007, Nature Reviews Genetics.

[59]  L. Donahue,et al.  Multiple quantitative trait loci for cortical and trabecular bone regulation map to mid‐distal mouse chromosome 4 that shares linkage homology to human chromosome 1p36 , 2012, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[60]  Gary A. Churchill,et al.  Ten Years of the Collaborative Cross , 2012, G3: Genes | Genomes | Genetics.

[61]  S. Lewis,et al.  Uberon, an integrative multi-species anatomy ontology , 2012, Genome Biology.

[62]  John M. Hancock,et al.  Phenotype ontologies for mouse and man: bridging the semantic gap , 2010, Disease Models & Mechanisms.

[63]  J. Boeke,et al.  Transposon-mediated genome manipulation in vertebrates , 2009, Nature Methods.

[64]  Olivier Bodenreider,et al.  Two approaches to integrating phenotype and clinical information , 2009, AMIA.

[65]  Martin Oti,et al.  The biological coherence of human phenome databases. , 2009, American journal of human genetics.

[66]  H. Fuchs,et al.  Mouse phenotyping. , 2011, Methods.

[67]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

[68]  E. Callaway How to build a better mouse , 2011, Nature.

[69]  P Chambon,et al.  EMPReSS: standardized phenotype screens for functional annotation of the mouse genome , 2005, Nature Genetics.

[70]  R. Korstanje,et al.  Identifying novel genes for atherosclerosis through mouse-human comparative genetics. , 2005, American journal of human genetics.

[71]  Carol A. Bocchini,et al.  A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®) , 2011, Human mutation.

[72]  D. Pinto,et al.  Copy-number variation in control population cohorts. , 2007, Human molecular genetics.

[73]  A. Yoshiki,et al.  Mouse phenome research: implications of genetic background. , 2006, ILAR journal.

[74]  Ulf Leser,et al.  Phenoclustering: online mining of cross-species phenotypes , 2010, Bioinform..

[75]  Steve D. M. Brown,et al.  High-throughput mouse phenotyping. , 2011, Methods.

[76]  Georgi Georgiev,et al.  PhenomicDB: a new cross-species genotype/phenotype resource , 2007, Nucleic Acids Res..

[77]  Steve D. M. Brown,et al.  ENU mutagenesis, a way forward to understand gene function. , 2008, Annual review of genomics and human genetics.

[78]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[79]  Trudy Torto-Alalibo,et al.  What is functional annotation ? , 2006 .

[80]  John M. Hancock,et al.  Building Mouse Phenotype Ontologies , 2003, Pacific Symposium on Biocomputing.

[81]  Robert Hoehndorf,et al.  New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models. , 2011, Briefings in functional genomics.

[82]  Lynne Pearce,et al.  Breaking the silence. , 2011, Nursing standard (Royal College of Nursing (Great Britain) : 1987).

[83]  R. Finnell,et al.  Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. , 2008, Genome research.

[84]  John M. Hancock,et al.  The functional annotation of mammalian genomes: the challenge of phenotyping. , 2009, Annual review of genetics.

[85]  John M. Hancock,et al.  EuroPhenome: a repository for high-throughput mouse phenotyping data , 2009, Nucleic Acids Res..

[86]  Magalie S Leduc,et al.  The mouse QTL map helps interpret human genome-wide association studies for HDL cholesterol[S] , 2011, Journal of Lipid Research.

[87]  E. Lander Initial impact of the sequencing of the human genome , 2011, Nature.

[88]  Michel Dumontier,et al.  A common layer of interoperability for biomedical ontologies based on OWL EL , 2011, Bioinform..

[89]  B. Libby,et al.  Mouse mutants from chemically mutagenized embryonic stem cells , 2000, Nature Genetics.

[90]  M. H. Angelis,et al.  Towards better mouse models: enhanced genotypes, systemic phenotyping and envirotype modelling , 2009, Nature Reviews Genetics.

[91]  J. Harrow,et al.  A conditional knockout resource for the genome-wide study of mouse gene function , 2011, Nature.

[92]  Paul N. Schofield,et al.  PhenomeNET: a whole-phenome approach to disease gene discovery , 2011, Nucleic acids research.

[93]  Thomas M. Keane,et al.  Mouse genomic variation and its effect on phenotypes and gene regulation , 2011, Nature.

[94]  J. Sundberg,et al.  Exploring the elephant: histopathology in high-throughput phenotyping of mutant mice , 2011, Disease Models & Mechanisms.

[95]  W. F. Mathes,et al.  Advances in comparative genetics: influence of genetics on obesity. , 2011, The British journal of nutrition.

[96]  W. Wurst,et al.  Efficient conditional and promoter-specific in vivo expression of cDNAs of choice by taking advantage of recombinase-mediated cassette exchange using FlEx gene traps , 2010, Nucleic acids research.

[97]  Judith A. Blake,et al.  The Mouse Genome Database genotypes::phenotypes , 2008, Nucleic Acids Res..

[98]  H. Fuchs,et al.  Systemic first-line phenotyping. , 2009, Methods in molecular biology.

[99]  Jing Chen,et al.  PhenoHM: human–mouse comparative phenome–genome server , 2010, Nucleic Acids Res..

[100]  H. Fuchs,et al.  The German Mouse Clinic – Running an Open Access Platform , 2011 .