1
|
Hmeljak J, Justice MJ. From gene to treatment: supporting rare disease translational research through model systems. Dis Model Mech 2019; 12:12/2/dmm039271. [PMID: 30819728 PMCID: PMC6398488 DOI: 10.1242/dmm.039271] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Individual rare diseases may affect only a few people, making them difficult to recognize, diagnose or treat by studying humans alone. Instead, model organisms help to validate genetic associations, understand functional pathways and develop therapeutic interventions for rare diseases. In this Editorial, we point to the key parameters in face, construct, predictive and target validity for accurate disease modelling, with special emphasis on rare disease models. Raising the experimental standards for disease models will enhance successful clinical translation and benefit rare disease research. Summary: This Editorial discusses the importance of model systems with accurate face, construct, target and predictive validity for rare disease research.
Collapse
Affiliation(s)
- Julija Hmeljak
- Disease Models & Mechanisms, The Company of Biologists, Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK
| | - Monica J Justice
- Program in Genetics and Genome Biology, The Hospital for Sick Children, and Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5G 0A4 Canada
| |
Collapse
|
2
|
Brommage R, Liu J, Hansen GM, Kirkpatrick LL, Potter DG, Sands AT, Zambrowicz B, Powell DR, Vogel P. High-throughput screening of mouse gene knockouts identifies established and novel skeletal phenotypes. Bone Res 2014; 2:14034. [PMID: 26273529 PMCID: PMC4472125 DOI: 10.1038/boneres.2014.34] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 07/29/2014] [Accepted: 07/31/2014] [Indexed: 12/13/2022] Open
Abstract
Screening gene function in vivo is a powerful approach to discover novel drug targets. We present high-throughput screening (HTS) data for 3 762 distinct global gene knockout (KO) mouse lines with viable adult homozygous mice generated using either gene-trap or homologous recombination technologies. Bone mass was determined from DEXA scans of male and female mice at 14 weeks of age and by microCT analyses of bones from male mice at 16 weeks of age. Wild-type (WT) cagemates/littermates were examined for each gene KO. Lethality was observed in an additional 850 KO lines. Since primary HTS are susceptible to false positive findings, additional cohorts of mice from KO lines with intriguing HTS bone data were examined. Aging, ovariectomy, histomorphometry and bone strength studies were performed and possible non-skeletal phenotypes were explored. Together, these screens identified multiple genes affecting bone mass: 23 previously reported genes (Calcr, Cebpb, Crtap, Dcstamp, Dkk1, Duoxa2, Enpp1, Fgf23, Kiss1/Kiss1r, Kl (Klotho), Lrp5, Mstn, Neo1, Npr2, Ostm1, Postn, Sfrp4, Slc30a5, Slc39a13, Sost, Sumf1, Src, Wnt10b), five novel genes extensively characterized (Cldn18, Fam20c, Lrrk1, Sgpl1, Wnt16), five novel genes with preliminary characterization (Agpat2, Rassf5, Slc10a7, Slc26a7, Slc30a10) and three novel undisclosed genes coding for potential osteoporosis drug targets.
Collapse
Affiliation(s)
| | - Jeff Liu
- Lexicon Pharmaceuticals , The Woodlands, TX, USA
| | | | | | | | | | | | | | - Peter Vogel
- Lexicon Pharmaceuticals , The Woodlands, TX, USA
| |
Collapse
|
3
|
Oellrich A, Jacobsen J, Papatheodorou I, Smedley D. Using association rule mining to determine promising secondary phenotyping hypotheses. ACTA ACUST UNITED AC 2014; 30:i52-59. [PMID: 24932005 PMCID: PMC4059059 DOI: 10.1093/bioinformatics/btu260] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MOTIVATION Large-scale phenotyping projects such as the Sanger Mouse Genetics project are ongoing efforts to help identify the influences of genes and their modification on phenotypes. Gene-phenotype relations are crucial to the improvement of our understanding of human heritable diseases as well as the development of drugs. However, given that there are ∼: 20 000 genes in higher vertebrate genomes and the experimental verification of gene-phenotype relations requires a lot of resources, methods are needed that determine good candidates for testing. RESULTS In this study, we applied an association rule mining approach to the identification of promising secondary phenotype candidates. The predictions rely on a large gene-phenotype annotation set that is used to find occurrence patterns of phenotypes. Applying an association rule mining approach, we could identify 1967 secondary phenotype hypotheses that cover 244 genes and 136 phenotypes. Using two automated and one manual evaluation strategies, we demonstrate that the secondary phenotype candidates possess biological relevance to the genes they are predicted for. From the results we conclude that the predicted secondary phenotypes constitute good candidates to be experimentally tested and confirmed. AVAILABILITY The secondary phenotype candidates can be browsed through at http://www.sanger.ac.uk/resources/databases/phenodigm/gene/secondaryphenotype/list. CONTACT ao5@sanger.ac.uk or ds5@sanger.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Anika Oellrich
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB1 10SA, UK
| | - Julius Jacobsen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB1 10SA, UK
| | - Irene Papatheodorou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB1 10SA, UK
| | | | - Damian Smedley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB1 10SA, UK
| |
Collapse
|
4
|
Rathkolb B, Fuchs H, Gailus-Durner V, Aigner B, Wolf E, Hrabě de Angelis M. Blood Collection from Mice and Hematological Analyses on Mouse Blood. ACTA ACUST UNITED AC 2013; 3:101-19. [PMID: 26069060 DOI: 10.1002/9780470942390.mo130054] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Basic phenotyping of inbred mouse strains and genetically modified mouse models usually includes the determination of blood-based parameters as a diagnostic screen for genotype effects on metabolism and organ function. A broad range of analytes, including hematological parameters, can be reliably determined in mouse blood, if appropriate samples are available. Here we describe recommended techniques for blood collection from mice and the considerations that have to be taken into account to get adequate samples for hematological investigations. Furthermore, we describe established methods used in the German Mouse Clinic (GMC) to determine hematological parameters in the mouse. Curr. Protoc. Mouse Biol. 3:101-119 © 2013 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Birgit Rathkolb
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany.,Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany
| | - Valérie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany
| | - Bernhard Aigner
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany.,Institute of Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany.,German Research Center for Diabetes Research, Neuherberg, Germany
| |
Collapse
|
5
|
Rathkolb B, Hans W, Prehn C, Fuchs H, Gailus-Durner V, Aigner B, Adamski J, Wolf E, Hrabě de Angelis M. Clinical Chemistry and Other Laboratory Tests on Mouse Plasma or Serum. ACTA ACUST UNITED AC 2013; 3:69-100. [PMID: 26069059 DOI: 10.1002/9780470942390.mo130043] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Besides hematological analyses, many other parameters, including clinical chemistry and endocrinological values, can be determined from mouse blood samples. For most of these tests, plasma or serum samples are used. Data obtained by these investigations provide indications of genotype effects on metabolism and organ functions. Here we describe in detail the considerations that have to be taken into account to get adequate samples for plasma or serum analyses and the recommended sample processing for different investigations. Furthermore, we describe established methods used in the German Mouse Clinic (GMC) to determine clinical chemical parameters; for more in-depth analysis of specific classes of biomarkers, we provide instructions for ELISAs (sandwich and competitive) as well as LC-MS/MS, focusing on markers associated with bone or steroid metabolism in the mouse as working examples. Curr. Protoc. Mouse Biol. 3:69-100 © 2013 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Birgit Rathkolb
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany.,Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Hans
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany
| | - Cornelia Prehn
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany
| | - Valérie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany
| | - Bernhard Aigner
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jerzy Adamski
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany.,Institute of Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz-Zentrum München, German Research Center for Environmental Health, GmbH, Neuherberg, Germany.,Institute of Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany.,German Research Center for Diabetes Research, Neuherberg, Germany
| |
Collapse
|
6
|
Ramírez-Solis R, Ryder E, Houghton R, White JK, Bottomley J. Large-scale mouse knockouts and phenotypes. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:547-63. [PMID: 22899600 DOI: 10.1002/wsbm.1183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Standardized phenotypic analysis of mutant forms of every gene in the mouse genome will provide fundamental insights into mammalian gene function and advance human and animal health. The availability of the human and mouse genome sequences, the development of embryonic stem cell mutagenesis technology, the standardization of phenotypic analysis pipelines, and the paradigm-shifting industrialization of these processes have made this a realistic and achievable goal. The size of this enterprise will require global coordination to ensure economies of scale in both the generation and primary phenotypic analysis of the mutant strains, and to minimize unnecessary duplication of effort. To provide more depth to the functional annotation of the genome, effective mechanisms will also need to be developed to disseminate the information and resources produced to the wider community. Better models of disease, potential new drug targets with novel mechanisms of action, and completely unsuspected genotype-phenotype relationships covering broad aspects of biology will become apparent. To reach these goals, solutions to challenges in mouse production and distribution, as well as development of novel, ever more powerful phenotypic analysis modalities will be necessary. It is a challenging and exciting time to work in mouse genetics.
Collapse
|
7
|
Bassett JHD, Gogakos A, White JK, Evans H, Jacques RM, van der Spek AH, Ramirez-Solis R, Ryder E, Sunter D, Boyde A, Campbell MJ, Croucher PI, Williams GR. Rapid-throughput skeletal phenotyping of 100 knockout mice identifies 9 new genes that determine bone strength. PLoS Genet 2012; 8:e1002858. [PMID: 22876197 PMCID: PMC3410859 DOI: 10.1371/journal.pgen.1002858] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 06/11/2012] [Indexed: 01/08/2023] Open
Abstract
Osteoporosis is a common polygenic disease and global healthcare priority but its genetic basis remains largely unknown. We report a high-throughput multi-parameter phenotype screen to identify functionally significant skeletal phenotypes in mice generated by the Wellcome Trust Sanger Institute Mouse Genetics Project and discover novel genes that may be involved in the pathogenesis of osteoporosis. The integrated use of primary phenotype data with quantitative x-ray microradiography, micro-computed tomography, statistical approaches and biomechanical testing in 100 unselected knockout mouse strains identified nine new genetic determinants of bone mass and strength. These nine new genes include five whose deletion results in low bone mass and four whose deletion results in high bone mass. None of the nine genes have been implicated previously in skeletal disorders and detailed analysis of the biomechanical consequences of their deletion revealed a novel functional classification of bone structure and strength. The organ-specific and disease-focused strategy described in this study can be applied to any biological system or tractable polygenic disease, thus providing a general basis to define gene function in a system-specific manner. Application of the approach to diseases affecting other physiological systems will help to realize the full potential of the International Mouse Phenotyping Consortium. Chronic disease represents a global healthcare burden but its genetic basis is largely unknown. To address this, a massive international investment is generating a resource of mutant mice to investigate the function of every gene. Although current characterization of mutants is broadbased, it lacks specificity. Here, we describe a new and rapid functional screening approach to identify genes involved in disease susceptibility. Using bone and osteoporosis as a paradigm, we identify nine new genes that determine bone structure and strength from a screen of 100 knockout mice. Deletion of five of the genes leads to low bone mass, whereas deletion of four results in high bone mass. We also report a novel functional classification that relates bone structure to bone strength and opens the field to collaborative research between material scientists, bioengineers and biologists. Our rapid throughput phenotyping approach can be applied to complex diseases in other physiological systems, thus realizing the full potential of the International Mouse Phenotyping Consortium.
Collapse
Affiliation(s)
- J. H. Duncan Bassett
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, London, United Kingdom
| | - Apostolos Gogakos
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, London, United Kingdom
| | - Jacqueline K. White
- Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Holly Evans
- The Mellanby Centre for Bone Research, Department of Human Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Richard M. Jacques
- School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
| | - Anne H. van der Spek
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, London, United Kingdom
| | | | - Ramiro Ramirez-Solis
- Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Edward Ryder
- Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - David Sunter
- Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alan Boyde
- Queen Mary University of London, Oral Growth and Development, Institute of Dentistry, Bart's and The London School of Medicine, London, United Kingdom
| | - Michael J. Campbell
- School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
| | - Peter I. Croucher
- The Mellanby Centre for Bone Research, Department of Human Metabolism, University of Sheffield, Sheffield, United Kingdom
- Garvan Institute of Medical Research, Sydney, Australia
- * E-mail: (GRW), (PIC)
| | - Graham R. Williams
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, London, United Kingdom
- * E-mail: (GRW), (PIC)
| |
Collapse
|
8
|
Schofield PN, Hoehndorf R, Gkoutos GV. Mouse genetic and phenotypic resources for human genetics. Hum Mutat 2012; 33:826-36. [PMID: 22422677 DOI: 10.1002/humu.22077] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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.
Collapse
Affiliation(s)
- Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.
| | | | | |
Collapse
|
9
|
Schofield PN, Vogel P, Gkoutos GV, Sundberg JP. Exploring the elephant: histopathology in high-throughput phenotyping of mutant mice. Dis Model Mech 2012; 5:19-25. [PMID: 22028326 PMCID: PMC3255539 DOI: 10.1242/dmm.008334] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Recent advances in gene knockout techniques and the in vivo analysis of mutant mice, together with the advent of large-scale projects for systematic mouse mutagenesis and genome-wide phenotyping, have allowed the creation of platforms for the most complete and systematic analysis of gene function ever undertaken in a vertebrate. The development of high-throughput phenotyping pipelines for these and other large-scale projects allows investigators to search and integrate large amounts of directly comparable phenotype data from many mutants, on a genomic scale, to help develop and test new hypotheses about the origins of disease and the normal functions of genes in the organism. Histopathology has a venerable history in the understanding of the pathobiology of human and animal disease, and presents complementary advantages and challenges to in vivo phenotyping. In this review, we present evidence for the unique contribution that histopathology can make to a large-scale phenotyping effort, using examples from past and current programmes at Lexicon Pharmaceuticals and The Jackson Laboratory, and critically assess the role of histopathology analysis in high-throughput phenotyping pipelines.
Collapse
Affiliation(s)
- Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.
| | | | | | | |
Collapse
|
10
|
Larina IV, Larin KV, Justice MJ, Dickinson ME. Optical Coherence Tomography for live imaging of mammalian development. Curr Opin Genet Dev 2011; 21:579-84. [PMID: 21962442 DOI: 10.1016/j.gde.2011.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/24/2011] [Accepted: 09/06/2011] [Indexed: 02/08/2023]
Abstract
Understanding the nature and mechanism of congenital defects of the different organ systems in humans has heavily relied on the analysis of the corresponding mutant phenotypes in rodent models. Optical Coherence Tomography (OCT) has recently emerged as a powerful tool to study early embryonic development. This non-invasive optical methodology does not require labeling and allows visualization of embryonic tissues with single cell resolution. Here, we will discuss how OCT can be applied for structural imaging of early mouse and rat embryos in static culture, cardiodynamic and blood flow analysis, and in utero embryonic imaging at later stages of gestation, demonstrating how OCT can be used to assess structural and functional birth defects in mammalian models.
Collapse
Affiliation(s)
- Irina V Larina
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States.
| | | | | | | |
Collapse
|
11
|
Karp NA, Baker LA, Gerdin AKB, Adams NC, Ramírez-Solis R, White JK. Optimising experimental design for high-throughput phenotyping in mice: a case study. Mamm Genome 2010; 21:467-76. [PMID: 20799038 PMCID: PMC2974211 DOI: 10.1007/s00335-010-9279-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 07/26/2010] [Indexed: 12/16/2022]
Abstract
To further the functional annotation of the mammalian genome, the Sanger Mouse Genetics Programme aims to generate and characterise knockout mice in a high-throughput manner. Annually, approximately 200 lines of knockout mice will be characterised using a standardised battery of phenotyping tests covering key disease indications ranging from obesity to sensory acuity. From these findings secondary centres will select putative mutants of interest for more in-depth, confirmatory experiments. Optimising experimental design and data analysis is essential to maximise output using the resources with greatest efficiency, thereby attaining our biological objective of understanding the role of genes in normal development and disease. This study uses the example of the noninvasive blood pressure test to demonstrate how statistical investigation is important for generating meaningful, reliable results and assessing the design for the defined research objectives. The analysis adjusts for the multiple-testing problem by applying the false discovery rate, which controls the number of false calls within those highlighted as significant. A variance analysis finds that the variation between mice dominates this assay. These variance measures were used to examine the interplay between days, readings, and number of mice on power, the ability to detect change. If an experiment is underpowered, we cannot conclude whether failure to detect a biological difference arises from low power or lack of a distinct phenotype, hence the mice are subjected to testing without gain. Consequently, in confirmatory studies, a power analysis along with the 3Rs can provide justification to increase the number of mice used.
Collapse
Affiliation(s)
- Natasha A. Karp
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Lauren A. Baker
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- Present Address: Division of Cardiovascular Medicine, Level 6, Addenbrooke’s Centre for Clinical Investigation (ACCI), Addenbrooke’s Hospital, University of Cambridge, Hills Road, Box 110, Cambridge, CB2 0QQ UK
| | - Anna-Karin B. Gerdin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Niels C. Adams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | - Ramiro Ramírez-Solis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Jacqueline K. White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| |
Collapse
|
12
|
Schofield PN, Gkoutos GV, Gruenberger M, Sundberg JP, Hancock JM. Phenotype ontologies for mouse and man: bridging the semantic gap. Dis Model Mech 2010; 3:281-9. [PMID: 20427557 DOI: 10.1242/dmm.002790] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A major challenge of the post-genomic era is coding phenotype data from humans and model organisms such as the mouse, to permit the meaningful translation of phenotype descriptions between species. This ability is essential if we are to facilitate phenotype-driven gene function discovery and empower comparative pathobiology. Here, we review the current state of the art for phenotype and disease description in mice and humans, and discuss ways in which the semantic gap between coding systems might be bridged to facilitate the discovery and exploitation of new mouse models of human diseases.
Collapse
Affiliation(s)
- Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | | | | | | | | |
Collapse
|
13
|
Kim IY, Shin JH, Seong JK. Mouse phenogenomics, toolbox for functional annotation of human genome. BMB Rep 2010; 43:79-90. [PMID: 20193125 DOI: 10.5483/bmbrep.2010.43.2.079] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mouse models are crucial for the functional annotation of human genome. Gene modification techniques including gene targeting and gene trap in mouse have provided powerful tools in the form of genetically engineered mice (GEM) for understanding the molecular pathogenesis of human diseases. Several international consortium and programs are under way to deliver mutations in every gene in mouse genome. The information from studying these GEM can be shared through international collaboration. However, there are many limitations in utility because not all human genes are knocked out in mouse and they are not yet phenotypically characterized by standardized ways which is required for sharing and evaluating data from GEM. The recent improvement in mouse genetics has now moved the bottleneck in mouse functional genomics from the production of GEM to the systematic mouse phenotype analysis of GEM. Enhanced, reproducible and comprehensive mouse phenotype analysis has thus emerged as a prerequisite for effectively engaging the phenotyping bottleneck. In this review, current information on systematic mouse phenotype analysis and an issue-oriented perspective will be provided.
Collapse
Affiliation(s)
- Il Yong Kim
- Laboratory of Developmental Biology and Genomics, BK21 Program for Veterinary Science, Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | | | | |
Collapse
|
14
|
Abstract
The generation and analysis of germline mutations in the mouse is one of the cornerstones of modern biological research. The chemical supermutagen N-ethyl-N-nitrosourea (ENU) is the most potent known mouse mutagen and can be used to generate point mutations throughout the mouse genome. The progeny of ENU-mutagenized males can be screened for autosomal dominant phenotypes, or they can be used to generate multigeneration pedigrees to screen for autosomal recessive traits. The introduction of balancer chromosomes into the breeding scheme can allow for the selective capture of mutations in a specific chromosomal region. More recent work has demonstrated that the use of animals that already have a mutation of interest can lead to the successful isolation of additional mutations that modify the original mutant phenotype. Further, modern molecular techniques ensure that mutations can be readily identified. We describe here the procedures for mutagenizing male mice with ENU and explain the various types of screens that can be performed for different kinds of induced mutations. The currently published research on ENU mutagenesis in the mouse has only scratched the surface of what is possible with this powerful technique, and further work is certain to deepen our knowledge of the role of the individual components of the mouse genome and the myriad relationships between them.
Collapse
Affiliation(s)
- Frank J Probst
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | |
Collapse
|