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Simon MM, Moresco EMY, Bull KR, Kumar S, Mallon AM, Beutler B, Potter PK. Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. Mamm Genome 2015; 26:486-500. [PMID: 26449678 PMCID: PMC4602060 DOI: 10.1007/s00335-015-9603-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/01/2015] [Indexed: 02/07/2023]
Abstract
Mutagenesis-based screens in mice are a powerful discovery platform to identify novel genes or gene functions associated with disease phenotypes. An N-ethyl-N-nitrosourea (ENU) mutagenesis screen induces single nucleotide variants randomly in the mouse genome. Subsequent phenotyping of mutant and wildtype mice enables the identification of mutated pathways resulting in phenotypes associated with a particular ENU lesion. This unbiased approach to gene discovery conducts the phenotyping with no prior knowledge of the functional mutations. Before the advent of affordable next generation sequencing (NGS), ENU variant identification was a limiting step in gene characterization, akin to ‘finding a needle in a haystack’. The emergence of a reliable reference genome alongside advances in NGS has propelled ENU mutation discovery from an arduous, time-consuming exercise to an effective and rapid form of mutation discovery. This has permitted large mouse facilities worldwide to use ENU for novel mutation discovery in a high-throughput manner, helping to accelerate basic science at the mechanistic level. Here, we describe three different strategies used to identify ENU variants from NGS data and some of the subsequent steps for mutation characterisation.
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Affiliation(s)
- Michelle M Simon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Katherine R Bull
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Saumya Kumar
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Paul K Potter
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
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Sturm M, Becker A, Schroeder A, Bilkei-Gorzo A, Zimmer A. Effect of chronic corticosterone application on depression-like behavior in C57BL/6N and C57BL/6J mice. GENES BRAIN AND BEHAVIOR 2015; 14:292-300. [DOI: 10.1111/gbb.12208] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 02/21/2015] [Accepted: 02/26/2015] [Indexed: 02/01/2023]
Affiliation(s)
- M. Sturm
- Institute of Molecular Psychiatry; University of Bonn; Bonn Germany
| | - A. Becker
- Institute of Molecular Psychiatry; University of Bonn; Bonn Germany
| | - A. Schroeder
- Institute of Molecular Psychiatry; University of Bonn; Bonn Germany
| | - A. Bilkei-Gorzo
- Institute of Molecular Psychiatry; University of Bonn; Bonn Germany
| | - A. Zimmer
- Institute of Molecular Psychiatry; University of Bonn; Bonn Germany
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