Bull, Katherine RRimmer, Andrew JSiggs, Owen MMiosge, Lisa ARoots, Carla MEnders, AnselmBertram, Edward MCrockford, Tanya LWhittle, BelindaPotter, Paul KSimon, Michelle MMallon, Ann-MarieBrown, Steve D MBeutler, BruceGoodnow, Christopher CLunter, GertonCornall, Richard J2014-01-202014-01-201553-73901553-7404http://hdl.handle.net/1885/11186Forward genetics screens with N-ethyl-N-nitrosourea (ENU) provide a powerful way to illuminate gene function and generate mouse models of human disease; however, the identification of causative mutations remains a limiting step. Current strategies depend on conventional mapping, so the propagation of affected mice requires non-lethal screens; accurate tracking of phenotypes through pedigrees is complex and uncertain; out-crossing can introduce unexpected modifiers; and Sanger sequencing of candidate genes is inefficient. Here we show how these problems can be efficiently overcome using whole-genome sequencing (WGS) to detect the ENU mutations and then identify regions that are identical by descent (IBD) in multiple affected mice. In this strategy, we use a modification of the Lander-Green algorithm to isolate causative recessive and dominant mutations, even at low coverage, on a pure strain background. Analysis of the IBD regions also allows us to calculate the ENU mutation rate (1.54 mutations per Mb) and to model future strategies for genetic screens in mice. The introduction of this approach will accelerate the discovery of causal variants, permit broader and more informative lethal screens to be used, reduce animal costs, and herald a new era for ENU mutagenesis.The High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics is funded by Wellcome Trust grant reference 090532/Z/09/Z and MRC Hub grant G0900747 91070. This study was supported by Wellcome Trust Strategic Award 082030 (CCG), Wellcome Trust Studentship 094446/Z/10/Z (KRB), the Oxford NIHR Biomedical Research Centre, and the MRC Human Immunology Unit (RJC). AJR and GL were supported by Wellcome Trust grant 090532/Z/ 09/Z, CCG and AE by a Major initiative Award from the Clive and Vera Ramaciotti Foundation, and AE by an NHMRC Career Development Award. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.12 pageshttp://www.sherpa.ac.uk/romeo/issn/1553-7390/ From Sherpa/Romeo as at 21/1/14: author can archive pre-print (ie pre-refereeing); author can archive post-print (ie final draft post-refereeing); author can archive publisher's version/PDF.whole-genome sequencingforward genetics2013-01-3110.1371/journal.pgen.10032192015-12-11