Unlocking the Bottleneck in Forward Genetics Using Whole-Genome Sequencing and Identity by Descent to Isolate Causative Mutations

Katherine R. Bull, Andrew J. Rimmer, Owen M. Siggs, Lisa A. Miosge, Carla M. Roots, Anselm Enders, Edward M. Bertram, Tanya L. Crockford, Belinda Whittle, Paul K. Potter, Michelle M. Simon, Ann Marie Mallon, Steve D.M. Brown, Bruce Beutler, Christopher C. Goodnow, Gerton Lunter, Richard J. Cornall

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Forward 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.

Original languageEnglish
Article numbere1003219
JournalPloS Genetics
Volume9
Issue number1
DOIs
Publication statusPublished - Jan 2013
Externally publishedYes

Bibliographical note

Copyright: © 2013 Bull et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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    Bull, K. R., Rimmer, A. J., Siggs, O. M., Miosge, L. A., Roots, C. M., Enders, A., Bertram, E. M., Crockford, T. L., Whittle, B., Potter, P. K., Simon, M. M., Mallon, A. M., Brown, S. D. M., Beutler, B., Goodnow, C. C., Lunter, G., & Cornall, R. J. (2013). Unlocking the Bottleneck in Forward Genetics Using Whole-Genome Sequencing and Identity by Descent to Isolate Causative Mutations. PloS Genetics, 9(1), [e1003219]. https://doi.org/10.1371/journal.pgen.1003219