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Boles MK, Wilkinson BM, Wilming LG, Liu B, Probst FJ, Harrow J, Grafham D, Hentges KE, Woodward LP, Maxwell A, Mitchell K, Risley MD, Johnson R, Hirschi K, Lupski JR, Funato Y, Miki H, Marin-Garcia P, Matthews L, Coffey AJ, Parker A, Hubbard TJ, Rogers J, Bradley A, Adams DJ, Justice MJ. Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin. PLoS Genet 2009; 5:e1000759. [PMID: 20011118 PMCID: PMC2782131 DOI: 10.1371/journal.pgen.1000759] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 11/09/2009] [Indexed: 12/13/2022] Open
Abstract
An accurate and precisely annotated genome assembly is a fundamental requirement for functional genomic analysis. Here, the complete DNA sequence and gene annotation of mouse Chromosome 11 was used to test the efficacy of large-scale sequencing for mutation identification. We re-sequenced the 14,000 annotated exons and boundaries from over 900 genes in 41 recessive mutant mouse lines that were isolated in an N-ethyl-N-nitrosourea (ENU) mutation screen targeted to mouse Chromosome 11. Fifty-nine sequence variants were identified in 55 genes from 31 mutant lines. 39% of the lesions lie in coding sequences and create primarily missense mutations. The other 61% lie in noncoding regions, many of them in highly conserved sequences. A lesion in the perinatal lethal line l11Jus13 alters a consensus splice site of nucleoredoxin (Nxn), inserting 10 amino acids into the resulting protein. We conclude that point mutations can be accurately and sensitively recovered by large-scale sequencing, and that conserved noncoding regions should be included for disease mutation identification. Only seven of the candidate genes we report have been previously targeted by mutation in mice or rats, showing that despite ongoing efforts to functionally annotate genes in the mammalian genome, an enormous gap remains between phenotype and function. Our data show that the classical positional mapping approach of disease mutation identification can be extended to large target regions using high-throughput sequencing.
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Affiliation(s)
- Melissa K. Boles
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Bonney M. Wilkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Laurens G. Wilming
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Bin Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Frank J. Probst
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jennifer Harrow
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Darren Grafham
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Kathryn E. Hentges
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Lanette P. Woodward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Andrea Maxwell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Karen Mitchell
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Michael D. Risley
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Randy Johnson
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Karen Hirschi
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Yosuke Funato
- Laboratory of Intracellular Signaling, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hiroaki Miki
- Laboratory of Intracellular Signaling, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Pablo Marin-Garcia
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Lucy Matthews
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Alison J. Coffey
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Anne Parker
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Tim J. Hubbard
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Jane Rogers
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- * E-mail: (MJJ); (DJA)
| | - Monica J. Justice
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (MJJ); (DJA)
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