title: Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.
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.
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Melissa K
authors.initials: MK
authors.lastname: Boles
authors.forename: Bonney M
authors.initials: BM
authors.lastname: Wilkinson
authors.forename: Laurens G
authors.initials: LG
authors.lastname: Wilming
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Probst
authors.forename: Jennifer
authors.initials: J
authors.lastname: Harrow
authors.forename: Darren
authors.initials: D
authors.lastname: Grafham
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Hentges
authors.forename: Lanette P
authors.initials: LP
authors.lastname: Woodward
authors.forename: Andrea
authors.initials: A
authors.lastname: Maxwell
authors.forename: Karen
authors.initials: K
authors.lastname: Mitchell
authors.forename: Michael D
authors.initials: MD
authors.lastname: Risley
authors.forename: Randy
authors.initials: R
authors.lastname: Johnson
authors.forename: Karen
authors.initials: K
authors.lastname: Hirschi
authors.forename: James R
authors.initials: JR
authors.lastname: Lupski
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Funato
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Miki
authors.forename: Pablo
authors.initials: P
authors.lastname: Marin-Garcia
authors.forename: Lucy
authors.initials: L
authors.lastname: Matthews
authors.forename: Alison J
authors.initials: AJ
authors.lastname: Coffey
authors.forename: Anne
authors.initials: A
authors.lastname: Parker
authors.forename: Tim J
authors.initials: TJ
authors.lastname: Hubbard
authors.forename: Jane
authors.initials: J
authors.lastname: Rogers
authors.forename: Allan
authors.initials: A
authors.lastname: Bradley
authors.forename: David J
authors.initials: DJ
authors.lastname: Adams
authors.forename: Monica J
authors.initials: MJ
authors.lastname: Justice
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D005038:Ethylnitrosourea / Q000494:pharmacology*; D005091:Exons; D020869:Gene Expression Profiling; D005804:Genes, Lethal; D051379:Mice; D008817:Mice, Mutant Strains; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics*; D010088:Oxidoreductases / Q000235:genetics*
chemical_list: D009687:Nuclear Proteins; D010088:Oxidoreductases; C105231:nucleoredoxin; D005038:Ethylnitrosourea