Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.
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...
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2009-12-01
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doaj-1a22b98f229e441bb8fc377e6991707a2020-11-25T01:04:19ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042009-12-01512e100075910.1371/journal.pgen.1000759Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.Melissa K BolesBonney M WilkinsonLaurens G WilmingBin LiuFrank J ProbstJennifer HarrowDarren GrafhamKathryn E HentgesLanette P WoodwardAndrea MaxwellKaren MitchellMichael D RisleyRandy JohnsonKaren HirschiJames R LupskiYosuke FunatoHiroaki MikiPablo Marin-GarciaLucy MatthewsAlison J CoffeyAnne ParkerTim J HubbardJane RogersAllan BradleyDavid J AdamsMonica J JusticeAn 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.http://europepmc.org/articles/PMC2782131?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Melissa K Boles Bonney M Wilkinson Laurens G Wilming Bin Liu Frank J Probst Jennifer Harrow Darren Grafham Kathryn E Hentges Lanette P Woodward Andrea Maxwell Karen Mitchell Michael D Risley Randy Johnson Karen Hirschi James R Lupski Yosuke Funato Hiroaki Miki Pablo Marin-Garcia Lucy Matthews Alison J Coffey Anne Parker Tim J Hubbard Jane Rogers Allan Bradley David J Adams Monica J Justice |
spellingShingle |
Melissa K Boles Bonney M Wilkinson Laurens G Wilming Bin Liu Frank J Probst Jennifer Harrow Darren Grafham Kathryn E Hentges Lanette P Woodward Andrea Maxwell Karen Mitchell Michael D Risley Randy Johnson Karen Hirschi James R Lupski Yosuke Funato Hiroaki Miki Pablo Marin-Garcia Lucy Matthews Alison J Coffey Anne Parker Tim J Hubbard Jane Rogers Allan Bradley David J Adams Monica J Justice Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin. PLoS Genetics |
author_facet |
Melissa K Boles Bonney M Wilkinson Laurens G Wilming Bin Liu Frank J Probst Jennifer Harrow Darren Grafham Kathryn E Hentges Lanette P Woodward Andrea Maxwell Karen Mitchell Michael D Risley Randy Johnson Karen Hirschi James R Lupski Yosuke Funato Hiroaki Miki Pablo Marin-Garcia Lucy Matthews Alison J Coffey Anne Parker Tim J Hubbard Jane Rogers Allan Bradley David J Adams Monica J Justice |
author_sort |
Melissa K Boles |
title |
Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin. |
title_short |
Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin. |
title_full |
Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin. |
title_fullStr |
Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin. |
title_full_unstemmed |
Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin. |
title_sort |
discovery of candidate disease genes in enu-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Genetics |
issn |
1553-7390 1553-7404 |
publishDate |
2009-12-01 |
description |
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. |
url |
http://europepmc.org/articles/PMC2782131?pdf=render |
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