Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis

Carrie N. Arnold, Yu Xia, Pei Lin, Charles Ross, Martin Schwander, Nora G. Smart, Ulrich Müller, Bruce Beutler

Research output: Contribution to journalArticle

46 Citations (Scopus)

Abstract

In a pedigree of C57BL/6J mice homozygous for germline mutations induced by the mutagen N-ethyl-N-nitrosourea (ENU), numerous animals died under specific pathogen-free (SPF) conditions between 6 and 7 months of age. Death was caused by nephritic syndrome, which progressed to renal failure associated with focal segmental glomerulosclerosis. To identify the mutation responsible for renal disease, we sequenced genomic DNA from an affected animal using the Applied Biosystems SOLiD sequencing platform. Approximately 74% of the nucleotides comprising coding sequences and splice junctions in the mouse genome were covered at least three times. Within this portion of the genome, 64 discrepancies were flagged as potential homozygous mutations and 82 were flagged as potential heterozygous mutations. A total of 10 of these calls, all homozygous, were validated by capillary sequencing. One of the validated mutations disrupted splicing of the Col4a4 transcript. Genetic mapping by bulk segregation analysis excluded all mutations but this one as the cause of renal disease in Aoba mice. Col4a4 has not been targeted in the mouse, and this strain, named Aoba, represents the first functionally null allele in this species. Our study demonstrates the speed and utility of whole genome sequencing coupled with low resolution meiotic mapping as a means of identifying causative mutations induced by ENU.

Original languageEnglish (US)
Pages (from-to)633-641
Number of pages9
JournalGenetics
Volume187
Issue number3
DOIs
StatePublished - Mar 2011

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Alleles
Genome
Mutation
Ethylnitrosourea
Kidney
Specific Pathogen-Free Organisms
Focal Segmental Glomerulosclerosis
Germ-Line Mutation
Mutagens
Pedigree
Inbred C57BL Mouse
Renal Insufficiency
Nucleotides
DNA

ASJC Scopus subject areas

  • Genetics

Cite this

Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis. / Arnold, Carrie N.; Xia, Yu; Lin, Pei; Ross, Charles; Schwander, Martin; Smart, Nora G.; Müller, Ulrich; Beutler, Bruce.

In: Genetics, Vol. 187, No. 3, 03.2011, p. 633-641.

Research output: Contribution to journalArticle

Arnold, Carrie N. ; Xia, Yu ; Lin, Pei ; Ross, Charles ; Schwander, Martin ; Smart, Nora G. ; Müller, Ulrich ; Beutler, Bruce. / Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis. In: Genetics. 2011 ; Vol. 187, No. 3. pp. 633-641.
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