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.T HE laboratory mouse has been used as a model organism in forward genetic studies in which the point mutagen, N-ethyl-N-nitrosourea (ENU), is applied to generate phenotype, and positional cloning is used to find causative mutations. The availability of an annotated reference genome sequence for the C57BL/6J strain has greatly accelerated the identification of point mutations. However, it remains necessary to outcross mutations and formally map them. In the past, ''fine mapping'' was often needed to define a critical region that could be directly sequenced at the genomic level to identify causative mutations.Coarse mapping to a large chromosomal region coupled with whole genome sequencing using massively parallel short-read sequencing platforms may be sufficient to exclude all but a single ENU-induced mutation in a defined genetic background. Whole genome sequencing may thereby eliminate the need for fine mapping of mutations and exploration of large critical regions, both expensive and time-consuming steps in positional cloning. Whereas a year or more was formerly required to identify causative mutations, a month or less may now be needed.Over the past 4 years, such sequencing platforms, including the Roche (454) GS FLX sequencer, Illumina genome analyzer, and Applied Biosystems SOLiD sequencer, have become available. They all have in common the capability to process millions of sequence reads in parallel at relatively low cost and are being applied in a number of ways, from resequencing whole genomes, as in The 1000 Genomes Project and The Exome Project Here we have applied whole genome sequencing using the Applied Biosystems SOLi...