Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders

Abstract

Spontaneously arising mouse mutations have served as the foundation for understanding gene function for more than 100 years. We have used exome sequencing in an effort to identify the causative mutations for 172 distinct, spontaneously arising mouse models of Mendelian disorders, including a broad range of clinically relevant phenotypes. To analyze the resulting data, we developed an analytics pipeline that is optimized for mouse exome data and a variation database that allows for reproducible, user-defined data mining as well as nomination of mutation candidates through knowledge-based integration of sample and variant data. Using these new tools, putative pathogenic mutations were identified for 91 (53%) of the strains in our study. Despite the increased power offered by potentially unlimited pedigrees and controlled breeding, about half of our exome cases remained unsolved. Using a combination of manual analyses of exome alignments and whole-genome sequencing, we provide evidence that a large fraction of unsolved exome cases have underlying structural mutations. This result directly informs efforts to investigate the similar proportion of apparently Mendelian human phenotypes that are recalcitrant to exome sequencing.

Discovery and characterization of spontaneous mouse models of craniofacial dysmorphology

“…We used this approach to identify alleles of Alx4 ( lst-2J ) and Pfas ( Sofa-3J ), among others. A majority of our mutant lines enter a standardized HTS exome pipeline to identify putative causative mutations (Fairfield et al, 2011b; Fairfield et al, 2015). This has proven very successful, and more than half (18) of our 33 new mutant genes were identified using this approach (Figure 1C).…”

“…A mapping panel of 100 N:J substrain SNPs indicated a strong linkage to 11-114979024-S with an estimated LOD (score of 9.4308 (significance is LOD ≥ 3) and 37 of 38 animals were concordant with this marker. Whole exome sequencing (Fairfield et al, 2015) revealed a single mismatch allele of C to T on chromosome 11: 112,782,845 on (GRCm38/mm10). The SNV, located in exon one of SRY-box containing 9 ( Sox9 ), is predicted to result in the missense mutation T87M (Figure 3A).…”

“…Until the advent of high-throughput sequencing (HTS) approaches, identification of the causative gene was the major bottleneck in spontaneous and ENU-induced mutant discovery programs. Recent work (Fairfield et al, 2011a; Fairfield et al, 2015), has clearly demonstrated that exome and whole-genome sequencing can now be applied to efficiently identify potential causative variants. These advances have greatly enhanced our ability to identify numerous new spontaneous models of craniofacial dysmorphology that add to our understanding of the genes and pathways that are critical for craniofacial development.…”

Identification of a highly immunogenic mouse breast cancer sub cell line, 4T1-S

“…For example, Sakaguchi et al have described a mouse substrain showing spontaneously developed rheumatoid arthritis phenotype (SKG mice); subsequently SKG mice were shown to have a point mutation in ZAP-70 gene [15]. Additionally, recent exome sequencing revealed pathogenic mutations in 91 strains of mice with Mendelian disorders [16]. Similarly, 4T1-S line might have a substantial mutation which altered its immunogenicity.…”

Mutations in AP3D1 associated with immunodeficiency and seizures define a new type of Hermansky-Pudlak syndrome

“…36 However, the neurologic phenotype and severe hearing loss are also observed in other Ap3d1 mutant strains that do not carry these additional mutations. 37 Third, we show that the identified mutation significantly reduces expression levels of the AP3d protein. Apparently this has severe consequences for the stability of the AP3 complex because the other subunits (AP3b3A, AP3s, and AP3m) were also decreased in protein expression.…”