De novo mutational profile in RB1 clarified using a mutation rate modeling algorithm

• Published in: BMC genomics Vol. 18; no. 1; p. 155
• Main Authors: Aggarwala, Varun, Ganguly, Arupa, Voight, Benjamin F.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 14.02.2017; Springer Nature B.V
• Subjects: Algorithms; Animal Genetics and Genomics; Biomedical and Life Sciences; Cancer; Cell cycle; CpG islands; Depletion; Disease; Enrichment; Exons; Genes; Genomes; Genomics; Heterogeneity; Human and rodent genomics; Humans; Hypotheses; Hypothesis testing; Introns; Life Sciences; Microarrays; Microbial Genetics and Genomics; Missense mutation; Models, Genetic; Mutation; Mutation Rate; Mutation rates; Phenotypes; Plant Genetics and Genomics; Proteins; Proteomics; Research Article; Retina; Retinoblastoma; Retinoblastoma - genetics; Retinoblastoma Binding Proteins - genetics; RNA Splice Sites; Sequence Analysis, DNA; Statistics; Tumors; Ubiquitin-Protein Ligases - genetics; Mutation Rate; mutations; Retinoblastoma; Variant Prioritization; Variability in Mutation Rate; de novo mutations
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-017-3522-z

Background Studies of de novo mutations offer great promise to improve our understanding of human disease. After a causal gene has been identified, it is natural to hypothesize that disease relevant mutations accumulate within a sub-sequence of the gene – for example, an exon, a protein domain, or at CpG sites. These assessments are typically qualitative, because we lack methodology to assess the statistical significance of sub-gene mutational burden ultimately to infer disease-relevant biology. Methods To address this issue, we present a generalized algorithm to grade the significance of de novo mutational burden within a gene ascertained from affected probands, based on our model for mutation rate informed by local sequence context. Results We applied our approach to 268 newly identified de novo germline mutations by re-sequencing the coding exons and flanking intronic regions of RB1 in 642 sporadic, bilateral probands affected with retinoblastoma (RB). We confirm enrichment of loss-of-function mutations, but demonstrate that previously noted ‘hotspots’ of nonsense mutations in RB1 are compatible with the elevated mutation rates expected at CpG sites, refuting a RB specific pathogenic mechanism. Our approach demonstrates an enrichment of splice-site donor mutations of exon 6 and 12 but depletion at exon 5, indicative of previously unappreciated heterogeneity in penetrance within this class of substitution. We demonstrate the enrichment of missense mutations to the pocket domain of RB1 , which contains the known Arg661Trp low-penetrance mutation. Conclusion Our approach is generalizable to any phenotype, and affirms the importance of statistical interpretation of de novo mutations found in human genomes.