// publications / [2] signatures of selection in DNA sequences

Selection on nonsense variants:

Human genetic diseases differ in whether NMD typically aggravates or alleviates the phenotypic effects of nonsense variants // Failure to trigger NMD is a cause of ineffective gene inactivation by CRISPR–Cas9 gene editing // NMD strongly determines the efficacy of cancer immunotherapy, with only transcripts that escape NMD predicting a response
Matched exome and transcriptome data can systematically elucidate the rules of NMD targeting in human tumors, explaining ¾ of the variance in NMD efficiency. Applying our NMD model identifies signatures of positive and negative selection on nonsense mutations in human tumors, and provides a classification for tumor-suppressor genes.

Selection on synonymous mutations:

Enrichments of somatic mutations indicate that ~1 in 5 synonymous mutations in oncogenes are cancer drivers. Involvement in known exonic splicing motifs and association to RNA-Seq data implicates many causal synonymous mutations to altered splicing. The 3’ UTRs of dosage-sensitive oncogenes also harbour causal mutations.
Comparative analyses of genomes, from bacteria across fungi to humans and human tumors have revealed many links between genes' biological roles and the accrual of synonymous mutations. The evolutionary trace of codon bias patterns across homologous genes may be examined to learn about a gene’s relevance to various phenotypes, or, more generally, its function in the cell.

"Admit that complexity always increases, first from the model you fit to the data, thence to the model you use to think about and plan about the experiment and its analysis, and thence to the true situation." -- John Tukey