Whole-miRNome sequencing (WMS) - a panel for targeted sequencing of all human miRNA genes

There is a growing interest in the genetic variation of noncoding genomic elements, including miRNAs, and several mutations in miRNA genes implicated in human diseases, including cancer, have already been detected. However, the lack of dedicated analytical tools severely hampers progress in this area. In this study, we developed whole-miRNome sequencing (WMS), which enables targeted sequencing of all human miRNA genes (n[~]2000) and 28 miRNA biogenesis genes. Herein, by sequencing almost 600 samples, including [~]300 tumor/normal pairs of samples from different cancer types, we identified [~]2, 000 mutations, including 1, 435 cancer somatic mutations, with 879 occurring in miRNA genes. These mutations were located in all parts of the genes, including seed or cleavage sites essential for the functioning of miRNA genes. The high reliability of the mutations was confirmed through various approaches, including different sequencing methods. The analysis identified several miRNA genes with functional enrichment of cancer mutations, including MIR3928, specifically mutated in basal cell carcinoma (BCC), indicating its potential role in this cancer. WMS also allowed the identification of multiple copy number alterations, hotspots of which often encompassed miRNA genes. WMS provides highly effective, low-cost sequencing of all miRNA genes in different types of samples, including highly degraded FFPE samples.