Whole-miRNome sequencing: a panel for the targeted sequencing of all human miRNA genes

Interest in the genetic variation of noncoding genomic elements, including microRNAs (miRNAs), is growing, 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 the first whole-miRNome sequencing (WMS) platform, which enables the targeted sequencing of all human miRNA genes (n ∼2000) and 28 miRNA biogenesis genes. By sequencing various types of DNA samples, including ∼300 tumor/normal pairs, from lung, colorectal, ovarian, renal, and basal cell carcinomas, we identified ∼2000 mutations, including 879 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, which was specifically mutated in basal cell carcinoma, suggesting its potential role in this cancer. WMS also allowed the identification of multiple copy number alterations, which often encompassed miRNA genes. WMS provides highly effective, low-cost sequencing of all miRNA genes in different types of samples, including highly degraded ones.