Detection of Merkel cell polyomavirus using whole exome sequencing data

Merkel cell carcinoma (MCC) is a highly malignant neuroendocrine tumor of the skin in which Merkel cell polyomavirus (MCV) DNA virus insertion can be detected in 75-89% of cases. Etiologic and phenotypic differences exist between MCC tumors with and without the inserted virus, thus it is important to distinguish between MCV+ MCC and MCV-MCC cases. Currently, MCV insertions in MCC genomes are detected using laboratory techniques. Here we report a freely available bioinformatics methodology to identify MCV+ MCC tumors using whole exome sequencing (WES) data. WES data could be also used to infer the virus insertion site into the tumor genome. Our method has been validated in a set of MCC samples previously characterized in the laboratory as MCV+ or MCV-, achieving 100% sensitivity and 62,5% specificity. Thus, with enough depth of sequencing, it is possible to use WES to the presence of MCV insertions in cancer samples.