Okada, A. | bioRxiv Science

bioRxiv2017

A framework for generating interactive reports for cancer genome analysis

SummaryWe introduce paplot, the software for generating dynamic reports that are frequently necessary in the post analytical phases of cancer genome studies. The \"interactive\" nature of the paplot-generated reports enables users to extract much richer information than that obtained from static graphs via most conventional visualization tools.\n\nAvailability and implementationThe python implementation for paplot (MIT license) is available at https://github.com/Genomon-Project/paplot. The documentation is at http://paplot-doc.readthedocs.io/en/latest/.\n\nContactyshira@hgc.jp

bioinformatics↗

bioRxiv2017

A comprehensive characterization of cis-acting splicing-associated variants in human cancer

Although many driver mutations are thought to promote carcinogenesis via abnormal splicing, the landscape of these splicing-associated variants (SAVs) remains unknown due to the complexity of splicing abnormalities. Here we developed a statistical framework to identify SAVs disrupting or newly creating splice site motifs and applied it to sequencing data from 8,976 samples across 31 cancer types. We constructed a catalog of 14,438 SAVs, approximately 50% of which consist of SAVs disrupting non-canonical splice sites (including the 3rd and 5th intronic bases of donor sites) or newly creating splice sites. Smoking-related signature substantially contributes to SAV generation. As many as 14.7% of samples harbor at least one SAVs in cancer-related genes, particularly in tumor suppressors. Importantly, in addition to previously reported intron retention, exon skipping or alternative splice site usage more frequently affected these genes. Our findings delineate a comprehensive portrait of SAVs, providing a basis for cancer precision medicine.

genomics↗