RT Journal Article SR Electronic T1 OncoScape: Exploring the cancer aberration landscape by genomic data fusion JF bioRxiv FD Cold Spring Harbor Laboratory SP 041962 DO 10.1101/041962 A1 Andreas Schlicker A1 Magali Michaut A1 Rubayte Rahman A1 Lodewyk FA Wessels YR 2016 UL http://biorxiv.org/content/early/2016/03/02/041962.abstract AB Although large-scale efforts for molecular profiling of cancer samples provide multiple data types for many samples, most approaches for finding candidate cancer genes rely on somatic mutations and DNA copy number only. We present a new method, OncoScape, which, for the first time, exploits five complementary data types across 11 cancer types to identify new candidate cancer genes. We find many rarely mutated genes that are strongly affected by other aberrations. We retrieve the majority of known cancer genes but also new candidates such as STK31 and MSRA with very high confidence. Several genes show a dual oncogene-and tumor suppressor-like behavior depending on the tumor type. Most notably, the well-known tumor suppressor RB1 shows strong oncogene-like signal in colon cancer. We applied OncoScape to cell lines representing ten cancer types, providing the most comprehensive comparison of aberrations in cell lines and tumor samples to date. This revealed that glioblastoma, breast and colon cancer show strong similarity between cell lines and tumors, while head and neck squamous cell carcinoma and bladder cancer, exhibit very little similarity between cell lines and tumors. To facilitate exploration of the cancer aberration landscape, we created a web portal enabling interactive analysis of OncoScape results.