OncoScape: Exploring the cancer aberration landscape by genomic data fusion.
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 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 (http://ccb.nki.nl/software/oncoscape).
Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Andreas
A
Schlicker
Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Magali
M
Michaut
Research IT, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Rubayte
R
Rahman
Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.|Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands.
Lodewyk F A
LF
Wessels
D045744:Cell Line, Tumor; D056915:DNA Copy Number Variations; D019175:DNA Methylation / Q000235:genetics; D020869:Gene Expression Profiling; D016147:Genes, Tumor Suppressor; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D009154:Mutation / Q000235:genetics; D009369:Neoplasms / Q000145:classification / Q000235:genetics*; D009857:Oncogenes / Q000235:genetics*; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics
D034741:RNA, Small Interfering