A database for identifying and visualizing CNAs in cancers at any specific region within the human genome. CaSNP stores pre-computed raw copy numbers, and dynamically generates viewable and downloadable summaries of CNA status in response to user queries. A schema for uniformly processing, storing, annotating and presenting data sets across different data sets or platforms was successfully implemented, making CaSNP a useful tool for cancer genomic meta-study. The query results contain numerical values of cancer copy numbers and the frequencies of CNA events, which are well suited for more detailed analysis by other software or methods. Besides the tabular display, the heatmap view displays SNP copy numbers in colors, enabling users to intuitively and comprehensively visualize the results and facilitating finding novel CNA regions in subset of samples.
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA; Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China
CaSNP funding source(s)
The National Institutes of Health R01 (HG004069, GM077122); Chinese Scholarship Council (2008632067); State S & T Projects (11th Five Year) of China (2008ZX10002-007); National Basic Research Program of China (973 Program No. 2010CB944904)