CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data

Cancer is known to have abundant copy number alterations (CNAs) that greatly contribute to its pathogenesis and progression. Investigation of CNA regions could potentially help identify oncogenes and tumor suppressor genes and infer cancer mechanisms. Although single-nucleotide polymorphism (SNP) arrays have strengthened our ability to identify CNAs with unprecedented resolution, a comprehensive collection of CNA information from SNP array data is still lacking. We developed a web-based CaSNP (http://cistrome .dfci.harvard.edu/CaSNP/) database for storing and interrogating quantitative CNA data, which curated 11 500 SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each...

• Type: Journal
• Year: 2011
• Where: NAR
• Authors: Qingyi Cao, Meng Zhou, Xujun Wang, Clifford A. Meyer, Yong Zhang, Zhi Chen, Cheng Li, X. Shirley Liu
• Keywords: Genome Browser, NAR 2011, Tumor Suppressor Genes, Tumor Suppressors