CaSNP

CaSNP provides a curated database of quantitative copy number alteration (CNA) data derived from single-nucleotide polymorphism (SNP) arrays for comparative analysis of cancer genomes.

Key Features:

• Extensive data repository: Curates approximately 11,500 SNP array datasets spanning 34 cancer types from 104 studies.
• Region and gene-level querying: Accepts genomic regions or gene identifiers to retrieve CNA metrics for specified loci.
• CNA summary metrics: Reports frequencies of gain and loss and averaged copy numbers for each study.
• Marker-level copy number estimates: Provides estimated copy numbers at individual SNP markers around queried regions.
• Heatmap visualization: Presents estimated copy numbers across SNP markers and studies as heatmaps for comparative inspection.
• Data export and genome-browser integration: Offers downloadable data and links to visualize results in the UCSC Genome Browser.
• Gene-type coverage: Includes analyses for both protein-coding genes and LincRNA genes.

Scientific Applications:

• Oncogene and tumor suppressor identification: Supports detection of recurrent CNAs to nominate candidate oncogenes and tumor suppressor genes.
• Cancer mechanism inference: Enables comparative CNA analysis across 34 cancer types to inform hypotheses about underlying cancer mechanisms.
• Discovery of novel cancer-associated elements: Facilitates identification of noncoding elements, including LincRNA, that show recurrent CNAs in cancer.

Methodology:

Aggregation and curation of high-resolution SNP array data from ~11,500 datasets across 104 studies; estimation of copy numbers at individual SNP markers; calculation of frequencies of gains and losses and averaged copy numbers per study; generation of heatmaps and provision of downloadable data and UCSC Genome Browser tracks.