+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

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



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



Nucleic Acids Research 39(Database Issue): D968



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 SNP marker around the query region across all studies for a more comprehensive visualization. Finally, we used CaSNP to study the CNA of protein-coding genes as well as LincRNA genes across all cancer SNP arrays, and found putative regions harboring novel oncogenes and tumor suppressors. In summary, CaSNP is a useful tool for cancer CNA association studies, with the potential to facilitate both basic science and translational research on cancer.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 051902669

Download citation: RISBibTeXText

PMID: 20972221

DOI: 10.1093/nar/gkq997


Related references

Ultradense array CGH and discovery of micro-copy number alterations and gene fusions in the cancer genome. Methods in Molecular Biology 973: 15-38, 2013

The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome. Bmc Medical Genomics 4: 16, 2011

Whole genome tiling path array CGH analysis of segmental copy number alterations in cervical cancer cell lines. International Journal of Cancer 120(2): 436-443, 2007

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinformatics 21(15): 3308-3311, 2005

Using SAAS-CNV to Detect and Characterize Somatic Copy Number Alterations in Cancer Genomes from Next Generation Sequencing and SNP Array Data. Methods in Molecular Biology 1833: 29-47, 2018

SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Research 33(11): 3455-3464, 2005

Modeling recurrent DNA copy number alterations in array CGH data. Bioinformatics 23(13): I450, 2007

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics 28(1): 40-47, 2012

Genome-wide high-resolution analysis of DNA copy number alterations in NF1-associated malignant peripheral nerve sheath tumors using 32K BAC array. Genes Chromosomes and Cancer 48(10): 897-907, 2009

A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data. Computational Biology and Chemistry 29(1): 47-54, 2005

High-resolution genome-wide copy-number analyses identify localized copy-number alterations in Ewing sarcoma. Diagnostic Molecular Pathology 22(2): 76-84, 2013

Detection of DNA copy number alterations in cancer by array comparative genomic hybridization. Genetics in Medicine 9(9): 574-584, 2007

AscatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data. Current Protocols in Bioinformatics 56: 15.9.1, 2016

Sparse representation and Bayesian detection of genome copy number alterations from microarray data. Bioinformatics 24(3): 309-318, 2008

SNP array analysis in constitutional and cancer genome diagnostics--copy number variants, genotyping and quality control. Cytogenetic and Genome Research 135(3-4): 212-221, 2011