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A Comprehensive and Interactive Array Comparative Genomic Hybridization Database for Cancer Genomes
Raj Chari, BSc,(rchari@bccrc.ca) William W. Lockwood, BSc; Bradley P. Coe, BSc; Calum MacAulay, PhD; Wan L. Lam, PhD; Cancer Genetics and Developmental Biology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
Context: With the wide-spread use of array CGH as a means of assaying genomic alteration status in diseases such as cancer, there is an exponential generation of data corresponding to array CGH profiles. For example, one array CGH methodology utilizes a bacterial artificial chromosome (BAC)-based array platform that provides comprehensive copy number status of a given genome at tiling resolution. Cancer cell lines are frequently used in many different types of experiments to model the potential behavior of actual tumors. A detailed description of their genomes and transcriptomes is necessary for selecting appropriate cell lines for biological experiments. A publicly available, interactive array CGH database containing many commonly used cancer cell lines profiled on high resolution array CGH technologies would be useful to researchers using these particular cell lines as they would be able to obtain information pertaining to their genomic status.
Technology: Java Web Start technology was used for the implementation of the web-based application with MySQL used for data storage.
Design: Over 100 cell line profiles consisting of different types of cancers such as lung, breast, prostate, lymphoma, cervical, colon, ovarian, osteosarcoma and melanoma were used to populate the database. Utilizing a java-based application to interface this database, users can view individual genomic ideograms, view selected sets of samples to delineate the most frequent genomic alterations or compare two groups of samples. In addition, the current organizational scheme allows for relevant and sophisticated queries into the types and subtypes of the different types of cancers in the database. Visualization techniques such as frequency histograms and heatmaps allow for easy analysis and interpretation of array CGH profiles. Within the visualizations, users can query for specific genes or regions of interest.
Results: We have created the largest publicly available whole genome array CGH databases of cancer cell line profiles. With each profile containing over 27,000 measurements throughout the genome, a detailed assessment of the DNA copy number status of 100 of the most commonly used cancer cell lines is readily accessible. In addition, a web-based analytical tool has been developed to facilitate interactive analysis of genomic data in this growing database.
Conclusion: This database, open to all, should be a useful resource to facilitate cancer research.