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SIGMA Viewer: A Platform to Visualize and Analyze DNA Copy Number Microarray Data

Andrew Thomson1, (athomson@bccrc.ca) Anna Chu1, Devon Macey1, Raj Chari1, Bradley P. Coe1, Wan L. Lam1.  1British Columbia Cancer Research Centre, Vancouver, BC and University of British Columbia, Vancouver, BC

Context:  Array comparative genomic hybridization is a method of determining copy number changes by comparing the fluorescence ratio of tumor DNA to reference DNA at different locations in the genome.  Currently, few programs exist which allow users to visualize and analyze copy number array CGH data with an easy user interface.  However, these applications suffer from limited operating system interoperability, inadequate incorporation of segmentation algorithms, or support of only a small number of microarray platforms.

Technology:  We implemented a software package implemented in Java which uses a MySQL database for storage of data and results and the statistical package R for statistical analysis.

Design:  We have created a software platform, System for Integrated Genomic Microarray Analysis (SIGMA), developed in Java to facilitate use across all operating systems.  A secure, searchable database has been established to facilitate the backing-up and optional sharing of genomic data.  SIGMA is highly versatile, having the ability to view copy number data from a variety of microarray platforms.  Multiple visualizations, including ratio value and frequency plots, are available at different magnifications and aspects for the user to view data.  In addition, SIGMA utilizes existing segmentation algorithms such as DNAcopy [Biostatistics 2004 Oct 5(4):557-72] as well as a newly developed algorithm which is built in.  SIGMA is also designed for ease of extension so that new data types can be handled effortlessly and additional algorithms are simple to incorporate.  All of this allows for a unified pipeline: data can be loaded, processed, segmented, viewed, compared and exported all within the same framework, eliminating unnecessary movement and possibly conversion between multiple software programs.

Conclusion:  We developed a unified program for data storage, visualization, and integrated analysis of array CGH data.