Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP-arrays

We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by SNP arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Overall copy number assignments were verified by DNA indexes of breast carcinomas and karyotypes of cell lines. The method performs well even for poor quality data, low tumor content, and highly rearranged tumor genomes. To investigate the efficiency of the method 19 primary breast carcinoma samples and 2 breast cancer cell lines were analyzed using 300K Illumina SNP arrays (Illumina HumanHap300-Duov2 Genotyping BeadChip)