Assessment of palindromes as platforms for DNA amplification in breast cancer

DNA amplification, particularly of chromosomes 8 and 11, occurs frequently in breast cancer and is a key factor in tumorigenesis, often associated with poor prognosis. The mechanisms involved in the amplification of these regions are not fully understood. Studies from model systems have demonstrated that palindrome formation can be an early step in DNA amplification, most notably seen in the breakage-fusion-bridge (BFB) cycle. Therefore, palindromes might be associated with gene amplicons in breast cancer. To address this possibility, we coupled high-resolution palindrome profiling by the Genome-wide Analysis of Palindrome Formation (GAPF) assay with genome-wide copy-number analyses on a set of breast cancer cell lines and primary tumors to spatially associate palindromes and copy-number gains. We identified GAPF-positive regions distributed non-randomly throughout cell line and tumor genomes, often in clusters and associated with copy-number gains. Commonly amplified regions in breast cancer, chromosomes 8q and 11q, had GAPF-positive regions flanking and throughout the copy-number gains. We also identified amplification-associated GAPF-positive regions at similar locations in subsets of breast cancers with similar characteristics (e.g., ERBB2 amplification). These shared positive regions offer the potential to evaluate the utility of palindromes as prognostic markers, particularly in premalignant breast lesions. Our results implicate palindrome formation in the amplification of regions with key roles in breast tumorigenesis, particularly in subsets of breast cancers. DNA palindrome profiles generated using the Genome-wide Analysis of Palindrome Formation (GAPF) assay. Whole genome profiling was performed on Colo320DM vs HF and MCF7 vs HF. Prolifing of chromosomes 8, 11, and 12 was performed on BT474 vs PBL, MCF7 vs PBL, MDA231 vs PBL, UACC893 vs PBL and 4 primary invasive ductal carcinomas (IDCs) vs PBL. Copy-number analysis on SNP 6.0 arrays was performed on Colo320DM and the 4 primary IDCs. The CEL files for the 4 breast cancer cell lines were obtained from the Wellcome Trust Sanger Institute Cancer Genome Project web site (http://www.sanger.ac.uk/genetics/CGP). All SNP arrays were compared to the HapMap cellection reference.