Genomic profiling of breast cancer

Cancer and other genetic diseases are characterized by genome alterations, including DNA copy number changes. Comparative genomic hybridization (CGH) represents a powerful technique to detect and map these aberrations, and recent improvements in resolution and sensitivity have been possible through implementation of microarray-based platforms. Germline mutations in the two major breast cancer susceptibility genes, BRCA1 and BRCA2, account for a significant proportion of all hereditary breast cancers. Earlier studies have shown that inherited and sporadic tumors progress along different somatic genetic pathways and that global gene expression profiles distinguish between these groups. Using 1 Mbp resolution BAC-array CGH analysis, we now show that genomic copy number profiles similarly discriminate between BRCA1/BRCA2-related tumors and sporadic tumors. Overall, BRCA1 tumors had a higher frequency of copy number alterations than sporadic breast cancers. In particular, frequent losses on 4p, 4q and 5q in BRCA1 tumors and frequent gains on 7p and 17q24 in BRCA2 tumors distinguish these from sporadic breast cancer. Distinct amplicons at 3q27.1-q27.3 were identified in BRCA1 tumors, and amplicons at 17q23.3-q24.2 in BRCA2 tumors. Moreover, evidence of a homozygous deletion in a BRCA1 tumor on 5q12.1 was obtained. Using a set of 169 BAC clones that detect significantly different frequencies of copy number changes in inherited and sporadic tumors, these subsets could be discriminated into separate groups using hierarchical clustering. Further validation may prove this tumor classifier to be useful for selecting familial breast cancer cases, likely to carry BRCA1 or BRCA2 germline mutations, for further mutation screening, particularly as these data can be obtained using DNA prepared from archival tumor tissue.

Further improved genomic profiling was obtained by construction of microarrays comprising 32,433 BAC clones, offering complete genome coverage at single gene resolution, on average <50 kbp. These new tiling 32k-arrays were evaluated on breast cancer cell lines (BT-474, MCF7, HCC1937, SK-BR-3, L56Br, ZR-75-1), validated by FISH and gene expression analysis. Known amplicons were resolved and found to include complex patterns of narrow peaks, occasionally including a few or even single genes. Several amplified regions and genes on 17q and 20q were depicted and confirmed by demonstrating strong correlations between gene copy numbers and expression. Previously described as well as novel homozygous deletions, ranging from a few BAC clones (<300 kb) to several Mbp, were observed, including PTEN and other regions on 10q, CDH1/CDH3 on 16q22, and new regions on 4q34 and 19p12, emphasizing the power of array CGH in pinpointing genes of importance in tumor development. Array CGH is a promising diagnostic tool in profiling of somatic and constitutional genomic alterations.