Deletion of chromosomes 13q and 14q is a common feature of tumors with BRCA2 mutations

Abstract

Introduction: Germline BRCA1 or BRCA2 mutations account for 20-30% of familial clustering of breast cancer. The main indication for BRCA2 screening is currently the family history but the yield of mutations identified in patients selected this way is low.

Methods: To develop more efficient approaches to screening we have compared the gene expression and genomic profiles of BRCA2-mutant breast tumors with those of breast tumors lacking BRCA1 or BRCA2 mutations.

Results: We identified a group of 66 genes showing differential expression in our training set of 7 BRCA2-mutant tumors and in an independent validation set of 19 BRCA2-mutant tumors. The differentially expressed genes include a prominent cluster of genes from chromosomes 13 and 14 whose expression is reduced. Gene set enrichment analysis confirmed that genes in specific bands on 13q and 14q showed significantly reduced expression, suggesting that the affected bands may be preferentially deleted in BRCA2-mutant tumors. Genomic profiling showed that the BRCA2-mutant tumors indeed harbor deletions on chromosomes 13q and 14q. To exploit this information we have created a simple fluorescence in situ hybridization (FISH) test and shown that it detects tumors with deletions on chromosomes 13q and 14q.

Conclusion: Together with previous reports, this establishes that deletions on chromosomes 13q and 14q are a hallmark of BRCA2-mutant tumors. We propose that FISH to detect these deletions would be an efficient and cost-effective first screening step to identify potential BRCA2-mutation carriers among breast cancer patients without a family history of breast cancer.

Figure 1. Unsupervised hierarchical clustering of the 66 BRCA2 signature genes in the training set.

There are seven BRCA2-mutant tumors and 24 BRCAX tumors (tumors from patients lacking known BRCA1/2 mutations but with a familial history of breast cancer). The upper left quadrant contains many genes on 13q and 14q that show reduced expression in BRCA2 tumors.

Figure 2. ROC analysis of the BRCA2 signature in the validation set.

Each tumor was given a score that was a weighted sum of the mean centered gene expression levels for each gene in the signature. The validation set contained 19 BRCA2 and 12 BRCAX tumors. The AUC was 0.76.

Figure 3. Unsupervised hierarchical clustering of the 66 BRCA2 signature genes in the validation set.

There are 19 BRCA2-mutant tumors and 12 BRCAX tumors. The lower left quadrant contains many genes on 13q and 14q that show reduced expression in BRCA2 tumors.

Figure 4. Genomic profiles in the training set.

Upper panels: BAC-CGH profiles of BRCA2-mutant tumors showing gains in red, losses in green and modal copy number in yellow. Lower panels: BAF profiles of BRCA2-mutant tumors on Illumina SNP arrays. The boundaries of the common regions of deletion on chromosomes 13 and 14 are marked by vertical red lines.

Figure 5. Cumulative rates of gain and loss for tumors analyzed by CGH (red, 4 BRCA2-mutant tumors; black, 24 BRCAX tumors).

A, All chromosomes; B, Chromosome 13; C, Chromosome 14. Each vertical line in B & C corresponds to an individual BAC probe. When the red line reaches −1, all of the tumors showed loss for that probe.

Figure 6. FISH with probes in the region of common deletion in a BRCA2-mutant tumor.

A, chromosome 13; B, chromosome 14. Red: probe in the deleted region; Green, pericentromeric probe. Each nucleus contains two green spots and one red spot, indicating that the tumor is diploid for chromosomes 13 and 14 but has heterozygous deletions in the regions tested by the red probes.