Table 1.
Characteristics of patients and tumors.
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.
Table 2.
BRCA2 signature genes.
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.
Table 3.
GSEA for loss of chromosomal bands.
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.
Table 4.
FISH with probes in the region of common deletion on chromosomes 13 and 14.
Table 5.
Contingency table summarizing the FISH data for deletions on chromosomes 13 and 14.