Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer

Abstract

Background: Defects in BRCA1, BRCA2, and other members of the homologous recombination pathway have potential therapeutic relevance when used to support agents that introduce or exploit double-stranded DNA breaks. This study examines the association between homologous recombination defects and genomic patterns of loss of heterozygosity (LOH).

Methods: Ovarian tumours from two independent data sets were characterised for defects in BRCA1, BRCA2, and RAD51C, and LOH profiles were generated. Publically available data were downloaded for a third independent data set. The same analyses were performed on 57 cancer cell lines.

Results: Loss of heterozygosity regions of intermediate size were observed more frequently in tumours with defective BRCA1 or BRCA2 (P=10(-11)). The homologous recombination deficiency (HRD) score was defined as the number of these regions observed in a tumour sample. The association between HRD score and BRCA deficiency was validated in two independent ovarian cancer data sets (P=10(-5) and 10(-29)), and identified breast and pancreatic cell lines with BRCA defects.

Conclusion: The HRD score appears capable of detecting homologous recombination defects regardless of aetiology or mechanism. This score could facilitate the use of PARP inhibitors and platinum in breast, ovarian, and other cancers.

Conflict of interest statement

VA, KMT, JP, JC, TVT, DW, DI, SJ, LF, AG, and JSL are employees of Myriad Genetics, Inc. The remaining authors declare no conflict of interest.

Figures

Figure 1

Fraction of lengths of LOH regions vs length of these regions adjusted to the length of chromosome arm. Chromosomes 13, 14, 15, and 22 were excluded because SNPs are not available for the p arms of these chromosomes. The largest adjusted value of 2 corresponds to LOH over the entire chromosome.

Figure 2

Homologous recombination deficiency score in tumour samples. The number of long LOH regions is shown on the x axis. Blue circles: BRCA1- or BRCA2-deficient samples. Red circles: BRCA1- and BRCA2-intact samples. The combined area under the blue and red circles is the same. This normalisation is used only to facilitate visualisation of the circles. The size of each individual circle is proportional to the number of samples with the corresponding number of LOH regions. (A) Homologous recombination deficiency score for the first cohort (44 of 132 samples were BRCA1 or BRCA2 deficient). (B) Homologous recombination deficiency score for the second cohort (18 of 43 samples were BRCA1 or BRCA2 deficient). (C) Homologous recombination deficiency score for the third cohort (146 of 434 samples were BRCA1 or BRCA2 deficient). (D) Homologous recombination deficiency score for the combined data from all three cohorts. Row A: 221 samples with either BRCA1, or BRCA2, or RAD51C deficient genes; B: 80 BRCA1 mutants (a BRCA1 mutant with a BRCA2 mutation, a BRCA1 mutant with a methylated BRCA1 promoter, and a BRCA1 mutant with a methylated RAD51C promoter were excluded from this plot); C: 43 BRCA2 mutants (a BRCA2 mutant with a BRCA1 mutation was excluded from this plot); D: 82 samples with low expression or methylation of BRCA1 (a sample with a methylated BRCA1 promoter and a BRCA1 mutation was excluded from this plot); E: 13 samples with methylation of RAD51C (a sample with a methylated RAD51C promoter and a BRCA1 mutation was excluded from this plot). Red circles: 388 samples with BRCA1, BRCA2, and RAD51C intact genes.

Figure 3

Comparison of HRD scores in cancer cell lines. Red circles: cell lines with intact BRCA1 or BRCA2. (A) 28 non-ovarian cell lines; (B) 16 ovarian cell lines. Green circles: six carriers of heterozygous mutations in either BRCA1 or BRCA2. Violet circles: one carrier of a homozygous mutation with reversion in BRCA1. Blue circles: six carriers of homozygous mutations in either BRCA1 or BRCA2 or with methylated BRCA1. The combined area under the green, red, blue and violet circles is the same. The size of each individual circle is proportional to the number of samples with the corresponding number of LOH regions.

Figure 4

Kaplan–Meier plot of OS post surgery for HRD score split at it’s median. These data were generated using 507 samples from the TCGA data set for which copy number data and survival information were available. Median OS for samples with high and low HRD score were 1499 (95% CI=(1355–1769)) and 1163 (95% CI=(1081–1354)) days, respectively. The P-value was calculated using Cox model.