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Updated: Jun 5, 2025
Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Validation and Performance of Quantitative BRCA1 and RAD51C Promoter Hypermethylation Testing in Breast and Ovarian
J Lynn Fink1, Binny Jaradi1, Nathan Stone1
1XING Genomic Services, Sinnamon Park, Queensland, Australia.
Abstract:
Poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors represent a significant advancement in the treatment of epithelial ovarian cancer, triple-negative breast cancer, pancreatic cancer, and castrate-resistant prostate cancer, and they are poised to improve treatment in an increasing number of other cancer types. PARP inhibitor efficacy as monotherapy has been primarily observed in tumors with deleterious genetic variants in genes involved in the homologous recombination repair pathway. Tumors without these variants have also been shown to respond; notably, those with hypermethylation at all alleles of the BRCA1 or RAD51C promoter can respond to PARP inhibitors. These epigenetic biomarkers therefore represent a patient population that may also benefit from this targeted therapy. However, no robust test has been conducted to identify these biomarkers in routine clinical specimens that is amenable to implementation for decentralized testing. This study describes the analytical and clinical validation of a BRCA1 and RAD51C promoter methylation test that can be run with a single-day library preparation workflow for sequencing on any next-generation sequencing platform. The results show that this test can accurately quantitate the level of promoter methylation at the BRCA1 and RAD51C genes using formalin-fixed, paraffin-embedded samples, even when the extracted DNA is extremely degraded or the input amount is limited. This test increases the precision of diagnostic tests aimed at identifying patients who are likely and unlikely to respond to PARP inhibitor therapy.
Insights
A new test accurately detects BRCA1 and RAD51C promoter methylation in cancer patients. This epigenetic biomarker test helps identify individuals likely to benefit from poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitor therapy.
Area of Science:
- Oncology
- Molecular Diagnostics
- Epigenetics
Background:
- Poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors are effective in treating specific cancers, particularly those with homologous recombination repair (HRR) pathway genetic variants.
- Tumors with BRCA1 or RAD51C promoter hypermethylation, an epigenetic alteration, also respond to PARP inhibitors, indicating a potential patient subgroup for this targeted therapy.
- A validated, decentralized test for identifying these epigenetic biomarkers in routine clinical specimens is currently lacking.
Purpose of the Study:
- To analytically and clinically validate a novel test for detecting BRCA1 and RAD51C promoter methylation.
- To establish a method suitable for decentralized testing using routine clinical samples.
- To improve the precision of diagnostic tests for predicting response to PARP inhibitor therapy.
Main Methods:
- Development and validation of a BRCA1 and RAD51C promoter methylation test.
- Utilized a single-day library preparation workflow compatible with any next-generation sequencing platform.
- Tested the assay's performance on formalin-fixed, paraffin-embedded (FFPE) samples, including those with degraded DNA and limited input.
Main Results:
- The developed test accurately quantitates BRCA1 and RAD51C promoter methylation levels in FFPE samples.
- The assay demonstrates robustness even with extremely degraded DNA and limited sample input.
- The test provides precise diagnostic information for patient stratification regarding PARP inhibitor response.
Conclusions:
- This validated methylation test offers a reliable method for identifying patients who may benefit from PARP inhibitors based on epigenetic biomarkers.
- The assay's compatibility with standard FFPE samples and NGS platforms facilitates its implementation in clinical settings.
- This diagnostic tool enhances the ability to select patients likely to respond to PARP inhibitor therapy, optimizing treatment strategies.
