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Published on: February 24, 2023
Diagnosis of Ovarian Carcinoma Homologous Recombination DNA Repair Deficiency From Targeted Gene Capture Oncology
Niklas Krumm1, Nithisha S Khasnavis2, Marc Radke2
1Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA.
Purpose:
Homologous recombination DNA repair deficiency (HRD) is a therapeutic biomarker for sensitivity to platinum and poly(ADP-ribose) polymerase inhibitor therapies in breast and ovarian cancers. Several molecular phenotypes and diagnostic strategies have been developed to assess HRD; however, their clinical implementation remains both technically challenging and methodologically unstandardized.
Methods:
We developed and validated an efficient and cost-effective strategy for HRD determination on the basis of calculation of a genome-wide loss of heterozygosity (LOH) score through targeted, hybridization capture and next-generation DNA sequencing augmented with 3,000 common, polymorphic single-nucleotide polymorphism (SNP) sites distributed genome-wide. This approach requires minimal sequence reads and can be readily integrated into targeted gene capture workflows already in use for molecular oncology. We interrogated 99 ovarian neoplasm-normal pairs using this method and compared results with patient mutational genotypes and orthologous predictors of HRD derived from whole-genome mutational signatures.
Results:
LOH scores of ≥11% had >86% sensitivity for identifying tumors with HRD-causing mutations in an independent validation set (90.6% sensitivity for all specimens). We found strong agreement of our analytic approach with genome-wide mutational signature assays for determining HRD, yielding an estimated 96.7% sensitivity and 50% specificity. We observed poor concordance with mutational signatures inferred using only mutations detected by the targeted gene capture panel, suggesting inadequacy of the latter approach. LOH score did not significantly correlate with treatment outcomes.
Conclusion:
Targeted sequencing of genome-wide polymorphic SNP sites can be used to infer LOH events and subsequently diagnose HRD in ovarian tumors. The methods presented here are readily generalizable to other targeted gene oncology assays and could be adapted for HRD diagnosis in other tumor types.
Insights
A new method using genome-wide loss of heterozygosity (LOH) scores accurately identifies homologous recombination DNA repair deficiency (HRD) in ovarian tumors. This cost-effective approach aids in diagnosing HRD for targeted cancer therapies.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Homologous recombination DNA repair deficiency (HRD) is a key biomarker for platinum and PARP inhibitor sensitivity in breast and ovarian cancers.
- Current HRD diagnostic strategies face technical challenges and lack standardization, hindering clinical implementation.
Purpose of the Study:
- To develop and validate an efficient, cost-effective strategy for HRD determination using genome-wide loss of heterozygosity (LOH) scores.
- To integrate this method into existing targeted gene capture workflows for molecular oncology.
Main Methods:
- Calculation of a genome-wide LOH score using targeted, next-generation DNA sequencing of ~3,000 polymorphic SNP sites.
- Interrogation of 99 ovarian neoplasm-normal pairs and comparison with mutational genotypes and whole-genome mutational signatures.
Main Results:
- LOH scores ≥11% demonstrated >86% sensitivity for identifying HRD-causing mutations.
- The LOH score method showed strong agreement with genome-wide mutational signature assays (96.7% sensitivity, 50% specificity).
- Targeted gene panels alone showed inadequate concordance for HRD inference.
Conclusions:
- Targeted sequencing of genome-wide polymorphic SNPs can effectively diagnose HRD in ovarian tumors by inferring LOH events.
- The presented method is generalizable to other targeted gene oncology assays and tumor types for HRD diagnosis.
