A targeted genetic sequencing strategy effectively identified homologous recombination DNA repair deficiency in ovarian cancer patients, and may eventually help predict treatment response, a study suggests.
Previous research has identified homologous recombination DNA repair deficiency (HRD) as a biomarker for sensitivity to poly( ADP-ribose) polymerase inhibitors (PARPi) and platinum-based therapies in patients with ovarian and breast cancers, wrote Niklas Krumm, MD, of the University of Washington, Seattle, and colleagues.
Currently, direct genetic testing is the most widely used method to identify mutations in HRD-associated genes, but not all genes underlying HDD have been identified, therefore current HRD assays that don't rely on gene-specific information have been considered more diagnostically useful, the researchers noted. Two genetic tests are approved by the Food and Drug Administration, which are the FoundationFocus CDX BRCA and myChoice CDx, the researchers wrote. The Foundation Focus CDX BRCA was approved in 2016, and myChoice CDx was approved in 2019.
"However, transparent, well-defined methods and criteria for diagnosing HRD by genomic scarring that are practical for smaller, academic, or private laboratories have not yet been established or widely implemented," they said.
In the paper published in JCO Precision Oncology, the researchers said they developed a molecular testing strategy involving the use of common, polymorphic single-nucleotide polymorphisms (SNPs).
They used a panel of approximately 3,000 SNPs distributed across the genome to create a loss of heterozygosity (LOH) score that could identify HRD.
To determine the ability of LOH to diagnose HRD in ovarian cancers, the researchers examined 99 ovarian neoplasm–normal pairs using the LOH method, and compared results with patient mutational genotypes and HRD predictors. LOH scores of 11% or higher showed greater than 86% sensitivity for identifying tumors with HRD-causing mutations in an independent validation set, and a sensitivity of 90.9% across training and validation sets.
When LOH scores were compared to a validated genome-wide mutational signature assay (HRDetect) the sensitivity and specificity of an LOH score of 11% or higher were estimated at 96.7% and 50%, respectively, for determining HRD-positive tumors.
However, the researchers found poor concordance (statistically insignificant correlation) using their LOH capture design to diagnose HRD based on mutational signatures only from targeted regions. "We conclude that mutational signatures inferred from our diagnostic tumor panel are unable to accurately ascertain HRD status, likely because the absolute number of somatic variants that it is able to identify is insufficient," they said.
LOH scores were not significantly correlated with treatment outcomes, which suggests that LOH score can be used to infer HRD status, rather than serving as a direct predictor of patient response to primary platinum therapy, the researchers said. The average LOH score was higher in patients whose cancers responded to platinum therapy than in those with no treatment response (17% vs. 15%) but this difference was not significant.
Study limitations
The research was limited by several factors, including the validation only for high-grade non–clear cell ovarian carcinomas, and LOH scores likely vary across cancer types, therefore more studies will be needed to optimize the strategy for different cancers, the researchers noted. Other potential limitations include the high level of tumor cellularity needed (30%), which will eliminate some specimens, they said.
Finally, the poor predictive value of LOH itself for treatment outcomes suggests a limitation of the HRD biomarker in this respect, the researchers concluded.
Potential advantages of using LOH method
However, the potential advantages of the LOH method include the minimal sequence reads and the ability to integrate the LOH into current targeted gene capture workflows, the researchers wrote, and the LOH score appears to be a reliable predictor of HRD positivity.
"Although we have found that the regions targeted by our assay are insufficient to identify HRD-associated mutational signatures, future refinements to this approach could integrate minimal additional sequencing targets designed to robustly identify such signatures in concert with LOH events," they concluded.
Study shares the details of detection methodology
"Tumors with HRD are sensitive to certain cancer chemotherapeutic agents [PARP inhibitors]," said Dr. Krumm, in an interview. "Until recently, HR-deficient tumors were primarily identified via inactivating BRCA1 or BRCA2 mutations, but now it is understood that an entire repair pathway can be affected and can result in HRD. Therefore, we sought to implement an NGS-based approach that could detect the 'HRD phenotype' in the DNA of tumors," he said.
The approach developed by Dr. Krumm and colleagues and presented in the current study "is not the first in the field, as some commercial tests have similar approaches," he said. However, the current study is important, "because it openly publishes the methodology and detailed results of our validation work in bringing HRD detection online in our clinical lab," he said.
"One of the advantages of a genome-wide approach is that we can identify HR-deficient tumors, even when BRCA1 and BRCA2 do not have any detectable loss-of-function mutations," said Dr. Krumm. "HRD detection is a relatively young test in the field of next-generation sequencing (NGS)–based cancer diagnostics. One of the challenges currently is the lack of large, standardized reference data sets or reference materials that can be used to compare tests and methodology in a clinical setting. We hope that by publishing our methods, more data sets can be generated and published," he said.
Some specific challenges to using the test clinically today include the need for a paired tumor plus blood sample, and the need for a relatively high fraction of tumor content in the sample, Dr. Krumm noted.
"This test is currently being used in a clinical setting at the University of Washington, as it is a laboratory-developed test (LDT) and part of our clinically validated NGS platform," said Dr. Krumm. "This test highlights how LDTs can advance clinical testing capabilities and improve the care of our patients and illustrates the UW Medicine position that LDTs are a necessary and important part of the clinical care. That said, we anticipate that additional validation studies, including long-term clinical effectiveness and outcome studies, will be required to bring HRD testing into a commercial platform that undergoes FDA review," he explained.
The study was supported by the Brotman Baty Institute for Precision Medicine, the National Institutes of Health, and the Department of Defense, Ovarian Cancer Research Program Clinical Development Award. Dr. Krumm disclosed stock and ownership interests in Reference Genomics.
This article originally appeared on MDedge.com, part of the Medscape Professional Network.
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Cite this: Sequencing Strategy in Ovarian Cancer Helps Guide Treatment - Medscape - Jun 08, 2023.
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