In-house testing for homologous recombination repair deficiency (HRD) testing in ovarian carcinoma: a feasibility study comparing AmoyDx HRD Focus panel with Myriad myChoiceCDx assay

Abstract

Summary Background Homologous recombination repair (HRR) is the main mechanism of repair of DNA double-strand breaks. Its deficiency (HRD) is a common feature of epithelial ovarian cancers (EOCs). BRCA1/2 mutations and/or other aberrations in genes of HRR are well known causes of HRD and genomic instability. Poly ADP-ribose polymerase inhibitors (PARPi) have revolutionized the management of BRCA mutant EOCs and demonstrated activity in HRD tumor cells. Determining HRD status can provide informations on the magnitude of benefit for PARPi therapy. Myriad MyChoice CDx is a next generation sequencing- based in vitro diagnostic test that assesses the Genomic Instability Score (GIS) which is an algorithmic measurement of loss of heterozygosity, telomeric allelic imbalance, and large-scale state transitions using DNA isolated from formalin-fixed paraffin embedded tumor tissue specimens. However Myriad MyChoice CDx, is a centrally performed and costly assay, with no reimbursement scheduled, at least in Italy. Methods In this report, we described our experience in performing the HRD Focus AmoyDx (Amoy Diagnostics Ltd, Xiamen, Fujian, China) on the same samples of EOCs evaluated with Myriad MyChoiceCDx assay. Results The overall percent agreement between AmoyDx and Myriad was 87.8% (65 of 74 tumors tested). All the 36 AmoyDx negative cases were confirmed to be negative by Myriad (negative predictive value, 100%). Conclusions The concordance of the results with the gold standard Myriad MyChoice CDx assay suggest the feasibility and reliability of HRD testing in diagnostic laboratories with high-throughput NGS platforms and qualified personnel.

Somatic and germline aberrations in homologous recombination repair genes in Chinese prostate cancer patients

“…In terms of the quality control for calling, a sample would not pass the quality control if: the total depth of mutation and wild-type alleles was lower than 100× for somatic sequencing or 20× for germline sequencing; the depth of a mutation allele was lower than 5×; the allelic frequency was lower than 3% for somatic sequencing or 20% for germline sequencing; the base quality of a mutation was lower than 30; the base quality of mutation allele minus the average base quality of both mutation and wild-type alleles was smaller than -2; the read quality of mutation allele minus the average read quality of both mutation and wild-type alleles was smaller than -2; the mapping quality of mutation allele minus the average mapping quality of both mutation and wild-type alleles was smaller than -0.3. These parameters had been validated in previous studies ( 20 , 21 ).…”

Homologous Recombination Deficiency in Ovarian Cancer: from the Biological Rationale to Current Diagnostic Approaches

“…Regarding the implementation of this testing strategy in routine practice, this still represents an open challenge. In a previous experience, Fumagalli et al evaluated the technical feasibility of the HRD Focus Assay, provided by AmoyDx (AmoyDx, Xiamen, China), that is able to detect BRCA1/2 pathogenetic alterations and calculate HRD scores by adopting an optimized bioinformatic pipeline [ 75 ] on a retrospective series of n = 95 HGSCOC patients externally tested with Myriad’s myChoiceCDx solution [ 54 ]. Overall, a success rate of 84.2% for the HRD in-house testing strategy was assessed.…”

“…Remarkably, the in-house testing approach highlighted an outstanding negative predictive value (100.0%) and an encouraging positive predictive value (83.3%) in comparison with an externalized solution. The failures were mostly caused by small biopsies or less-than-ideal DNA quality, caused by the fixative procedure and preanalytical conditions that affected DNA deamination and fragmentation [ 75 ]. Fumagalli et al also compared the average reporting time of the in-house kit to Myriad, focusing on the accessibility and accuracy of in-house HRD testing.…”

“…The results showed excellent concordance with the Myriad assay and short turnaround times [ 76 ]. These aspects highlight the fact that HRD in-house testing approaches provide a technically comparable analytic solution for HRD calculation on real-world clinical samples [ 75 ].…”

Genomic testing in high-grade serous ovarian cancer: current options and future development

“…31 The only exception to this observation is PAOLA-1, where homologous recombination proficient patients derived no significant benefit (1.00; 0.75 to 1.35); however, the addition of bevacizumab within this study may be a compounding factor. Finally, these assays are expensive and require central analysis, two factors which are driving the development of academic assays such as AmoyDx HRD Focus Panel 32 and Leuven HRD test. 33 Alongside these institutional efforts, there is an international academic effort underway to identify more reliable, cost-effective HRD assays using samples from the PAOLA-1 trial.…”