TEST:

AmoyDx® HRD Focus Panel

However, the efficacy and survival of Olaparib in some patients is dismal, in which the effective molecular biomarkers remain to be explored. Total 60 patients (January 2016 to March 2021) received Olaparib (300 mg, BID) with or without Bevacizumab (7.5-15 mg/kg, once every 21 days) (PSR OCs, N=19; Non-PSR OCs, N = 41), and undergo HRD test by AmoyDx® HRD Focus Panel (HRD-positive, GSS score ≥ 50 or BRCA1/2 mutated). In the study, we confirmed that HRD-positive patients can benefit from Olaparib therapy, and have a good prognosis. ICOSLGhigh and ICOSLGhigh & DLX2high, as potential biomarkers of survival and Olaparib efficacy, may help to better identify patients who will benefit most from Olaparib treatment and require further validation in clinical studies.

There is new hope for BRCA -negative ovarian cancer patients receiving targeted therapy. Up to 50% of patients could benefit from PARP inhibitor treatment, depending on their HRD status. However, there are important factors to consider when choosing the right test method.

In our preliminary validation cohor t, we observed a 90% concordance rate between assays, consistent with the results of other series (81.6% to 87.8%). When applying the AmoyDX HRD focus panel in HGSOC, we detected HRD positivity in 48.22% of tumors, similar with the incidences reported in PAOLA1 (48%), PRIMA (50.9%), and VELIA (50.1%) trials. While the global prevalence of BRCA1/2 alterations in ovarian cancer ranges from 20% to 25%, we found that 32% of positive cases in our series exhibited gene variants consistent with previous reports of BRCA variant frequencies in Mexican patients.

Resistance mechanism of PARPi is complex. BRCA restoration mutation is a frequent cause of PARPi resistance. PARPi resistance could be driven without DNA mutation.

A trend for a clinical benefit of second-line therapy with re-exposure to platinum-based agents as compared to irinotecan-based regimens was observed (HR= 0.79, 95%CI 0.34-1.8, P= 0.56)... Platinum-based chemotherapy associates with more favorable outcomes in HRRm BTC patients. Further investigation is needed to delineate HRD in the context of personalizing systemic therapies of BTC.

False-positive rates were 31.6% (6/19) for AmoyDx GI status and 31.9% (7/22) for OncoScanâ„¢, while false-negative rates were 0% (0/28, AmoyDx) and 11.1% (2/18, OncoScanâ„¢) compared with the Myriad MyChoice GI status. While substantial concordance between Myriad MyChoice and alternative assays was demonstrated, prospective validation of the analytical performance and clinical relevance of these assays is warranted.

Our data shows that the implementation of in-house HRD testing in diagnostic laboratories is technically feasible and can be reliably performed with commercial assays. Also, the turnaround time is compatible with clinical needs, making it an ideal alternative to offer to a broader number of patients while maintaining high-quality standards at more accessible price tiers.

"We developed the Seraseq HRD reference materials to meet the needs of laboratories looking to analyze HRD in cancer patient samples. The HRD status of each material was evaluated using several assays using different measurement approaches. Although the materials showed similar trends and concordance among formats, there was variability in GIS across the methods tested."

Pathogenic alterations in DDR pathway genes were seen in 13.5% of the cases studied. DDR-deficient BTC patients showed a trend for better OS and TTE representing a potential subgroup that could benefit from targeted treatment strategies, like PARP-inhibitors. and more prospective data are needed.

"Chinese diagnostics firm Amoy Diagnostics said...that it has entered into a collaboration agreement with AstraZeneca to advance its AmoyDx HRD Complete Panel as a companion diagnostic for the pharma firm's PARP inhibitor Lynparza (olaparib)."

Preliminary functional experiments in HRP (HR proficient, n=5) and HRD (n=4) PDX and organoids (n=3 and n=3 for HRD and HRP respectively) indicate that HRD tumors present low RAD51 foci count (p=0.03 after damage induction) and favorable response to Olaparib and CDDP. Conclusions These data suggest that homologous recombination may be deficient in a substantial proportion of early-stage NSCLC patients, supporting the potential use of PARPi in HRD patients in the adjuvant or maintenance setting.

Analytical performance was assessed with reference cell lines: specificity with wildtype cell lines, sensitivity with gradient HD-positive cell lines (tumor cellularity: 20%, 30%, 40%, 50%) with varying DNA input (30ng, 50ng, 100ng), reproducibility of intra- and inter-runs, and anti-interference against hemoglobin, triglycerides, xylene, paclitaxel, and ethanol...Conclusions A machine learning based method was successfully developed and adopted in multiple NGS assays to detect HD of HRR genes in PC tissues. It provides a reliable approach to effectively identify PC patients with HRR HD.

Accuracy of BRCA1/2 SNV/InDel was further verified with 100% concordance with BRCA1/2 kit. Conclusions With high sensitivity and specificity, short TAT and high success rate, the CE marked (CE-IVD) HRD Complete assay provides a robust and reliable test approach to PC patients that may guide them for a better treatment option.

DDR-deficient BTC patients showed a trend for better OS and TTE representing a potential subgroup that could benefit from targeted treatment strategies, like PARP-inhibitors. Moreover the slight benefit of DDR-mutated BTC under platinum-based therapy supports the hypothesis of better response of DDR-mutated tumours to platinum.

Using the cut-off value of 42 for a new algorithm, the accordance rate between the two tests was 78.9%.Conclusion We successfully developed NGS cancer panel-based HRD test algorithms. The incorporation of the new algorithm on NGS cancer panels might be useful to identify HRD-positive EOC cases.

The analysis shows that biallelic BRCA alterations had higher GSS compared with those with monoallelic inactivation, consistent with positive HRD status. The study indicates that grades 1-2 of the pathological response caused by chemotherapy affect HRD scores and suggests controlling for tumor purity of 40% or more as a critical factor for GSS measurement.

"HRDirect predictions on tumor-only samples reproduced the expected results with a very low discordance (Cohen's kappa: 0.97).After having confirmed that our tool performs well also on matched CRC organoids, we obtained scores from HRDirect and AmoyDX HRD: both approaches resulted equivalent at predicting the sensitivity of CRC cell lines to PARPi.Both tests were unable to identify HRD in samples characterized by ATM loss, a feature characterized by lack of molecular scars. For this reason, we propose to combine the HRDirect scoring with ATM immunohistochemistry (IHC) analysis to improve the overall HRD prediction.ConclusionOur results highlight that combining HRDirect and ATM IHC can potentiate the identification of HRD tumors, with an immediate translational and clinical impact.This finding results of interest not only for the analysis of clinical samples missing the germline DNA, but also for preclinical models that have been demonstrated to be valuable platforms..."

Our small-scale study confirmed that BRCA reversion mutation is one of the important resistance mechanisms of PARPi, and the reversion mutation is located near the germline pathogenic mutation to counteract the reading frame change caused by the frameshift mutation. The up-regulation of B-cell receptor, NK cytotoxic cytokine receptor interaction and other related pathways suggested that PARPi may activate immune response, and the changes in the levels of memory B cells, C7 and neutrophils also confirmed the results above. Epithelial mesenchymal transition induced by CCL18 may also lead to PARPi resistance and activate the NF-κb pathway simultaneously, increasing the inflammatory characteristics of TME.

In addition, to further deepen the mechanisms behind HRD, we analyzed the study cohort by using both a custom NGS panel that analyzed 21 HRR-related genes and FISH analysis to determine the copy numbers of PTEN and EMSY. We found complete concordance in HRD status detected by the Amoy and the Myriad assays, supporting the feasibility of internal HRD testing.

We report a well-characterized cohort of BTC patients analyzed with three molecular assays. The 7% of BTC patients with DDR deficiency might be another subgroup suitable for targeted therapies, i.e. PARP inhibition.

Clinical trial outcomes undoubtedly urge companion diagnostics tests' and newly developed HRD assays' optimization. Nonetheless, sample quality is critical for all methods, especially when complex traits, such as HRD, are measured, as shown by our analyses. Sample quality is adversely affected in numerous steps, from surgery to DNA extraction.

All the 36 AmoyDx negative cases were confirmed to be negative by Myriad (negative predictive value, 100%). 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.

"The HRD status of advanced epithelial ovarian cancer patients may be influenced by platinum-based chemotherapy. So, it should be detected by surgical sample after NACT."

Ten of twelve cell lines harbored alterations in common HRR-related genes, and five cell lines were HRD-positive, although this parameter did not correlate well with Olaparib sensitivity. Moreover, functionally relevant APC and β-catenin mutations were registered, which were also detected in 4/176 (2.3%) samples on a CCA microarray. Although rare, these alterations were exclusive to large duct type CCA with associated intraductal papillary neoplasms of the bile duct (IPNB) in 3 cases, pointing at a distinct form of cholangiocarcinogenesis with potential specific vulnerabilities.

This option may address main concerns related to U.S. Food and Drug Administration (FDA) approved therapy with established companion diagnostics such as cost, test send-out and optimized performance. Our real-life experience underlines the technical challenges related to specimen quality and highlights the necessity for multidisciplinary education and collaboration throughout the patient care pathway.

The HRD status assessed by AmoyDx HRD Focus Panel is highly concordant with that obtained using the current standard reference method. Commercial in-house test may offer a cost-effective, reliable and robust alternative to the centralized assay for the evaluation of HRD status in patient with EOC.

HRD status tested by AmoyDx HRD Focus Panel is significantly correlated with the efficacy of Olaparib, and our results demonstrated a significant PFS benefit for HRD-positive patients compared with HRD-negative patients, especially for patients received Olaparib first-line maintenance therapy.

Conclusion* F1CDx and AmoyDx HRD Focus Panel molecular HRD assays demonstrated concordance with, but not full equivalence to, myChoice CDx. Having multiple assays (providing their performance is adequate) to identify patients whose tumours harbour HRD is important to inform treatment decisions, as well as providing greater choice for clinicians and clinical laboratories.