1199P - Developing and systematically validating homologous recombination repair gene detection method based on next-generation sequencing

Background

Homologous recombination repair (HRR) genes play a critical role in tumor DNA damage repair. Loss-of function HRR alternation, including SNV/Indel and homozygous deletion (HD), could predict sensitivity of poly ADP-ribose polymerase (PARP) inhibitor. Therefore, developing a comprehensive and reliable HRR detection approach is necessary.

Methods

In this study, prostate samples (cancer tissue specimens and cell lines) carrying HRR SNV/Indel/HD alterations or wild-type genomes were used to assess the performance of a Next Generation Sequencing (NGS) kit (AmoyDx HRD Complete Panel) for the SNV/Indel/HD detection, which covers 17 HRR genes and 3 tumor-associated genes. The AmoyDx master panel was used as a reference test.

Results

Of the 102 prostate cancer samples (including 19 BRCA1/2 SNV/indel-positive samples and 1 BRCA2 HD-positive sample), positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement (OPA) of the two NGS kits for BRCA1/2 detection were all 100%. 8 SNV/Indel-positive samples were constructed into 576 reactions that were validated by gradient dilution and repetition. The limit of detection (LOD) criterion for SNV/Indel were ≥ 5% and the amount of DNA input was 30 ng. Detection sensitivity for HD at the exon level was 100% when tumor purity was greater than 40% and DNA input was 100ng. For gene level HD, tumor purity ≥ 30% was required. 8 SNV/Indel/HD positive or negative (4 SVN/Indel positive, 2 HD positive, 2 SNV/Indel/HD negative) samples were tested repeatedly with different batches of reagents in different time periods. The coefficient of variance (CV) of positive samples was less than 10%, and the negative samples were all negative for repeat testing. In the presence of hemoglobin, triglyceride, and paclitaxel during the extraction process, or ethanol (found in DNA samples), xylene, or proteinase K during the DNA addition, the OPA of testing samples was 100% compared to the reference.

Conclusions

This study demonstrated that Amoydx human homologous recombination repair gene panel exhibited high concordance with AmoyDx master panel and could provide reliable HRR SNV/Indel/HD detection.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

The authors.

Funding

Has not received any funding.

Disclosure

X. Lin, Y. Guo, P. Cheng, Z. Huang, C. Zhu: Financial Interests, Institutional, Full or part-time Employment: Amoy Diagnostics Co., Ltd. All other authors have declared no conflicts of interest.