1213P - HRD complete: A novel NGS assay for detecting homologous recombination repair (HRR) gene alterations in prostate cancer

Background

HRR gene alterations, which are enriched in prostate cancer (PC), are associated with sensitivity to PARP inhibitors. However, the tests available to detect HRR gene alterations are limited and usually large NGS panels with high cost and long turnaround time (TAT). A novel HANDLE (Halo-shape ANnealing and Defer-Ligation Enrichment) based NGS assay, AmoyDx HRD Complete was established to evaluate single nucleotide variant (SNV), short insertion and deletion (InDel) and homozygous deletion (HD) of 17 HRR genes in PC tissues, with 4 days TAT.

Methods

Sensitivity was validated in serially diluted cell lines with varying DNA input: with gradient mutation allele frequency (MAF) (7%, 5%, 3%) for SNV/InDel; with different tumor content (50%, 40%, 30%, 20%) for HD. Specificity was validated in wild type cell lines. Testing success rate was evaluated using 100 formalin-fixed paraffin-embedded (FFPE) PC tissues (up to 10 years old). A “three-tube” library process was developed for samples which failed DNA, library, or sequencing QC with standard process. Accuracy was assessed in >200 FFPE PC tissues, using commercially available AmoyDx HRD54 NGS kit (hybridization capture based) and AmoyDx BRCA1/2 NGS kit (CE-IVD) as reference tests.

Results

Sensitivity of HRR SNV/InDel was 99.4% (179/180, MAF 5%) with 30ng DNA. Sensitivity of HRR HD was 100% at gene level with 30% tumor content and at exon level with 40% tumor content with 100ng DNA. Specificity was 100%. 54/100 (54%) PC tissues had valid sequencing results using standard process, whereas the “three-tube” library improved the success rate to 84%. For HRR SNV/InDel accuracy, 98/100 PC tissues showed concordant results with HRD54 kit (PPA 96.8%, NPA 98.6%, OPA 98.0%). For HRR HD accuracy, 130/132 PC tissues showed concordant results with HRD54 kit (PPA 100%, NPA 98.4%, OPA 98.5%). 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.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

The authors.

Funding

Janssen.

Disclosure

X. Ye, U. Singh, K. Bell, K. Urtishak, L. Luo, X. Lyu, M. Gormley, D.A. Smirnov, L. Zhou: Financial Interests, Institutional, Full or part-time Employment: Johnson and Johnson. P. Cheng, Y. Guo, J. Wang, W. Xu, Z. Huang, X. Chen, S. Liu, S. Yang, W. Shi, C. Zhu: Financial Interests, Personal, Full or part-time Employment: Amoy Diagnostics.