117P - Homologous recombination deficiency (HRD) by shallow whole genome sequencing (sWGS): Seamless integration in an existing NGS somatic oncology workflow

Background

PARP inhibitors are now the standard of care for patients with ovarian cancer. The determination of HRD status has become essential to predict sensitivity to these targeted therapies, and has to be integrated in routine oncology assays, beyond the search for BRCA1/2 pathogenic variants. We present the integration of an HRD assay based on tumor shallow whole genome sequencing (sWGS) fully integrated in an existing NGS workflow dedicated to somatic oncology.

Methods

25 samples from ovarian cancer with HRD status was determined using two CE-IVD assays (5 Sofia Genetics / 20 Myriad Genetics). Samples have been re-analysed, starting from FFPE blocks. We performed new DNA extractions from FFPE blocks followed by our dedicated workflow for solid tumor using NGS sequencing. DNA samples were prepared using hybridation method (Twist BioScience®) with Unique Molecular Identifiers (UMI). Part of libraries from HRD samples were collected before the capture step, and directly pooled for sequencing on Illumina® NextSeq 500. sWGS produced were analysed by a dedicated CE-IVD Bioinformatic pipeline for HRD status determination (SeqOne®).

Results

3 different runs of 10 samples each have been sequenced for replicability evaluation. No failure were encountered on any of the sequenced samples. The mean depth, Q30 quality and duplicate rates for sWGS produced were respectively 1.12X / 88.8% / 1.94%, far above the minimum requirements for analysis (> 0.1X). Replicability analysis show an average variation of 4% of the final HRD score. Regarding the HRD status determination, our results show an agreement of 93.3% with the status previously determined, in line with the results obtained by SeqOne during the validation of their bioinformatic analysis (93%).

Conclusions

Theses results demonstrate innovative integration into routine genetics’s laboratory. This implemented methodology allows us to provide a full report with both BRCA1/BRCA2 variant identification and the HRD status for each patient, in an efficient and cost-effective workflow.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

The authors.

Funding

Has not received any funding.

Disclosure

All authors have declared no conflicts of interest.