Shallow Whole Genome Sequencing (sWGS) pipeline for the assessment of Homologous Recombination Deficiency (HRD) score in Hereditary Breast and Ovarian Cancer (HBOC) patients

Introduction: the Homologous Recombination Repair (HRR) system is essential for DNA repair and genomic stability. Homologous Recombination Deficiency (HRD) arises upon the inactivation of several genes involved in HRR, and it is commonly observed in breast and ovarian cancer. The detection of HRD is a valuable tool of clinical relevance, indicative of sensitivity to agnostic therapy and DNA damaging reagents. Methods: shallow Whole Genome Sequencing (sWGS) was performed on 26 ovarian cancer (OC) samples divided into training (n=13) and test group (n=13). The training set included 7 somatic and 6 germline carrying BRCA+ve (n=8) and BRCA-ve (n=5) status. In particular, the BRCA+ve were 3/7 somatic and 5/6 germline samples; the BRCA-ve were 4/7somatic and 1/6 germline. All samples were prepared using the KAPA HyperPlus Library Preparation kit (Roche), pooled and sequenced on NextSeq550 Dx (Illumina). Large-Scale Transitions (LST) profiles were calculated using WGS data at low coverage (<1x) using different sliding window sizes spanning 10-1 000 Kbases. The HRD score was estimated using our bioinformatics pipeline. Results: the BRCA status was assessed in 22/26 OC samples, and the HRD score was evaluated in all somatic samples. In the test group, 7 BRCA+ve samples were classified as HRD+ve, 2 BRCA-ve were classified as HRD-ve, and 4 BRCA unknown samples were predicted as HRD+ve in two cases and HRD-ve in the other half. Discussion: germline BRCA1/2 mutation status is currently the main genetic biomarker of HRD, but it has its drawbacks: HRD can be driven purely by somatic events. A bioinformatics pipeline to evaluate the HRR system status in breast and ovarian cancer has been completed; it is based on sWGS to support therapeutics and follow up strategies.