A Single Cell Genomic Signature to Detect Homologous Recombination Deficiency (HRD) and PARP Inhibitors Sensitivity Using Patient's Circulating Tumor Cells (Ctcs).

e23015 Background: PARPi have been successfully exploited as therapeutic agents in breast and ovarian tumors with HRD associated with germline BRCA mutations, and recently in metastatic castration resistance prostate cancer (mCRPC). Stratification of patients sensitive to PARPi is often based on the detection of HRD inactivating mutations and/or genomic scarring conducted in tumor tissue biopsies. These methods lack sensitivity due to their intrinsic limitation to resolve intra-tumor heterogeneity. To circumvent this, we developed a single cell HRD genomic signature aim to predict PARPi response in patients. Methods: 3 breast cancer cell lines (2 PARP sensitive BRCA mutant, MDA-MB-436 and HCC1395, and 1 BRCA wild type MDA-MB-231), and 3 BRCA wild type PARP resistant prostate cancer cell lines (VCaP, LnCaP and PC3) were identified and analyzed using Epic’s proprietary technology. Single cell DNA sequencing libraries were constructed to detect genome-wide Large Scale Transitions (LSTs) while target enrichment was performed to simultaneously assess for HRD inactivating mutations and loss of heterozygosity (LOH). Results: The highest median LSTs were observed in the BRCA mutant cell lines (50 ± 1; 58 ± 4, in HCC1395 and MDA-MB-436, respectively). Among BRCA wild type, the LSTs were highest in VCaP (33 ± 3) and PC3 (33 ± 4), both harboring p53 and/or PTEN alterations. The lowest LSTs were detected in VCaP (12 ± 1) and MDA-MBA-231 (21 ± 4). All detected LSTs were validated in comparison to gDNA. Concordantly, the highest number of LOHs were detected in BRCA mutant cell lines. All known point mutations (TP53, PTEN, BRCA) were recapitulated. Conclusions: We consistently detect genomic scars and inactivating HRD mutations at single cell resolution. Overall, our data indicates that high genomic instability as measured by the numbers of LSTs and LOHs may help to select for PARP sensitive patients.