Abstract P5-13-09: Identifying homologous recombination deficiency in breast cancer: Genomic instability score thresholds differ in breast cancer subtypes
Authors: Kirsten M Timms, Lauren Lenz, Chris Neff, Cara Solimeno, Darl Flake, Judy C Boughey, Matthew P Goetz, Andrea Richardson, Anna Maria Storniolo, Alexander Gutin, Roisin M Connolly, Vered Stearns, Jerry S Lanchbury
Journal: Cancer Research (2022)

Abstract Background: Patients with homologous recombin ation (HR) deficient tumors may benefit from treatment with DNA damaging agents. Markers of genomic instability can be used to identify HR deficiency, including a 3-biomarker Genomic Instability Score (GIS). For patients with ovarian cancer (OC), the FDA-approved GIS threshold for identifying HR deficiency is 42, set as the 5th percentile for BRCA deficient tumors. Recently, a lower 1st percentile cutoff of 33 was explored in OC; this threshold was significantly associated with improved outcome after platinum-based treatment.1,2 Determining an optimal GIS threshold for different types of tumors is crucial, as the GIS distribution may vary between different cancers and even between different cancer subtypes. We propose GIS thresholds for breast cancer separately for triple-negative breast cancer (TNBC) and estrogen receptor-positive (ER+) breast cancer, using the exploratory threshold of 33 for OC as a comparator. Methods: GISs in BRCA deficient tumors were determined for patients newly diagnosed with varying stages of OC, TNBC, or ER+ breast cancer across 5 cohorts (Timms et al,3 TCGA,4 Abkevich et al,5 TBCRC008,6 the OlympiaD trial7). GIS was determined as a combination of loss of heterozygosity, telomeric-allelic imbalance, and large-scale state transitions. BRCA deficiency was defined by loss of function resulting from a pathogenic variant in BRCA1 or BRCA2 or by methylation of the BRCA1 promoter region, with loss of heterozygosity in the affected gene. GIS distributions in different cancer types and subtypes were compared using the Kolmogorov-Smirnov test. A normal distribution was fit to GISs in BRCA deficient ER+ breast tumors. The 1st percentile of the fitted distribution was chosen as the threshold. Results: A total of 561 OC tumors (190 BRCA deficient), 99 TNBC tumors (44 BRCA deficient), and 406 ER+ breast tumors (76 BRCA deficient) were included across the 5 cohorts. When score distributions were evaluated for BRCA deficient tumors, the GIS distribution within ER+ breast cancer was significantly different than for OC (p=9.6x10-5) and TNBC (p=3.2x10-4). This indicates that different GIS thresholds are appropriate for breast cancer subtypes and that the GIS threshold developed for OC is not appropriate for ER+ breast cancer. The 1st percentile of a normal distribution fit in BRCA deficient ER+ breast cancer tumors yields a threshold of 24. Using this threshold, 45.1% (183/406; 75 BRCA deficient, 108 BRCA intact) of ER+ breast tumors were HR deficient. In contrast, the GIS distribution for TNBC was not significantly different than for OC (p=0.77). Using the exploratory threshold of 33, 63.6% (63/99; 44 BRCA deficient, 19 BRCA intact) of TNBC tumors were HR deficient. Conclusions: When compared to OC, the distribution of GIS in BRCA deficient tumors was different for ER+ breast cancer, but not for TNBC. These findings are consistent with the fact that OC and TNBC are known to have similar molecular signatures.8 Exploratory thresholds of 24 for ER+ breast cancer, and 33 for TNBC and OC could be examined to determine if these cutoffs are associated with a benefit from treatment with DNA targeting agents. Clinical validity and utility of these more inclusive 1% thresholds would require demonstration of correlation with clinical outcomes. The threshold difference observed between these cancer subtypes also suggests that cancer or cancer subtype specific thresholds may be needed as evaluations of HR deficiency expands beyond OC to identify candidates for PARP inhibitors. References: 1 Mol Cancer Res. 2018;16(7):1103-11. 2 Cancers. 2021;13(5):946. 3 Br J Cancer. 2012;107(10):1776-82. 4 Nature. 2012;490(7418):61-70. 5 Breast Cancer Res. 2014;16(145):1-9. 6 J Nucl Med. 2015;56(1):31-7. 7 NEJM. 2017;377(17):1700. 8 Int J Mol Sci. 2016;17(5):759. Citation Format: Kirsten M Timms, Lauren Lenz, Chris Neff, Cara Solimeno, Darl Flake, Judy C Boughey, Matthew P Goetz, Andrea Richardson, Anna Maria Storniolo, Alexander Gutin, Roisin M Connolly, Vered Stearns, Jerry S Lanchbury. Identifying homologous recombination deficiency in breast cancer: Genomic instability score thresholds differ in breast cancer subtypes [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-13-09.