Abstract P4-03-03: Germline potentially pathogenic variants in breast cancer intrinsic molecular subtypes are not associated with somatic TMB
Authors: Obeid E , Reddy SB , Goldstein LJ , Daly MB , Benz SC , Hall MJ , Szeto C 
Published: May 2019

Abstract
Background: Breast cancer (BC) is a heterogeneous disease. It is estimated that 5 to 10% of all BC to have a germline genetic predisposition. A 50-gene assay (PAM50) identifies 5 intrinsic molecular subtypes (IMS): Luminal A, Luminal B, HER2-enriched, Basal-like, and Normal-like. Basal-like breast cancers are enriched for BRCA1/2 germline mutations. Deleterious mutations in BRCA1/2 or other DNA-damage repair (DDR) genes may increase tumor mutational burden (TMB), a biomarker for response to checkpoint inhibition therapy. We sought to determine the spectrum of germline mutations in molecular BC subtypes (IMS), and their relation to somatic TMB. Methods: We performed a retrospective analysis of data from NantHealth database. RNAseq was used to classify breast tumors into IMS. Germline variants within putative driver genes (COSMIC v.76) were detected in analysis of 181 whole-genomes and 89 whole-exomes sequenced using Illumina chemistry. Classification of germline variants into potentially pathogenic variants (pPv) was determined using ClinVar database annotation. Patients were categorized as TMB-high by thresholding on &gt;200 non-synonymous exonic somatic mutations as was previously reported. Results: A total of 270 BC patients with comprehensive omics profiling (germline DNAseq, somatic DNAseq, and somatic RNAseq) were available for this analysis. The mean age (±SD) was 56.4 (± 12.5) years (range 20.8-86.5). Forty-six patients (17.0%) were classified TMB-high. The IMS distribution was 40.7% Luminal A, 31.5% Luminal B, 5.9% HER2-enriched, 21.5% Basal-like, and 0.37% Normal-like. Over 200 unique germline variants were detected of which 98 were pPv according to ClinVar annotation. These pPv spanned 21 genes, 7 of which are directly related to DDR. One hundred and four patients had ≥1 pPv (78 had only 1 pPv, and 26 had &gt;1 pPv). The most common pPv were APC (5.9%), BRCA2 (5.2%), TSC2 (4.4%), BRCA1 (3.7%), SDHB (3.3%), SDHD (3.3%), TSC1 (3.0%), PMS2 (3.0%), MUTYH (2.6%), MSH2 (1.5%) and MSH6 (1.5%). BRCA1 and especially BRCA2 pPv were mostly seen in the basal-like patients. Luminal B had distinctly more germline pPv in PMS2, BRCA1 & BRCA2 than Luminal A. TMB-high patients were not significantly enriched for germline pPv (OR 0.73, p=0.41), even when limited to pPv in DDR genes (OR 0.69, p=0.52). TMB-high patients were present in all 4 major IMS types; Her2-enriched 37.5%, Luminal B 23.5%, Basal-like 17.2%, and Luminal A 9.1%. Conclusion: We identified differential distribution of germline pPv in BC IMS. Of the pPv found, APC was the most commonly detected pPv across subtypes, while BRCA1/2 pPv were clustered in Basal-like subtype, and PMS2 in Luminal B subtype. 17% of all patients had a pPv within at least one DDR gene, that potentially may benefit from targeted therapy. Despite IMS types having distinct germline pPv profiles especially in DDR genes, there was no association with subsequent somatic TMB. This suggests that either 1. somatic events are the primary drivers of TMB, or 2. that germline variants with either unknown or benign significance need to be revisited. Future analysis in a larger demographically well-annotated dataset (commercial data, ExAC, other) or via functional studies should be considered.
Citation Format: Obeid E, Reddy SB, Goldstein LJ, Daly MB, Benz SC, Hall MJ, Szeto C. Germline potentially pathogenic variants in breast cancer intrinsic molecular subtypes are not associated with somatic TMB [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-03-03.