The Landscape of Somatic Genetic Alterations in Breast Cancers from Carriers of Germline Pathogenic Variants in DNA-repair Genes

SABCS 2023 Presentation
Authors Siddhartha Yadav, Ali Arafa, Emily A. Teslow, Minxuan Huang, Melissa C. Stoppler, Calvin Chao, Emmanuel S. Antonarakis, Fergus J. Couch


Hereditary breast cancer in carriers of germline pathogenic or likely pathogenic variants (PVs) in ATM, BRCA1, BRCA2, CHEK2, and PALB2 have unique clinicopathological characteristics compared to sporadic breast cancer. However, very little is known about the underlying differences in somatic genetic alterations between hereditary and sporadic breast cancer.


The study included 7,533 individuals with breast cancer subjected to Tempus xT tumor-normal matched sequencing (596-648 genes). The frequencies of the somatic genetic alterations in each gene were compared separately between tumors arising in individuals with incidental germline PVs (gATM, gBRCA1, gBRCA2, gCHEK2, gPALB2) and sporadic breast tumors. Sporadic tumors were identified as individuals with no detected incidental germline PVs in these 5 genes. Comparisons were made by either Pearson’s Chi-squared or Fisher’s exact test, with false discovery rate (FDR) correction for multiple testing. Breast cancer subtype was determined based on the record of IHC positivity for ER, PR, or HER2. Detection of ERBB2 (HER2) gene amplifications via DNA sequencing was also used to classify samples as HER2+ in the absence of available IHC data.


The median age at breast cancer diagnosis for the cohort was 56 years. More than two-thirds of the patients were White (73%) while 14% identified as Black or African American. The overall frequency of incidental germline PVs in each gene was 0.8% for gATM, 1.4% for gBRCA1, 2.1% for gBRCA2, 1.0% for CHEK2, and 0.7% for PALB2. A total of 3,648 (48.4%) tumors were ER+/PR+/HER2-, 1,297 (17.2%) were triple-negative (TNBC), 841 (11.2%) were HER2+ and 1,747 (23.2%) could not be classified due to missing ER, PR or HER2 status, or absence of detected ERBB2 amplifications. Among ER+/PR+/HER2- breast cancers, compared to sporadic tumors, ESR1 mutations were significantly enriched in gATM carriers (33% vs. 11%, q- value 0.05), TP53 alterations were significantly enriched in gBRCA1 PV carriers (69% vs. 30%, q-value < 0.001) but depleted in gATM (12% vs. 30%, q- value 0.4) and gCHEK2 PV carriers (5.4% vs. 30%, q-value 0.06), and PIK3CA (14% vs. 35%, q-value 0.001) and CCND1 (3.4% vs. 17%, q-value 0.02)
alterations were significantly lower in gBRCA2 PV carriers. Among TNBC, TP53 alterations were also significantly higher in gBRCA1 PV carriers compared to sporadic tumors (96% vs. 69%, q-value 0.004). In HER2+ breast cancers, ERBB2 alterations were observed in approximately two-thirds of the tumors, and a significant difference was not observed between incidental hereditary and sporadic tumors. Among ER+/PR+/HER2- tumors, although not statistically significant, the frequency of ESR1 (3.1% vs. 11%, q-value >0.9), PIK3CA (12% vs. 35%, q-value 0.2) alterations were lower in incidental gBRCA1 versus sporadic tumors, FGFR1 alterations were lower in incidental gBRCA1 (6.2% vs. 13%, q-value >0.9) and incidental gBRCA2 (3.4% vs. 13%, q-value 0.13) but enriched in incidental gATM (33% vs. 13%, q-value 0.05).


The observed differences in the frequencies of CCND1, ESR1, PIK3CA, TP53, and other key genetic alterations between incidental hereditary and sporadic breast cancer highlight the unique tumor biology of breast cancer in germline PV carriers and have significant implications for understanding tumorigenesis and identifying therapeutic strategies for the management of hereditary breast cancer.