Abstract P4-05-03: Mutational analysis of triple-negative breast cancer (TNBC): CALGB 40603 (Alliance)
Authors: Hoadley Katherine A , Powell Bradford C. , Kanavy Dona , Marron David , Mose Lisle E. , Hyslop Terry , Berry Donald A. , Hahn Olwen , Tolaney Sara M. , Sikov William M. , Perou Charles M. , Carey Lisa A. 
Published: March 2020

Abstract
Background: Triple-negative breast cancer is an aggressive disease with limited treatment options beyond chemotherapy. In CALGB 40603, adding either carboplatin (Cb) or bevacizumab (Bev) to standard neoadjuvant chemotherapy (NACT) increased pathologic complete response (pCR) rates in TNBC and the subset of Basal-like breast cancers. Transcriptomic studies have previously found that evidence of immune activation was significantly associated with pCR. We are now examining frequency and pCR impact of germline and somatic mutations as secondary analyses.
Methods: 281 pretreatment tumors and matched blood samples were sequenced using a 1,123 cancer-associated gene panel. Germline and somatic mutations were determined and somatic mutations were further evaluated and filtered using a previously identified list of likely false positives (Bailey, Cell 2019) and RNA expression of the variant. We examined mutation frequency and association of mutations with overall in-breast pCR (result available for 274 of our cohort) and for benefit of addition of Cb or Bev on pCR.
Results: The pCR rate in patients with DNA sequencing was 53.6% in TNBC (147 pCR, 127 non-pCR) and 53.3% in Basal-like (131 pCR, 115 non-pCR). Total number of somatic mutations per sample from our targeted cancer panel ranged from one to 1,041, with a median of 18 mutations per patient. Ten samples had more than 100 mutations, of which six had POLE or POLD1 mutations. Focusing on non-silent coding mutations reduced the number of variants in the entire cohort from 10,483 to 4,275. A second filter was used to remove likely false positives. Mutations in TP53 were identified in 90% of samples. Only two other genes - KMT2C (12%) and MACF1 (11%) - were mutated in more than 10% of the samples. Mutations were also identified in NF1 (8%), PIK3CA (8%), PTEN (7%), FAT1 (7%), and RB1 (7%). Somatic alterations in BRCA1 and BRCA2 were observed in 6% and 5% of samples, respectfully. We also found that 40% of the tumors had one or more mutations in a set of 18 histone modification genes. However, these mutations were not associated with pCR in the entire cohort or in the Basal-like subset (n=246). The mutations were also not associated with response to Cb or Bev. The germline was also analyzed for inherited variants. We identified 35 (12%) patients with pathogenic or likely pathogenic variants in BRCA1 (n=23), BRCA2 (n=6), PALB2 (n=3), ATM (n=2), and CHEK2 (n=1). Germline variants were not associated with pCR in the entire cohort (n=33) or Basal subset (n=32), but there was a trend toward higher pCR in germline carriers (n=15) versus non-germline carriers (n=123) within the Bev-treated cohort (80% vs 54%, p=0.09). The pCR rate in patients with a pathogenic germline or somatic BRCA1/2 mutation (n=55) was similar to that for the overall study population (53% pCR rate), as was the increase in pCR seen with the addition of Cb (61% vs. 41% pCR rate) (Sikov, JCO 2015).
Conclusions: Analysis of recurrently mutated genes in TNBC among patients treated in CALGB 40603 revealed high rates of mutation and very high TP53 mutation frequency but failed to identify mutations significantly associated with pCR rate. Integrated analyses with copy number, immune and other RNA features are underway. Support for the project came from U10CA180821, U10CA180882; BCRF, Susan G. Komen, and Genentech. https://acknowledgments.alliancefound.org
ClinicalTrials.gov Identifier: NCT00861705
Citation Format: Katherine A Hoadley, Bradford C. Powell, Dona Kanavy, David Marron, Lisle E. Mose, Terry Hyslop, Donald A. Berry, Olwen Hahn, Sara M. Tolaney, William M. Sikov, Charles M. Perou, Lisa A. Carey. Mutational analysis of triple-negative breast cancer (TNBC): CALGB 40603 (Alliance) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-05-03.