Abstract P2-18-03: Breast cancer treatment and association with clinicopathologic features in TCGA
Authors: Liu Jianfang , Fantacone-Campbell J. Leigh , Kovatich Albert J. , Deyarmin Brenda , Mostoller Bradley J. , Hooke Jeffrey A. , Rui Hallgeir , Shriver Craig D. , Hu Hai 
Published: March 2020

Abstract
Background: For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data were analyzed and a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource was created. However, TCGA treatment data are not systematically analyzed. Here we focus on TCGA primary breast cancer (TCGA-BC) treatment data to assess their completeness, regimen patterns, and association with clinicopathologic features.
Method: 814 TCGA-BC patients with treatment data diagnosed from 2001 to 2013 were selected for this study. The treatment data were prepared and classified to be adjuvant Chemotherapy (CT), adjuvant Radiation Therapy (RT), and adjuvant Hormone Therapy (HT). An in-house Clinical Breast Care Project (CBCP) treatment dataset (n=1051 from 2001 to 2017), which were relatively complete, were used as a reference for data completeness. Multinomial logistic regression was used to analyze the associations between different therapies and clinical features.
Results: There is no consistent treatment data difference between TCGA-BC and CBCP. In TCGA-BC, 68.7%, 64.4%, and 64.5% of patients received CT, RT, and HT respectively, whereas in CBCP, the corresponding percentages were 59.0%, 71.2%, and 77.1%. The percentages of patients receiving combined therapies are even more comparable between the two cohorts (data not shown due to many combinations).
The associations between treatment and clinicopathologic features were analyzed using multinomial logistic regressions with age, race, menopausal status, AJCC stage, and PAM50 subtype as covariates. Several of these covariates significantly associate with the use of therapies. Compared to patients with age &lt; 50, patients with age ≥ 65 were significantly more likely to receive HT, HT+RT, or RT than CT only (OR=11.34, 9.25, 4.82; p=0.001, 0.002, and 0.024 respectively); Compared to pre-menopausal patients, post-menopausal patients were significantly more likely to receive HT+RT than CT only (OR=4.12, p=0.034); Compared to patients with early stages (I, II), patients with advanced stages (III, IV) were more likely to receive CT+HT+RT (OR=1.92, p=0.038) or CT+RT (OR=2.38, p=0.010) than CT only, and less likely to receive CT+HT (OR=0.39, p=0.033) or HT (OR=0.30, p=0.008) than CT only. PAM50 subtype also significantly associates with the use of therapies. Compared to Luminal A patients, patients with Basal subtype were significantly less likely to receive CT+HT (OR=0.14, p=1.3e-05), CT+HT+RT (OR=0.06, p=3.0e-10), HT+RT (OR=0.01, p=9.2e-06), or HT (OR=0.02, p=3.8e-07) than CT alone. Patients with HER2+ subtype showed similar patterns (note targeted therapies were classified as CT). In addition, patients with Basal subtype were significantly more likely to receive CT+RT (OR=2.47, p=0.01) than CT only.
Conclusion: TCGA-BC patient treatment data are relatively as complete as our in-house CBCP patient treatment data, enabling us to perform a preliminary analysis of the former for association with clinicopathologic features of the patients. The significant associations of age, menopausal status, AJCC stage, and PAM50 subtype with treatment regimens are consistent with clinical knowledge, suggesting potential validity of TCGA BC treatment data for research use.
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Citation Format: Jianfang Liu, J. Leigh Fantacone-Campbell, Albert J. Kovatich, Brenda Deyarmin, Bradley J. Mostoller, Jeffrey A. Hooke, Hallgeir Rui, Craig D. Shriver, Hai Hu. Breast cancer treatment and association with clinicopathologic features in TCGA [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 P2-18-03.