Abstract Intratumoral genetic heterogeneity leads to tumor progression and therapeutic resistance. However, due to the difficulty associated with its assessment, application of intratumoral genetic heterogeneity as a prognostic or predictive marker is limited. We investigated the significance of Shannon diversity index as a tool for measuring genetic heterogeneity by performing fluorescence in situ hybridization of c-Myc gene in invasive breast cancers, and correlated the Shannon diversity index for c-Myc copy number variation with clinicopathologic features of tumor including patient survival. Shannon index for c-Myc copy number variation strongly correlated with average c-Myc copy number and was significantly higher in tumors with c-Myc genetic or regional heterogeneity than in those without c-Myc amplification. High Shannon index was associated with high histologic grade, lymphovascular invasion, p53 overexpression, high Ki-67 proliferation index, hormone receptor negativity, and HER2 amplification. In survival analyses, c-Myc amplification or c-Myc copy number gain was not associated with patient survival. However, a high level of Shannon index was associated with poor disease-free survival. In subgroup analyses, it was found to be an adverse prognostic factor in hormone receptor-positive group, but not in hormone receptor-negative group. In a validation set, high Shannon diversity index for c-Myc copy number variation was also found to be associated with poor survival of the patients. We further investigated the correlation with clinicopathologic features and predictive power of Shannon index using another gene, fibroblast growth factor receptor 1 (FGFR1) and observed that high Shannon index for FGFR1 gene copy number variation was an independent prognostic factor for poor clinical outcome in a whole group and in hormone receptor-positive subgroup. In conclusion, this study demonstrated that higher diversity index was associated with adverse pathologic parameters of breast cancer and poor clinical outcome suggesting that Shannon diversity index, which represents intratumoral genetic heterogeneity, can be used as a potential biomarker for tumor progression and prognostication in patients with breast cancer. Citation Format: Yul Ri Chung, Hyun Jeong Kim, Young A Kim, Mee Soo Chang, Ki-Tae Hwang, So Yeon Park. Diversity index as a novel predictor of tumor progression in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3937. doi:10.1158/1538-7445.AM2017-3937