Abstract P6-07-01: Multigene profiling to identify clinically relevant actionable mutations in breast cancer: An Indian study
Authors: Ghosh M , Sheela ML , Choudhury S , Bahadur U , Patil S , Satheesh CT , Murugan K , Nayak R , Sridhar PS , Rao N , Mahesh B , Shashidhara HP , Krishnamoorthy N , Gupta V , Sankaran S , Subramanian K , Ajaikumar BS 
Published: May 2016

Abstract
Background: Numerous chemotherapeutic agents are available against breast cancer (BC), but a vast majority of patients diagnosed with this disease still develop treatment resistance and eventually succumb to disease. It remains an unmet need to identify specific molecular defects against which targeted therapy are available for improving clinical outcomes in BC. Our study aims to identify frequent hotspot mutations in BCs and determine their clinical impact.
Methods: 200 women with BC(early diagnosed and/or metastatic) aged 26-75 yrs (median age 50.5yrs) diagnosed at HCG from April 2013-15 were consented to be profiled by targeted deep sequencing for hotspot mutations in 48 cancer-related genes using Illumina's TSCAP panel and MiSeq technology in an IRB-approved prospective study in a CLIA compliant laboratory. All the cases had pathology review for stage, histological type, hormonal status and Ki67. The average coverage across 220 hot spots was greater than 1000X. Data was processed using Strand Avadis NGS™. Mutations identified in the tumor were assessed for 'actionability' i.e. response to therapy and impact on prognosis. Results: Somatic variants were detected in 75% of cases with direct impact on therapy or prognosis. Genetic aberrations were identified in PI3K/AKT/ mTOR signalling pathway in substantial fraction (27%) of breast cancer cases, out of which 17% had PIK3CA activating mutations,13 and 5 cases had PTEN and AKT deletions or truncating mutations respectively. Aberration in this pathway was more prevalent in HR+ve (53%) and HER2-ve including TNBC (61%) than in HR+/HER2+ve tumors (10.6%) of IDC histology. However, no correlation was found with stage and Ki67 index of the tumor. Notably 80% of BC cases presented with liver metastasis at the time of diagnosis were detected with PIK3CA mutation indicating its role as a surrogate marker of organ specific metastasis. PIK3CA was found to be co mutated with p53 in 16 cases (9%) of which 4 cases showed npCR post NACT. Also disruptive and non-disruptive mutations in TP53 alone were found in 25% of BC, varying widely among different histologies. A follow up of few cases showed shorter PFS and poor outcome in resected BC treated with NACT indicating its robust prognostic value in NACT setting. Furthermore, two patients were detected with cKIT mutations indicating sensitivity to imatinib and therefore enrolled on a clinical trial. The other variants were found in RB1(n=8),Her2 (n=2),FGFR amplification(n=1), KRAS(n=2),NRAS(n=3)CDH1(n=1),FBXW7(n=2) and EGFR(n=1).All these variants detected indicated resistance to conventional therapy and suggested sensitivity to available targeted therapy, either approved or in clinical trials. The response and outcome are being monitored in about 20 (10%) patients who have been enrolled in clinical trials and receiving mutation specific targeted therapy. Conclusions: This study confirms the utility of multigene profiling in early diagnosed and advanced BC patients, to stratify them on their molecular profile who could potentially benefit from targeted therapy. Prospective studies and randomized clinical trials are ongoing to confirm the independent prognostic and therapeutic value of the mutations in a larger cohort of Indian population.
Citation Format: Ghosh M, Sheela ML, Choudhury S, Bahadur U, Patil S, Satheesh CT, Murugan K, Nayak R, Sridhar PS, Rao N, Mahesh B, Shashidhara HP, Krishnamoorthy N, Gupta V, Sankaran S, Subramanian K, Ajaikumar BS. Multigene profiling to identify clinically relevant actionable mutations in breast cancer: An Indian study. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-07-01.