Abstract 4564: Assessment of genetic alterations using next-generation sequencing in postmenopausal women with hormone receptor-positive, HER2-negative advanced breast cancer: results from the BOLERO-2 phase III trial.
Authors: Jose Baselga, Martine Piccart, Hope Rugo, David Chen, Howard A. Burris, Mario Campone, Shinzaburo Noguchi, Alejandra Perez, Inas Deleu, Mikhail Shtivelband, Louise Provencher, Adnan Derti, Alan Huang, Rob McDonald, Creton Kalfoglou, Douglas Robinson, Tetiana Taran, Tarek Sahmoud, David Lebwohl, Gabriel N. Hortobagyi
Journal: Cancer Research (2013)

Abstract The BOLERO-2 phase III trial compared the combination of everolimus and exemestane to placebo and exemestane in 724 postmenopausal women with hormone receptor-positive, HER2-negative advanced breast cancer. Results showed significant improvement in progression-free survival, response rate, and clinical benefit rate. Although significant benefit has been observed in all prospectively defined subgroups, variations were seen among patients. As the first step to delineate the molecular determinants of sensitivity to everolimus and interactions between estrogen receptor and mTOR pathways, we used next-generation sequencing technology to comprehensively assess the genetic alterations in archival tumor specimens. Formalin-fixed, paraffin-embedded archival tumor samples were obtained from 496 patients. DNA was extracted from 348 samples of sufficient quantity and 230 samples (representing approximately 1/3 of all patients) qualified for the analysis. No indication of sampling bias was observed when the data were assessed and compared against several covariates as well as to the full trial data. The coding regions of 182 cancer-related genes were analyzed using an Illumina HiSeq 2000. Mutations and copy number variations were evaluated in 230 samples for which DNA extraction, library construction, and hybrid capture were successful and sequencing depth was sufficient (250-1500×). Alterations predicted to be germline events were discarded. One hundred seventy-three genes were found to be altered in at least one tumor sample. The number of alterations per sample varied from 1 to 24 (average 9 ± 4). Sequence variations (N = 1565) consisted primarily of point mutations (85%), followed by deletions (9%) and insertions (6%). 225 of 230 (98%) patients had at least two sequence variations. The most frequently mutated genes included PIK3CA (49%), TP53 (24%), and ARID1A (16%). ESR1 and IGF1R mutations were detected in 9% and 4% of the cohort, respectively. PIK3CA and AKT1 (6%) mutations were found to be mutually exclusive. Copy-number alterations comprised of 524 amplifications and 27 bi-allelic deletions. The most frequently amplified genes included CCND1 (32%) and FGFR1 (18%). Specific rearrangements assayed in 14 genes occurred infrequently (9% of the samples). These results demonstrated the feasibility of performing large-scale next-generation sequencing in a global phase III clinical trial. High alteration frequencies were observed in specific genes, resulting in activated PI3K, FGFR1, and estrogen receptor pathways, corroborating the rationale of concomitant targeting of the mTOR and estrogen receptor pathways. The results generate testable hypotheses for the development of combinations of new targeted therapies in this patient population. Citation Format: Jose Baselga, Martine Piccart, Hope Rugo, David Chen, Howard A. Burris, Mario Campone, Shinzaburo Noguchi, Alejandra Perez, Inas Deleu, Mikhail Shtivelband, Louise Provencher, Adnan Derti, Alan Huang, Rob McDonald, Creton Kalfoglou, Douglas Robinson, Tetiana Taran, Tarek Sahmoud, David Lebwohl, Gabriel N. Hortobagyi. Assessment of genetic alterations using next-generation sequencing in postmenopausal women with hormone receptor-positive, HER2-negative advanced breast cancer: results from the BOLERO-2 phase III trial. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4564. doi:10.1158/1538-7445.AM2013-4564