ABSTRACT: There is need for a technology platform that has the capability to simultaneously characterize all classes of genomic alterations in a single assay. The use of next-generation sequencing (NGS) offers such a platform.
This study evaluated the ability of targeted NGS to identify unanticipated targetable genomic alterations among patients with relapsed epithelial ovarian cancer OC. Comprehensive NGS-based DNA sequencing was performed on 3320 exons of 182 cancer-related genes and 37 introns of 14 genes frequently rearranged in cancer on indexed, adaptor ligated, hybridization-captured libraries using DNA isolated from 48 chemorefractory relapsed OC specimens. Genomic alterations evaluated included base substitutions, insertions, deletions, copy-number alterations (amplifications and homozygous deletions), and select gene fusions/rearrangements. DNA was sequenced from 26 (54%) primary OC and from 22 (46%) recurrent and metastatic tumor sites. Genomic alterations identified were divided into 2 actionability classes: (1) those that predict sensitivity or resistance to approved or standard therapies and (2) those that are inclusion or exclusion criteria for specific experimental therapies in National Cancer Institute–registered clinical trials.
Histological phenotypes included the following carcinomas: papillary serous (79%, n = 38), endometrioid (10%, n = 5), clear cell (6%, n = 3), mucinous (2%, n = 1), and undifferentiated (2%, n = 1). A total of 141 alterations were identified in the 48 OCs, with an average of 2.9 alterations per tumor (range, 0–8); 67 of these alterations were actionable, with an average of 1.4 per patient (range, 0-5). At least 1 actionable gene alteration was found in 69% (33/48) of the OC specimens. The most common alterations were in TP53 mutation (79%), MYC amplification (25%), BRCA1/2 truncation (23%), KRAS mutation/amplification (16.6%), and NF1 mutation truncating alterations (14.5%). A cMET amplification was featured in 1 (33%) of the clear cell tumors; this was validated by both fluorescence in situ hybridization and immunohistochemistry.
This study demonstrates that NGS identifies an unexpectedly high frequency of actionable genomic alterations that may influence targeted therapy selection for conventional therapy–resistant ovarian carcinomas.
Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY (J.S.R.); Foundation Medicine, Inc., Cambridge, MA (J.S.R., S.M.A., K.W., G.P., R.Y., D.L., V.A.M., P.J.S.); and The Clearity Foundation, San Diego, CA (D.Z., L.K.S.)