Abstract B35: Australian Ovarian Cancer Assortment Trial–Allocating ovarian cancer patients into clinical trials based on molecular profiling
Authors: Kondrashova Olga , Au-Yeung George , Leas Leakhena , Ho Gwo-Yaw , Lunke Sebastian , Alsop Kathryn , Scott Clare , Hamilton Anne , Ananda Sumitra , Freimund Alison , Quinn Michael , McNally Orla , Traficante Nadia , Cowie Tiffany , Wakefield Matthew , Hsu Arthur , Dobrovic Alex , Christie Michael , Taylor Graham , Bowtell David , Mileshkin Linda , Waring Paul 
Published: August 2018

Abstract
Background: The Australian Ovarian Cancer Assortment Trial (ALLOCATE) was designed as a pilot study to demonstrate feasibility of molecularly profiling patients with recurrent ovarian cancer with the aim of allocating patients to targeted therapies based on the genomic profile of their tumors.
Materials and Methods: Two next-generation sequencing (NGS) panels, as well as a BRCA1 methylation assay, were used for molecular profiling of most common subtypes of ovarian cancer. A custom Illumina TruSeq Amplicon Low Input (v2) panel with dual-strand coverage was designed to target 38 genes commonly mutated and clinically important in ovarian cancer. The second assay was a NGS modification of the Multiplex Ligation-dependent Probe Amplification (MLPA) assay that was designed to target 11 genes with common copy number alterations (CNA) in ovarian cancer, including extensive BRCA1/2 coverage for large exonic deletions (Kondrashova et al., 2015). A thorough analytic validation was performed to ensure that both tests were fit for diagnostic use.
Patients with recurrent epithelial ovarian cancer were eligible for the study. Where feasible, patients underwent biopsies of recurrent tumor that were snap frozen. Otherwise, archival FFPE tumor blocks were retrieved. Sequencing was performed using Illumina Miseq and HiSeq 2500 with target median coverage of 2000x (amplicon panel) and 800x (MLPA-Seq). Data were analyzed using an internally built pipeline, an upgraded version of AmpliVar (Hsu et al 2015), with Variant Effect Predictor (Mclaren et al., 2016) used for variant annotation.
Results: Between December 2013 and October 2016, 113 patients with recurrent ovarian cancer were recruited from two tertiary hospitals, with 15 cases (13%) excluded due to insufficient tumor material or poor-quality DNA. Ninety-eight cases (87%) were analyzed and reports issued back to the referring clinician.
Fifty-six patients (61%) in the study had recurrent high-grade serous ovarian cancer (HGSC). Of these, TP53 mutations were identified in 91%. Events in genes other than TP53 were detected in 44 cases, most commonly MYC and CCNE1 amplifications and BRCA1/2 mutations. BRCA1/2 reversions were identified in two cases, explaining their lack of response to platinum/PARPi.
Fifteen patients (16%) had recurrent low-grade serous ovarian cancer (LGSC), with KRAS or BRAF mutations identified in four cases. Two HGSC tumors were reclassified as LGSC on the basis of a lack of TP53 mutation, presence of KRAS mutation, and subsequent pathology review. Other cases in the study included mucinous, clear cell, and mixed-histology carcinomas and a metastatic carcinosarcoma.
In terms of clinical utility, 6 patients (7%) received a matched therapy. Three HGSC patients with somatic BRCA1/2 mutations were treated with PARP inhibitors. Another HGSC patient with ERBB2 amplification was treated with trastuzumab. One LGSC patient with a BRAF mutation was enrolled on a BRAF inhibitor clinical trial. A second LGSC patient was enrolled in a trial of anastrazole. Furthermore, 7 patients (14%) with HGSC who were previously untested were found to have a germline BRCA1/2 mutation and were subsequently referred to a familial cancer clinic for further management and cascade testing.
The limitations in the study included the turnaround time and advanced stage of disease at enrolment, which significantly affected the clinical utility of the test.
Conclusion: We demonstrated that molecular profiling of recurrent ovarian cancer using the ALLOCATE panel was feasible and reflected the known genomic characteristics of the different subtypes. However, challenges remain, including appropriate patient selection and efficient turnaround time for reporting. Furthermore, improved access to targeted therapies or clinical trials will also enhance the clinical utility of the ALLOCATE panel.
Citation Format: Olga Kondrashova, George Au-Yeung, Leakhena Leas, Gwo-Yaw Ho, Sebastian Lunke, Kathryn Alsop, Clare Scott, Anne Hamilton, Sumitra Ananda, Alison Freimund, Michael Quinn, Orla McNally, Nadia Traficante, Tiffany Cowie, Matthew Wakefield, Arthur Hsu, Alex Dobrovic, Michael Christie, Graham Taylor, David Bowtell, Linda Mileshkin, Paul Waring. Australian Ovarian Cancer Assortment Trial–Allocating ovarian cancer patients into clinical trials based on molecular profiling. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B35.