Elsevier

Gynecologic Oncology

Volume 155, Issue 3, December 2019, Pages 473-482
Gynecologic Oncology

Comprehensive genomic sequencing of paired ovarian cancers reveals discordance in genes that determine clinical trial eligibility

https://doi.org/10.1016/j.ygyno.2019.10.004Get rights and content

Highlights

  • Ovarian cancer samples collected during clinical care were analyzed using a diagnostic next-generation sequencing gene panel.

  • For most patients, the detected genomic alterations were stably maintained over time.

  • No discordant alterations were found in genes currently used for therapy selection.

  • 30% had discordant alterations in genes used for clinical trial eligibility; 23% were detected by repeat tumor testing.

  • Low discordance was detected in assays for tumor mutation burden and loss of heterozygosity.

Abstract

Objective

We analyzed comprehensive genomic sequencing results from paired ovarian cancer samples to identify changes in mutational events over time.

Methods

DNA from paired FFPE tumor samples from 50 ovarian cancer patients in the Clearity Foundation Data Repository was analyzed for genomic mutations (GM), copy number alterations (CNA), microsatellite status (MS), tumor mutation burden (TMB), and loss of heterozygosity (LOH) by hybrid-capture, next-generation sequencing of up to 315 genes. Genomic profiles were compared between samples from the same patient. Poor quality results excluded 6 pairs from all analyses and 9 from CNA or LOH.

Results

Forty-four patients with predominantly advanced stage disease (34, 77%) and serous histology (31, 70%) received a median of 3 intervening treatment regimens (range 1–13). Analysis of 22 primary and recurrent sample pairs and 22 recurrent tumor pairs detected a median of 2 GM (range 0–5) and 1 CNA (range 0–6)/sample. TMB, MS, and LOH results were mostly concordant across paired samples. GM were consistent across most pairs [32/44 (73%) concordant], while CNA concordance was less [18/35 (51%)]. No changes were detected in therapeutically relevant GM, but 23% of patients had GM or CNA in the second sample that affect clinical trial eligibility.

Conclusions

Paired ovarian cancer samples demonstrate stable genomic alterations across time. However, discordance was observed for some genes used as eligibility criteria for molecularly targeted clinical trials. Repeat tumor testing may be useful in cases where eligibility for such trials is deemed important after consideration of testing costs and potential clinical benefit.

Introduction

Advanced stage ovarian cancer patients are typically treated with cytoreductive surgery and platinum-based chemotherapy at the time of diagnosis and are initially platinum-sensitive, but the majority will experience disease recurrence [1,2]. Prior studies have demonstrated that ovarian tumors are characterized by a high prevalence of TP53 mutations, copy number alterations and low mutation burdens, but can be clonally heterogeneous [[3], [4], [5]]. Genomic events that are associated with improved patient prognosis have been identified, such as defects in homologous recombination DNA repair (e.g., BRCA1 and BRCA2), as well as with poor prognosis, such as CCNE1 amplification [3,[6], [7], [8]]. Genomic alterations can also be associated with opportunities for therapeutic intervention (e.g., PARP inhibitors for patients with BRCA 1 and BRCA2 mutations).

Relatively few studies have investigated changes in genomic profiles over time and these studies are largely limited to patients with high grade serous carcinomas [[9], [10], [11]]. In whole exome analyses of tumors sampled at diagnosis and first recurrence after platinum-based chemotherapy, significant genomic variability between samples was observed. Despite observing frequent loss of heterozygosity (LOH) in genes associated with homologous recombination repair deficiency, these studies did not detect any genetic alterations that would restore such repair processes in the recurrent specimens [11,12]. Among patients whose tumors have acquired resistance to chemotherapy, higher mutational burdens and an increased frequency of structural variants were observed in relapse compared to primary samples [10].

Some literature suggests specific genomic changes occur in response to treatment, particularly BRCA1 or BRCA2 reversion mutations leading to resistance to platinum-based chemotherapy and PARP inhibitors [10,[13], [14], [15]]. For non-platinum chemotherapy, less is known about the relationship between somatic mutations and specific treatments [16]. Promoter fusion of ABCB1, which encodes the MDR1 protein, a rapid efflux pump for many chemotherapy agents used to treat ovarian cancer, including paclitaxel, etoposide, and doxorubicin, has been noted in 8% of ovarian cancer patients with resistant disease [10,17].

Tumor molecular analysis is becoming increasingly common to inform treatment decisions for ovarian cancer patients in order to determine eligibility for targeted therapies or clinical trial participation. National Comprehensive Cancer Network (NCCN) guidelines now recommend tumor molecular testing prior to initiating therapy for persistent or recurrent disease, using the most recent available tumor tissue. Historically it has not been standard practice to perform repeat tumor sampling at the time of recurrence outside of secondary cytoreduction or clinical trial participation [18], so tissue sent for molecular analysis is often from surgery at the time of diagnosis. Unless repeat tumor sampling is performed at the time of recurrence, the tissue tested reflects the tumor’s mutations prior to exposure to chemotherapy rather than capturing any additional genomic alterations accumulated in response to treatment or through selection of a resistant clone from the parental population. Furthermore, since many ovarian cancer patients experience multiple recurrences and are exposed to multiple different therapies, it is unclear how an individual’s tumor might change over time or how accurately the profile of the primary tumor sample may reflect the disease later in the clinical course.

The objective of this study was to analyze paired recurrent ovarian cancer tumor samples by comprehensive genomic profiling (CGP) using a multi-gene panel test that interrogates ovarian cancer driver genes and genomic biomarkers [e.g., BRCA1/2, tumor mutation burden (TMB), microsatellite instability (MSI), loss of heterozygosity (LOH)] to identify any changes in genomic alterations and multi-gene biomarker scores over time and to assess the potential impact on therapy options and patient management.

Section snippets

Patient samples and clinical histories

50 ovarian cancer patients with two or more genomically profiled samples collected serially during the course of routine clinical care (2012–2018) were identified in the Clearity Foundation Data Repository of more than 600 ovarian cancer patients. This repository contains de-identified data from clinical histories and various tumor profiles, including those from next generation sequencing gene panels. Patient informed consent was obtained for the use of this data for research purposes under a

Results

Of 44 patients with evaluable sample pairs, 22 had primary-recurrent specimens and 22 had multiple recurrent tissue specimens (Table 1). Three patients had three specimens available for analysis. Ovarian cancer was diagnosed at a median age of 58.7 years (range 34.5–76.9 years). The majority of patients had stage III/IV (34/77%) and primary platinum-sensitive disease (32/73%). Most tumors demonstrated serous histology (31/70%); there were four cases (9%) with clear cell and three cases (7%)

Discussion

In a cohort of patients with recurrent ovarian cancer, the majority of mutation events were preserved between different samples over time, but nearly half had at least one discordant mutation or copy number alteration event. No discordant alterations were clinically actionable, but approximately 30% of patient samples demonstrated variable detection of mutations or copy number alterations that could affect clinical trial eligibility. In 23 % (10/44), a new alteration was detected in the second

Author contributions

Conception and design: JEF, DAL, DAZ.

Collection and assembly of data: JEF, LJ, JE, DAZ.

Data analysis and interpretation: JEF, AAB, LJ, JE, DAL, DAZ.

Manuscript writing: All authors.

Final approval of manuscript: All authors.

Conflict of interest disclosures

Drs. Fehniger, Berger, and Zajchowski have no disclosures.

Dr. Elvin reports employment and stock from Foundation Medicine, Inc.

Dr. Juckett reports employment by Foundation Medicine, Inc.

Dr. Levine reports personal fees from Tesaro, personal fees from Merck, grants from Splash Pharmaceuticals, outside the submitted work; In addition, Dr. Levine has a Patent Application US20130078319A1 - Detection of ovarian cancer pending, and a Patent application WO2015103431A9 - Compositions and methods for

Acknowledgements

We gratefully acknowledge the programming assistance of M. Whitlow, database management by K. Zajchowski, and all of the patients who contributed their data to The Clearity Foundation Data Repository. We are grateful for funding provided in part by the US Department of Defense Award: W81XWH-15-1-0429, NIH:P30 CA016087, and Arnold Chavkin and Laura Chang.

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