Abstract MIP-075: SOMATIC MUTATIONS AND COPY-NUMBER VARIATIONS IN OVARIAN CANCERS VIA TARGETED SEQUENCING OF EXONS OF 300 CANCER-ASSOCIATED GENES, INCLUDING MULTIPLE DNA DAMAGE REPAIR GENES
Authors: Stover Elizabeth , Howitt Brooke , Garraway Levi , Matulonis Ursula 
Published: June 2017

Abstract
INTRODUCTION: Recent studies demonstrated frequent alterations in DNA damage repair (DDR) genes in ovarian cancer, from well-established variants in BRCA1/2 to rarely altered genes in various DDR pathways that may be clinically relevant. Here we summarize somatic alterations in DDR related genes identified by targeted sequencing of several hundred ovarian cancers.
EXPERIMENTAL PROCEDURES: Targeted next-generation sequencing was performed on formalin-fixed tumor tissues from &gt;500 patients with ovarian cancer enrolled in an IRB-approved protocol at Dana-Farber Cancer Institute (DFCI). The current dataset includes 269 patients whose tumors underwent gynecologic pathology review. Targeted sequencing via hybrid capture was performed for exons of 300 cancer-associated genes. Sequence data was analyzed at Brigham and Women's Hospital to identify single-nucleotide variants (SNVs) and insertions/deletions (indels). Putative copy number variants (CNVs) were computationally inferred from sequencing coverage in a subset of patients (n=219). Germline analysis was not performed in this study, but SNVs were filtered against variant databases. Corresponding clinical data is undergoing analysis.
RESULTS: In the 269-patient cohort, 67% of samples were primary tumors, 25% metastatic recurrences, and 3% local recurrences. Histologies included high-grade serous (34%), endometrioid (12%), clear cell (9%), malignant mixed mesodermal tumor (MMMT, carcinosarcoma) (9%), low-grade serous (7%), granulosa cell (7%), mucinous (3%), and borderline variants (6%). We focused upon alterations in DDR related genes in the targeted panel. Of the 269 patients, ~9% harbored BRCA1 variants and ~13% harbored BRCA2 variants; frameshift and nonsense mutations were frequent. Copy losses in BRCA1 or BRCA2 were predicted in up to 1/3 of patients, some of whom also carried SNVs/indels in the same gene. BRCA1/2 alterations were more frequent in high-grade serous cancers, but were also observed in other histologic subtypes. SNVs/indels in ATM were common, present in ~9% of patients. Another ~10% of patients had a variant in one of the Fanconi Anemia (FA) genes (FANCA,B,C,D2,E,F,G,I) or BRIP1. Alterations in MMR genes (MLH1, MSH2, MSH6, PMS2) were present in ~12%. SNVs in genes encoding DDR associated helicases BLM or WRN were observed in ~8%. PRKDC, encoding the DNA-PK catalytic subunit involved in non-homologous end joining, was altered in up to 7%. The SNVs in these DDR genes were observed in all histologic subtypes at varying frequencies. CNVs in DDR related genes were common, including predicted amplifications of CCNE1 and 2-copy deletions in several FA genes. Several limitations of this dataset may result in overestimates of the frequency of clinically significant alterations, e.g. some SNVs may represent benign variants (specific mutations are undergoing more detailed analysis to eliminate these); some patients harbor multiple mutations; and CNVs are predicted but need to be confirmed by orthogonal methods.
CONCLUSIONS: Targeted sequencing data from a large cohort of ovarian cancer patients collectively support previous work indicating a significant frequency of alterations in DDR related genes in ovarian cancer, across multiple histologic subtypes. Further analysis of specific mutations and clinical correlations with DDR gene alterations are ongoing. Identifying alterations in DDR genes in ovarian cancer patients is feasible and may have clinical relevance, particularly regarding DNA repair targeted agents and chemotherapeutics.
Citation Format: Elizabeth Stover, Brooke Howitt, Levi Garraway, Ursula Matulonis. SOMATIC MUTATIONS AND COPY-NUMBER VARIATIONS IN OVARIAN CANCERS VIA TARGETED SEQUENCING OF EXONS OF 300 CANCER-ASSOCIATED GENES, INCLUDING MULTIPLE DNA DAMAGE REPAIR GENES [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr MIP-075.