Abstract 445: Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues

Abstract

Abstract The detection of subclonal tumor-specific somatic mutations in clinical samples could revolutionize cancer diagnostics, but is limited by insufficiently sensitive sequencing methods. Duplex Sequencing is a novel next-generation sequencing (NGS) technology that implements single-molecule barcoding of both strands of DNA to allow internal error correction. This modification reduces the error rate of NGS from 1 in 1000 to less than 1 in 10 million nucleotides, an unprecedented sensitivity that enables accurate ultra-deep sequencing for clinical applications. In this study we sought to determine whether Duplex Sequencing could detect extremely rare TP53 mutated cancer cells disseminated into the peritoneal cavity of women with high-grade serous ovarian carcinoma (HGSOC). HGSOC is the most common and most aggressive type of ovarian cancer, shows early transperitoneal dissemination, and is characterized by near-universal prevalence of driver TP53 mutations. We analyzed 17 peritoneal fluid samples from women with HGSOC and known TP53 tumor mutation (cases) and 20 peritoneal fluid samples from women without cancer (controls). The tumor-specific TP53 mutation was detected in matched peritoneal fluid from 94% of cases (16/17), including 2 patients with occult tubal intraepithelial neoplasia, 7 patients with early stage HGSOC, and 8 with negative peritoneal fluid cytopathology. Tumor-specific alleles were detected as low as <1/25,000. Surprisingly, we also detected additional extremely low-frequency somatic TP53 mutations in peritoneal fluid from nearly all (35/37) cases and controls. These mutations were more abundant in cases than in controls, and in the latter correlated with age. The total burden of somatic TP53 mutations (tumor specific and non-specific) in a peritoneal fluid sample could distinguish cases from controls with 82% sensitivity (14/17) and 90% specificity (18/20). Duplex Sequencing also revealed low-frequency, age-associated somatic TP53 mutations in 100% (15/15) of matched peripheral blood samples. Our results demonstrate the ability of Duplex Sequencing to detect very rare cancer cells, but also provide evidence of widespread, low frequency somatic TP53 mutation in non-cancerous tissue. This compromises the specificity of TP53 mutation tests for cancer detection in liquid biopsies. Citation Format: Jeffrey D. Krimmel, Michael W. Schmitt, Scott R. Kennedy, Maribel I. Harrell, Kathy J. Agnew, Larry A. Loeb, Elizabeth M. Swisher, Rosa Ana Risques. Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 445.