Abstract 3156: NGS-based screening for TP53 mutations in circulating cell-free DNA: A first step towards early detection of lung cancers

Abstract

Abstract Background The US National Lung Cancer Screening Trial (NLST) demonstrated in 2011 that screening with computed tomography (CT) scans could reduce lung cancer mortality by 20%, but with important financial costs and high number of false positives. The identification of novel biomarkers is a need to obtain the maximum benefit from CT screening. Given its economical and minimally invasive nature, screening for somatic mutations in circulating tumor DNA (ctDNA) using next-generation sequencing may complement existing screening tools. However, for application in early detection, variant detection must also be done agnostically, i.e. without prior knowledge from tumour tissue of the mutations expected and unfortunately, most currently available variant callers are not adapted for this task. Methods We performed multiplex PCR on circulating free DNA (cfDNA) extracted from the plasma of 35 lung squamous cell carcinoma (SCC) and 64 small-cell carcinoma (SCLC) patients. We additionally included 133 hospital controls to evaluate the specificity of ctDNA. We applied (>10,000X) Ion torrent targeted sequencing on the full-coding region of TP53 since this gene is known to be mutated in more than 70% and 90% of SCC and SCLC, respectively. Each amplification, library preparation, and sequencing was performed in duplicate to control for amplification and sequencing errors. Detecting mutations on ctDNA raises important statistical and bioinformatics challenges as it represents only a small fraction of cfDNA. We therefore developed and applied a method based on the idea that a data-derived model of sequencing errors has the potential to improve our ability to detect low-allelic fraction (AF) somatic variants. Results We detected TP53 non-synonymous coding mutations with AFs between 0.04% and 85% (median 1.7%) in 8 (23%) SCC patients, 28 (44%) SCLC patients, and 8 (6%) controls. We estimated odds ratios of 4.6 (p = 0.006) for SCC and 12.0 (p = 6.7×10-10) for SCLC. Observations in controls are surprising, but in this instance there was no information regarding a subsequent cancer diagnosis. Conclusion We show that it is possible to detect ctDNA in the cfDNA of lung cancer patients. Since only patients with early stage (I-IIA) SCC tumours were included, these results support the potential utility of the approach for early detection. Nevertheless, if such mutations are found prior to diagnosis has not been explored in a prospective study design with pre-diagnostic plasma samples and individuals without a cancer diagnosis through a follow-up period. Citation Format: Patrice H. Avogbe, Tiffany Delhomme, Noémie Leblay, Florence Le Calvez-Kelm, Priscilia Chopard, Valérie Gaborieau, Ghislaine Scelo, Behnoush Abedi-Ardekani, David Zaridze, Anush Mukeria, Graham Byrnes, Paul Brennan, Lynnette Fernandez-Cuesta, Matthieu Foll, James D. McKay. NGS-based screening for TP53 mutations in circulating cell-free DNA: A first step towards early detection of lung cancers. [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 3156.