Abstract A23: Ultrasensitive mutation detection in FFPE tissues and circulating tumor DNA using SiMSen-Seq

Abstract

Abstract Novel diagnostic tools in oncology, prenatal diagnostics, and transplantation medicine depend on the detection of ultrarare variants. The analysis of cell-free DNA has the potential to revolutionize diagnosis, treatment monitoring, and recurrence and resistance of cancer. Yet these analysis remains challenging due to limited amounts of material and low allele frequencies of targeted variants. Simple, Multiplexed, PCR-based barcoding of DNA for Sensitive mutation detection using Sequencing (SiMSen-Seq) enables easy generation of libraries containing unique molecular identifiers (UMI) with minimal DNA input across several kilobases of DNA using two rounds of PCR and allows the detection of rare variants below 0.1% allele frequency. Clinical applications of ctDNA require highly optimized workflows to ensure high sensitivity and reproducibility. Here we present our state-of-the-art liquid biopsy workflow using SiMSen-Seq and simple quality control steps, applicable to almost any liquid biopsy protocol. In a series of case studies with melanoma patients we find that ctDNA mirrors the time-course of established protein markers such as S-100 and in some cases detects minimal residual months in advance of standard clinical diagnostics. SiMSen-Seq efficiently determined even rare mutations across multiple tumor forms in challenging sample types, such as FFPE tissue or cfDNA. We identified mutations in highly degraded FFPE tissue using a 60-plex SiMSen-Seq panel and then analyzed longitudinal cfDNA samples using patient-specific panels in a cohort of metastatic breast cancer patients. Our data indicate that ctDNA might be used as a biomarker for early detection of recurrence in these patients. We were able to detect treatment resistance variants as well as observe tumor recurrence well in advance of the onset of clinical symptoms. Thus, SiMSen-Seq offers an affordable, minimally invasive method for monitoring treatment efficiency and determination of drug resistance development in cancer. Citation Format: Stefan Filges, Daniel Andersson, Helena Kristiansson, Christoffer Vannas, Gustav Johansson, Junrui Li, Tony E. Godfrey, Max Levin, Barbro Linderholm, Anders Ståhlberg. Ultrasensitive mutation detection in FFPE tissues and circulating tumor DNA using SiMSen-Seq [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A23.