Assessment of clinical applications of circulating tumor DNA using an enhanced TAm-Seq platform

Abstract:

Abstract Novel biomarkers are required to assess tumor burden and response in cancer as conventional biopsies are invasive, costly and only provide a snapshot of the mutational profile at a given time and location. A promising biomarker is the detection of genomic material released from tumors into the blood plasma of patients, known as circulating tumor DNA (ctDNA). ctDNA has been detected in plasma for a wide range of solid tumors and can be distinguished from other (germline) cell-free DNA by the presence of tumor-specific DNA alterations or known hotspot mutations. However, the potential of ctDNA as a biomarker has not yet been fully realized due to technical challenges associated with its detection and analysis, including the short fragment sizes (140-170 bp), small number of amplifiable copies and low/variable allele fractions of ctDNA. We have developed an enhanced platform for tagged-amplicon deep sequencing (TAm-Seq™). Using a combination of improved library preparation and bespoke data analysis methods, this platform can be used to sequence established cancer hotspots and the entire coding regions of selected genes, while preserving high levels of specificity and sensitivity. Using this approach, we have developed an assay that analyzes ∼20 kb of the genome (including regions of interest in more than 30 genes) with sensitivity down to a few mutant copies. Performance of this assay has been demonstrated using spike-in experiments, dilution series and clinical sample cohorts. Proof of concept studies have shown the potential of ctDNA to be used to assess tumor mutation status, monitor tumor dynamics, assess response to treatment and identify mutations associated with acquired drug resistance and disease progression. This non-invasive approach - a “liquid biopsy” - offers a revolution in how cancer can be detected, monitored and treated. Citation Format: Andrew RJ Lawson, Vincent Plagnol, Abdelaziz Fahem, Tim Forshew, James D. Brenton, Davina Gale, Nitzan Rosenfeld. Assessment of clinical applications of circulating tumor DNA using an enhanced TAm-Seq platform. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2412. doi:10.1158/1538-7445.AM2015-2412

Authors:

ARJ Lawson, V Plagno, A Fahem, T Forshew, JD Brenton, D Gale, N Rosenfeld

Journal:

Cancer Research

Citation info:

75(15_Supplement):2412-2412

Publication date:

1st Aug 2015

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