Abstract SY11-02: Detection of tumor-associated mutations in circulating DNA: clinical applications and experiences.
Authors: Jeffers Michael , Lathia Chetan D. , Wilhelm Scott M. , Voliotis Dimitris , Laurent Dirk , Pena Carol E. 
Published: August 2014

Abstract
The detection of tumor-associated mutations is of paramount importance in the era of personalized medicine. Mutational testing is now a prerequisite for the use of some approved therapies (e.g., KRAS for cetuximab in colorectal cancer [CRC]; BRAF for vemurafenib in melanoma), and these clearly established correlations between tumor mutational status and drug response elevate the importance and urgency of evaluating such associations in clinical trials of investigational drugs.
While archival primary tumor tissue is often used for mutational evaluation, such material has inherent limitations, which may be overcome by recent technological developments enabling the detection of tumor-associated mutations using plasma-derived DNA. For example, when a tumor tissue specimen is unavailable, use of plasma DNA would allow mutational status to be ascertained without the need for an invasive procedure to obtain a new tumor sample. In addition, it is now apparent that most patients treated with targeted therapies will eventually develop drug resistance, often via the acquisition of new tumor-associated mutations; these mutations may vary not only between patients but also between metastases within an individual patient. As such, the mutational status of an archival primary tumor specimen may not be relevant to guide the selection of subsequent therapies, and obtaining fresh tumor tissue from each metastasis that arises following the development of drug resistance is impractical. In such instances, mutational analysis of DNA derived from a real-time plasma sample obtained after the onset of drug resistance may offer advantages in terms of both availability and biological relevance, since new mutations acquired in response to a particular targeted therapy may be detectable in plasma DNA. Finally, mutational analysis of plasma DNA may be useful in clinical trials to evaluate potential correlations between mutational status and clinical outcome. For such exploratory analyses, the collection of archival tumor specimens from a high proportion of enrolled patients can be logistically and ethically difficult to achieve, not to mention of questionable relevance given that acquired mutations would not be detectable in these specimens. Collection of fresh tumor tissue samples at study entry would provide biologically relevant material, but can be problematic and costly to obtain in large, global clinical trials. Thus, the utility of plasma DNA for real-time mutational analysis in the clinical-trial setting offers several distinct advantages.
Since DNA derived from both normal and tumor cells exists in the circulation, the detection of tumor-associated mutations in plasma DNA requires the ability to identify a relatively small number of mutant alleles among an excess of wild-type alleles. With the goal of identifying the most suitable technology for this purpose, we conducted a comparison of available methodologies and found that BEAMing technology (Beads, Emulsions, Amplification, and Magnetics) offered very sensitive detection of known tumor-associated mutations using plasma DNA, although this technique is not well suited for the discovery of previously unknown mutations. We have now used BEAMing to analyze more than 2,000 patient samples collected from oncology clinical trials, allowing us to evaluate a number of genes (e.g., KRAS, NRAS, HRAS, BRAF, PIK3CA, AKT1, EGFR, KIT, and PDGFRA) in different cancer types (e.g., CRC, gastrointestinal stromal tumors, hepatocellular carcinoma, non-small-cell lung cancer, and breast cancer). We have used BEAMing of plasma DNA both prospectively, to enroll patients into a phase I trial based on a molecular profile of interest, and retrospectively, to evaluate potential associations between mutational status and clinical outcome in phase II and III trials. In many of these trials, collection of both fresh plasma and archival tumor tissue from a subset of patients has enabled us to compare mutational status in patient-matched plasma and tumor samples. Our experiences with BEAMing of plasma DNA to determine tumor-associated mutational status will be discussed.
Citation Format: Michael Jeffers, Chetan D. Lathia, Scott M. Wilhelm, Dimitris Voliotis, Dirk Laurent, Carol E. Pena. Detection of tumor-associated mutations in circulating DNA: clinical applications and experiences. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY11-02. doi:10.1158/1538-7445.AM2013-SY11-02