Editors: Donna E. Hansel, MD, PhD, chief, Division of Anatomic Pathology, and professor, Department of Pathology, University of California, San Diego; John A. Thorson, MD, PhD, associate professor, Department of Pathology, UCSD; Sarah S. Murray, PhD, associate professor, Department of Pathology, and director of genomic technologies, Center for Advanced Laboratory Medicine, UCSD; and James Solomon, MD, PhD, resident, Department of Pathology, UCSD.
Noninvasive diagnosis of mutations by deep sequencing of cfDNA in NSCLC
Mutation analysis of actionable oncogenes in solid tumors commonly uses human tissue samples obtained through invasive procedures, such as biopsy or surgery. The authors demonstrated that circulating free DNA (cfDNA) obtained from patients in the BioCAST/IFCT-1002 lung cancer study could be used to detect clinically actionable somatic mutations in several genes of relevance to lung cancer that develop in patients who never smoked. CfDNA was successfully extracted from 106 of 107 patient plasma samples, and cfDNA concentration was shown to significantly correlate with clinical stage. It was also associated with the overall number of metastatic sites. Using a technique based on multiplex polymerase chain reaction and Life Technologies’ Ion Torrent Personal Genome Machine for deep sequencing (at a target average read depth of 10,000 times for plasma DNA and 1,000 times for tumor DNA), the authors tested for mutations in EGFR, KRAS, BRAF, ERBB2, and PI3KCA in cfDNA and compared the results to tumor-derived DNA in a subset of 68 cases. Most of the cfDNA-detected mutations were identified in the EGFR gene, with overall sensitivity of 58 percent and specificity of 87 percent when compared to tumor DNA as a reference. The authors noted that point mutations were more readily detected than insertions or deletions in this analysis. Despite this early success, additional studies are needed to expand the number of detectable mutations in actionable oncogenes using this approach. Furthermore, software modifications, such as those that allow modification of the variant calling strategy to detect uncommon mutations, need to be developed for common use. The use of cfDNA is likely to expand into clinical application given the ease of blood draw for cfDNA isolation and the ability to isolate cfDNA from most samples. In addition to being used for molecular profiling at initial diagnosis, these methods could potentially be used to monitor the efficacy of targeted therapy.
Couraud S, Paniagua FV, Villar S, et al. Non-invasive diagnosis of actionable mutations by deep sequencing of circulating-free DNA in non-small cell lung cancer: Findings from BioCAST/IFCT-1002 [published online ahead of print July 10, 2014]. Clin Cancer Res. doi:10.1158/1078-0432.CCR-13–3063.
Correspondence: Dr. Sebastien Couraud at sebastien.couraud@chu-lyon.fr