Clinical applications of circulating tumor DNA analysis
Keywords: Stem Cell Biology and Regenerative Medicine.

Circulating tumor DNA (ctDNA) represents an exquisitely specific biomarker due to the fact that tumors harbor somatic mutations that are not present in other cell-types in the body. We begin with a review of the existing methodologies and applications of ctDNA, highlighting studies that illustrate the diverse clinical utility of ctDNA. Next we focus on a method for ctDNA detection developed by our lab called Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq). CAPP-Seq is a targeted next-generation sequencing approach for ctDNA detection that does not require patient specific optimization and is amenable to a variety of cancer types. We first employ CAPP-Seq based ctDNA analysis to study resistance mechanisms in 43 non-small cell lung cancer (NSCLC) patients treated with the third-generation EGFR tyrosine kinase inhibitor (TKI) rociletinib. Multiple resistance mechanisms were present in 46% of patients after treatment with front-line EGFR TKIs, representing a previously unrecognized high frequency of molecular heterogeneity of resistance mechanisms following treatment with EGFR TKIs. Rociletinib resistance recurrently involved MET, EGFR, PIK3CA, ERRB2, KRAS and RB1. We observed a novel EGFR L798I mutation, and EGFR C797S, which arises in ~1/3 of patients treated with another third-generation inhibitor (osimertinib), was observed in only one patient. Increased MET copy number was the most frequent rociletinib resistance mechanism and patients with multiple pre-existing mechanisms (i.e. T790M and MET) experienced inferior responses. Congruently, rociletinib-resistant xenografts developed MET amplification that could be overcome with the MET inhibitor crizotinib. These results underscore the importance of tumor heterogeneity in NSCLC and the clinical utility of ctDNA-based resistance mechanism assessment. Next we apply ctDNA analysis to a less common cancer type, Leiomyosarcoma (LMS). LMS is a soft-tissue sarcoma that represents a tumor type with a heterogeneous spectrum of genomic abnormalities. As such, targeting hotspot mutations in a narrow genomic region for ctDNA detection is suboptimal. For this reason we developed a combinatorial approach that integrates different sequencing protocols for the orthogonal detection of single nucleotide variants (SNVs), small indels and copy number alterations (CNAs) in ctDNA. We employed CAPP-Seq for the analysis of SNVs and indels, together with a genome-wide interrogation of CNAs by Genome Representation Profiling (GRP). We profiled 28 longitudinal plasma samples and 25 tumor specimens from 7 patients with LMS. We detected ctDNA in 6 of 7 of these patients with > 98% specificity for mutant allele fractions down to a level of 0.01%. We found that ctDNA quantitation by CAPP-Seq and GRP was highly concordant, and the combination of these methods allows for more comprehensive monitoring of ctDNA by profiling a wide spectrum of tumor-specific markers. Through analysis of multiple tumor specimens from individual patients we observed evidence for both spatial and temporal tumor heterogeneity that was reflected in ctDNA profiles. This strategy allows for comprehensive monitoring of a broad spectrum of tumor-specific markers in plasma and may be clinically useful not only in LMS but in other tumor types that lack recurrent genomic alterations.