Background
Available methods for MRD detection in CTCL utilize primarily circulating cellular DNA, and sensitivity of MRD in cfDNA has been poorly characterized for CTCL. Genomic heterogeneity of CTCL limits the utility of disease-specific MRD panels, and existing hybrid capture based cell-free MRD methods exclude TCR detection. Therefore, we developed a personalized cfDNA sequencing strategy than integrates detection of patient-specific somatic variants with detection of cell-free TCR molecules (cfTCR).
Methods
Based on WES of diagnostic samples, we generated customized hybrid-capture panels that included 62 shared, recurrently altered CTCL genes, as well as 25-389 personalized somatic mutations, and 3-6 lymphoma TCR clonotypes per patient. MRD detection was compared between cellular and cfDNA isolated from the same blood sample.
Results
Detection of circulating tumor DNA by somatic variant tracking was more sensitive in plasma versus cells (78% vs. 33%, p=0.0176), and tumor DNA fractions were significantly more abundant in plasma (p=0.0419). Similarly, detection of TCR clonotypes was significantly more sensitive using cfTCR compared to cellular TCR (72% vs. 28%, p=0.0437). MRD detection through integrated assessment of somatic variants and cfTCR suggested better detection of molecular disease by our cfDNA NGS approach as compared to commercial TCR high-throughput sequencing assays using cellular DNA (84% vs 63% sensitivity, p=0.27). Analysis of serial plasma samples during treatment, demonstrated levels of molecular disease corresponded to treatment response.
Conclusions
Overall, our findings suggest that detection of circulating tumor cfDNA including cfTCR may improve MRD detection and has potential clinical utility for disease surveillance in CTCL.
