We designed a targeted NGS panel based on a single-primer extension protocol to analyze the lengths of cfDNA fragments. The panel comprised 81 primers covering COAD-specific open-chromatin regions extracted previously from TCGA data.
Results:We developed a novel approach for targeted cfDNA fragmentation analysis in multiply regions of interest. We have experimentally identified 10 genomic regions with significant (p<0.01) differences in cfDNA fragmentation in patients with stage IV colorectal cancer and healthy controls.Conclusions: Our evidence supports the concept that targeted analysis of cfDNA fragmentation may facilitate the detection of tumor presence. This strategy may reveal a novel class of cost-effective biomarkers that will serve as analytes themselves or might be incorporated into multidimensional liquid biopsy assays in combination with somatic mutations or aberrant methylation.Legal entity responsible for the study: The authors.
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