Error-corrected deep targeted sequencing of circulating cell-free DNA from colorectal cancer patients for sensitive detection of circulating tumor DNA

Abstract

IntroductionCirculating tumor DNA (ctDNA) is a promising biomarker, reflecting the presence of tumor cells. Sequencing-based detection of ctDNA at low tumor fractions is challenging due to the crude error rate of sequencing. To mitigate this challenge, we developed UMIseq, a fixed-panel deep-targeted sequencing approach, which is universally applicable to all colorectal cancer (CRC) patients.MethodsUMIseq features UMI-mediated error correction, exclusion of mutations related to clonal hematopoiesis, a panel of normals for error modeling, and signal integration from single-nucleotide variations, insertions, deletions, and phased mutations. UMIseq was trained and independently validated on pre-operative (pre-OP) plasma from CRC patients (n=364) and healthy individuals (n=61).ResultsUMIseq displayed an area under the curve surpassing 0.95 for allele frequencies (AF) down to 0.05%. In the training cohort, the pre-OP detection rate reached 80% at 95% specificity, while in the validation cohort, it was 70%. UMIseq enabled the detection of AFs down to 0.004%. To assess the potential for detection of residual disease, 26 post-operative plasma samples from stage III CRC patients were analyzed. Detection of ctDNA was associated with recurrence (p =0.08).ConclusionUMIseq demonstrated robust performance with high sensitivity and specificity, enabling the detection of ctDNA at low allele frequencies.