The potential of combined mutation sequencing of plasma circulating cell‐free DNA and matched white blood cells for treatment response prediction

Abstract

Highly sensitive mutation detection methods enable the application of circulating cell‐free DNA for molecular tumor profiling. Recent studies revealed that sequencing artifacts, germline variants, and clonal hematopoiesis confound the interpretation of sequencing results and complicate subsequent treatment decision making and disease monitoring. Parallel sequencing of matched white blood cells promises to overcome these issues and enables appropriate variant calling. Comment on: https://doi.org/10.1002/1878-0261.12617

Circulating tumor DNA as a biomarker for monitoring early treatment responses of patients with advanced lung adenocarcinoma receiving immune checkpoint inhibitors

“…Longitudinal monitoring of a single tumor‐derived variant beyond the currently proposed interval might assist in early detection of disease progression and its clinical applicability, probably in combination with multiple available biomarkers, should be investigated in future (prospective) studies. Besides, as ccfDNA is shed into circulation from various tissues, DNA fragments from hematopoietic and germline origin are prone to affect analytical results with NGS, as well as inconsistent preanalytical handling and sample processing [ 23 , 49 , 50 , 51 ]. Although the majority of clonal hematopoietic variants occur in nontargetable genes, these variants are also identified in targetable genes such as KRAS , BRAF , and PIK3CA as well [ 16 ].…”

“…Deep sequencing of plasma may therefore identify more mutations, but these might not all be derived from the tumor. To this extent, parallel sequencing of a patient‐matched bloodborne reference material, for example, white blood cells, is of importance [ 50 ], further increasing the costs for routine clinical practice. Therefore, monitoring ctDNA with a ddPCR assay is as sensitive as NGS to monitor therapy response but in a cost‐effective manner.…”

Validation of a Circulating Tumor DNA-Based Next-Generation Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing

“…This makes it possible to encounter genomic alterations in cfDNA but not in tissue DNA. Those unique plasma variations were thought to be entirely because of tumor heterogeneity and clonal evolution, but recent reports have added clarification to the complex picture: such events might reflect clonal hematopoiesis [25] or simply are reported because of technical errors [26]. By analyzing replicate sets of tissue‐plasma samples through four NGS‐based plasma assays, Stetson et al documented variability among results from the four plasma NGS vendors revealing technical errors or differences in sensitivities as potential causes of discrepant alterations between the plasma NGS vendors [26].…”

Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients

“…Furthermore, total ccfDNA concentrations can be influenced dramatically not only by technical factors such as hemolysis, but also by unrelated factors such as exercise and inflammation [32,33]. Finally, post-analytical determinants such as detection methods that differ in, e.g., sensitivity, complexity, and mutation coverage may also affect the clinical outcome [17,27,34,35].…”