Adapting Clinical Chemistry Plasma as a Source for Liquid Biopsies

Background Circulating cell-free DNA (cfDNA) has become a valuable analyte for molecular testing but requires specialized collection tubes or immediate processing. We investigated the feasibility of using residual plasma from heparin separators, which are routinely used in clinical chemistry, as an accessible and underutilized source for cfDNA testing. Methods We analyzed matched plasma samples collected in EDTA, Streck, and heparin separators in a Healthy Cohort (n = 5) and matched samples collected in EDTA and heparin separators from a Hospital Cohort derived from viral PCR-positive patients (n = 34). Whole-genome sequencing and genome-wide enriched methylation sequencing were performed to evaluate concordance across multiple benchmarks, including metagenomics, chromosomal copy number, methylome, and fragmentomics. Results In the Healthy Cohort, methylation patterns were correlated (Pearson’s r = 0.92–0.93) between tube types, and fragmentation features were preserved with a modal size peak at 166 bp and a consistent top 10 end motif ranking across tube types (n = 5). In the Hospital Cohort, heparin separators showed a strong concordance with matched EDTA tubes for viral detection (n = 34, Pearson’s r = 0.99), copy number alteration profiling (n = 6, Pearson’s r = 0.86-0.98), and methylation patterns (n = 12, r = 0.83-0.93). Conclusions Residual plasma from routine clinical chemistry tests can provide a vast, untapped resource for cfDNA analysis.