Influence of Isolation Techniques on the Quality of Plasma Samples: Implications for Cancer Biobanking

Biobanks are essential for precision oncology, providing high-quality materials for biomedical research. Liquid biopsy has become a key tool for non-invasive detection of tumor-derived biomarkers, including circulating tumor DNA, proteins, and extracellular vesicles. However, the reliability of these assays critically depends on standardized preanalytical procedures. In this study, we evaluated the impact of two plasma isolation methods—direct centrifugation (DC) and density gradient centrifugation (DGC)—on the overall quality of breast cancer samples collected at the Bruno Boerci Biobank (Maugeri, Italy). Plasma obtained with the two methods was analyzed by spectrometry for hemolysis and lipemia, biochemical analysis for protein and lipoprotein composition, flow cytometry for cellular debris and platelet contamination. Preanalytical nonconformities due to hemolysis, icterus, and lipemia were comparable between methods. However, DGC was associated with a higher platelet contamination and reduced albumin and cholesterol levels. Inter-individual variability was preserved, supporting the robustness of patient-specific molecular signatures, despite absolute discrepancies. This study highlights the pivotal role of the isolation techniques in shaping the quality and overall composition of plasma samples. Harmonized, “fit-for-purpose” biobanking protocols are required to ensure reproducibility of downstream analyses, support biomarker discovery, and ultimately advance the identification of novel therapeutic targets in cancer.