Laboratory practices for next-generation sequencing-based circulating tumor DNA analysis: insights from a...

Since large efforts have been done in recent years to promote the standardization of next-generation sequencing (NGS)-based circulating tumor DNA (ctDNA) analysis, the current status of its laboratory practices in clinical settings has become a topic worthy of inquiry. To address this, we conducted a comprehensive survey on the clinical laboratory practices of NGS-based ctDNA analysis. Between May and June 2024, an online questionnaire consisting of 62 questions was distributed to laboratories that had previously participated in the proficiency testing schemes for NGS-based ctDNA analysis in China. Information on the laboratory characteristics, detailed analytical workflows, and quality assurance measures were collected. Out of 137 initial responses, 106 laboratories (77.4%) reported performing NGS-based ctDNA analysis for clinical purposes. While there was considerable variability in methodologies and workflows among these laboratories, 96.2% (102/106) of laboratories adhered to standardized pre-analytical workflows and more than 84.9% (90/106) implemented diverse quality assurance approaches to maintain testing quality. Nevertheless, critical gaps in laboratory practices were still identified, including a lack of specific criteria for sample collection timing and sample rejection, inadequate filtration measures, absence of orthogonal confirmations, incomplete validation plans, insufficient quality control metrics, and infrequent internal quality control assessments. The data revealed both strengths and critical gaps in the currently clinical laboratory practices of NGS-based ctDNA analysis in China. Albeit former efforts, future care must still be taken in establishing standardized workflows, implementing robust validation, and enforcing robust quality control measures.