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

Area of Science:

• Clinical Diagnostics
• Molecular Oncology
• Genomic Medicine

Background:

• Standardization efforts for next-generation sequencing (NGS)-based circulating tumor DNA (ctDNA) analysis are ongoing.
• Assessing current laboratory practices is crucial for clinical implementation.

Purpose of the Study:

• To investigate the current status of clinical laboratory practices for NGS-based ctDNA analysis in China.
• To identify strengths and critical gaps in these laboratory workflows and quality assurance measures.

Main Methods:

• A comprehensive online survey with 62 questions was distributed to laboratories in China.
• Data collected included laboratory characteristics, analytical workflows, and quality assurance (QA) measures.
• 106 laboratories performing clinical NGS-based ctDNA analysis were included in the final analysis.

Main Results:

• While 96.2% of labs followed standardized pre-analytical workflows and 84.9% used diverse QA approaches, significant variability in methodologies was observed.
• Identified gaps include lack of specific criteria for sample collection/rejection, inadequate filtration, absence of orthogonal confirmations, incomplete validation, and insufficient quality control metrics.
• Internal quality control assessments were infrequently performed in many laboratories.

Conclusions:

• Clinical laboratory practices for NGS-based ctDNA analysis in China demonstrate both adherence to some standards and critical deficiencies.
• Further standardization of workflows, robust validation strategies, and stringent quality control measures are essential for improving clinical practice.