️ Episode 151: EQA of ctDNA Mutation Testing Across the COIN Consortium

In this episode of PaperCast Base by Base, we explore how 16 Dutch laboratories evaluated their real‑world workflows for circulating tumor DNA (ctDNA) mutation testing across BRAF, EGFR, and KRAS using a coordinated external quality assessment within the COIN consortium.

Study Highlights:
The team distributed six plasma samples—three commercial references with predefined variants and three patient‑derived diagnostic leukapheresis samples—to participating labs, asking them to run their routine preanalytical and analytical pipelines, including ddPCR, small PCR panels, and next‑generation sequencing. Performance was scored on protocol adherence, overall detection, and precise genotyping, revealing broad variability in plasma input, extraction methods, and elution volumes and showing that only 38% of labs achieved a performance score above 0.90. Although 81% reached a 100% overall detection rate for the variants they assayed, clinically actionable mutations such as EGFR p.(S752_I759del), EGFR p.(N771_H773dup), and KRAS p.(G12C) were frequently mis‑genotyped, largely reflecting assay design limits. NGS approaches generally enabled more accurate variant‑level calls but carried a higher risk of false positives, while single‑target assays demonstrated sensitivity yet lacked breadth to cover all guideline‑relevant loci.

Conclusion:
Harmonizing preanalytical handling and selecting assays with adequate breadth and specificity are essential to deliver reproducible, clinically actionable liquid biopsy results in routine practice.

Reference:
van der Leest P, Rozendal P, Hinrichs J, van Noesel CJM, Zwaenepoel K, et al. External Quality Assessment on Molecular Tumor Profiling with Circulating Tumor DNA‑Based Methodologies Routinely Used in Clinical Pathology within the COIN Consortium. Clinical Chemistry. 2024;70(5):759–767. https://doi.org/10.1093/clinchem/hvae014

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

Chapters

• (00:00:00 ) - Chopping Through the DNA of Cancer
• (00:03:18 ) - Commemorating the COIN Consortium
• (00:03:56 ) - The challenge of standardization in cancer DNA testing
• (00:07:56 ) - The EGFR Genotyping Study
• (00:10:59 ) - Liquid DNA standardization