151: EQA of ctDNA Molecular Tumor Profiling in the COIN Consortium

van der Leest P et al., Clinical Chemistry - An interlaboratory external quality assessment across 16 laboratories in the Dutch COIN consortium evaluated how diverse (pre)analytical workflows and analytical platforms affect detection and genotyping of ctDNA mutations in plasma. Key terms: ctDNA, liquid biopsy, external quality assessment, NGS, preanalytical standardization.

Study Highlights:
Six of 16 laboratories achieved a performance score >0.90 while others scored between 0.26 and 0.80, reflecting wide variability in results. Thirteen laboratories reached a 100% overall detection rate for analyzed variants, but actionable mutations such as EGFR p.(S752_I759del), EGFR p.(N771_H773dup), and KRAS p.(G12C) were frequently not accurately genotyped. A broad range of plasma input volumes, extraction kits, elution volumes, and analytical methods (ddPCR, small panels, and NGS) were used across sites. The study indicates that divergent (pre)analytical and analytical choices can lead to discrepant clinical outcomes.

Conclusion:
Standardization of (pre)analytical workflows and careful selection of analytical assays are needed to ensure reproducible and clinically reliable ctDNA-based molecular profiling.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
External Quality Assessment on Molecular Tumor Profiling with Circulating Tumor DNA-Based Methodologies Routinely Used in Clinical Pathology within the COIN Consortium

First author:
van der Leest P

Journal:
Clinical Chemistry

DOI:
10.1093/clinchem/hvae014

Reference:
van der Leest P, Rozendal P, Hinrichs J, van Noesel CJM, Zwaenepoel K, Deiman B, Huijsmans CJJ, van Eijk R, Speel EJM, van Haastert RJ, Ligtenberg MJL, van Schaik RHN, Jansen MPH, Dubbink HJ, de Leng WW, Leers MPG, Tamminga M, van den Broek D, van Kempen LC, Schuuring E. 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. doi: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:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/eqa-of-ctdna-mutation-testing-across-the-coin-consortium

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-09-28.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript’s representation of the COIN EQA study’s design, numeric results, and implications for standardization in ctDNA testing, including specific mutation-genotype findings and methods.
- transcript topics: Interlaboratory variability in preanalytical workflows; DLA patient-derived plasma vs artificial reference samples; Loci analyzed: BRAF exon 15, EGFR exons 18–21, KRAS exons 2–3; Analytical methods: ddPCR, small-panel PCR, NGS; Genotyping accuracy vs detection rate and actionable mutations; Specific mutation misses: EGFR S752_I759del, EGFR N771_H773dup, KRAS G12C

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- 16 laboratories participated in the COIN EQA across plasma-derived ctDNA analysis
- Three artificial reference (spiked-in) plasma samples and three DLA (patient-derived) plasma samples were distributed
- Loci of interest: BRAF exon 15, EGFR exons 18–21, KRAS exons 2–3
- Eight different extraction methods and ten different analytical methodologies were used
- 13 of 16 laboratories (81%) achieved 100% overall detection rate for the analyzed variants
- Genotyping accuracy for actionable mutations was frequently lacking, with specific misses including EGFR S752_I759del (69%), EGFR N771_H773dup (50%), and KRAS G12C (33/64 calls, 52

QC result: Pass.