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Updated: Aug 5, 2026
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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
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Integrating Formalin-Fixed, Paraffin-Embedded-Derived Whole-Genome Sequencing into Routine Molecular Pathology:
Cassandra Litchfield1, Ronny Nienhold1, Andreas Wicki2
1Department of Pathology and Molecular Pathology, University Zürich and University Hospital Zürich, Zürich, Switzerland.
The Journal of Molecular Diagnostics : JMD
|July 27, 2025
Summary
Whole-genome sequencing (WGS) of formalin-fixed, paraffin-embedded (FFPE) tumor tissue is a valid diagnostic tool for metastatic melanoma. FFPE-derived WGS provides comprehensive insights and enhances therapeutic options, potentially becoming a routine diagnostic method.
Area of Science:
- Oncology
- Genomics
- Pathology
Background:
- Formalin-fixed, paraffin-embedded (FFPE) tissue is standard in pathology.
- Whole-genome sequencing (WGS) has diagnostic potential but is underexplored in FFPE samples.
Purpose of the Study:
- To evaluate the validity and utility of FFPE-derived WGS in metastatic melanoma.
- To compare FFPE-derived WGS with targeted sequencing panels.
Main Methods:
- Developed a diagnostic pipeline for FFPE-derived WGS quality control and variant annotation.
- Compared WGS results with FoundationOneCDx (F1CDx) and MelArray in 78 melanoma samples.
Main Results:
- FFPE-derived WGS showed high concordance with F1CDx for various variant types.
- Tumor mutational burden strongly correlated with F1CDx, especially at clinical thresholds.
- WGS identified complex biomarkers and suggested treatments/trials for all cases, revealing additional markers and novel therapeutic opportunities.
Conclusions:
- FFPE-derived WGS demonstrates robust analytical validity and clinical utility in melanoma.
- WGS offers comprehensive genomic insights beyond targeted panels, enhancing therapeutic strategies.
- WGS is poised to become a powerful routine diagnostic tool with decreasing costs.
