Genome Sequencing Outperforms Exome Sequencing in Formalin‐Fixed Paraffin Embedded Tumors Leading to Improved Treatment Options
5 affiliations
- 1Institute of Medical Genetics and Applied Genomics University Hospital Tübingen Tübingen Germany
- 2NGS Competence Center Tübingen (NCCT) Tübingen Germany
- 3Department of Pathology and Neuropathology University Hospital Tübingen Tübingen Germany
- 4Center for Personalized Medicine University Hospital Tübingen Tübingen Germany
- 5Department of Internal Medicine I University Hospital Tübingen Tübingen Germany
Abstract
Precision oncology is based on comprehensive molecular characterization of a patient's tumor. This is mostly realized by next‐generation sequencing panels or exome sequencing. Data on the value of genome sequencing from formalin‐fixed paraffin embedded (FFPE) material in a clinical setting is still scarce. In this pilot, we generated datasets of matched exome and genome sequencing of FFPE tumor samples from 15 cancer patients to benchmark quality metrics, clinical feasibility, and added value for a molecular tumor board. Despite the reduced sequencing depth, diagnostic detection of small nucleotide variations, copy number variations, and complex biomarkers was maintained in genome sequencing compared to exome sequencing with the exception of hard‐to‐sequence regions. Evaluation by the local molecular tumor board identified additional treatment recommendations with high priority in 20% (3/15) of patients and additional molecular markers to support existing treatment recommendations in another 20% (3/15) of patients. Our work underscores the diagnostic superiority of genome sequencing even for FFPE samples and therefore supports its integration into clinical practice.
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BibTeX
@article{ballin2026genome,
title = {{Genome Sequencing Outperforms Exome Sequencing in Formalin‐Fixed Paraffin Embedded Tumors Leading to Improved Treatment Options}},
author = {Nadja Ballin and Alexander Ott and Michaela Pogoda and Florian Harmuth and Vijay Kumar Ulaganathan and Anton Karelin and Cristiana Roggia and Irina Bonzheim and Stephan Singer and Holly Sundberg‐Malek and Pavlos Missios and Stephan Ossowski and Tobias B. Haack and Olaf Riess and Michael Bitzer and Nisar Malek and Christopher Schroeder and Sorin Armeanu‐Ebinger},
journal = {Cancer Medicine},
year = {2026},
month = oct,
doi = {10.1002/cam4.72448},
url = {https://doi.org/10.1002/cam4.72448},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Genome Sequencing Outperforms Exome Sequencing in Formalin‐Fixed Paraffin Embedded Tumors Leading to Improved Treatment Options
AU - Nadja Ballin
AU - Alexander Ott
AU - Michaela Pogoda
AU - Florian Harmuth
AU - Vijay Kumar Ulaganathan
AU - Anton Karelin
AU - Cristiana Roggia
AU - Irina Bonzheim
AU - Stephan Singer
AU - Holly Sundberg‐Malek
AU - Pavlos Missios
AU - Stephan Ossowski
AU - Tobias B. Haack
AU - Olaf Riess
AU - Michael Bitzer
AU - Nisar Malek
AU - Christopher Schroeder
AU - Sorin Armeanu‐Ebinger
PY - 2026
DA - 2026/10/27
JO - Cancer Medicine
DO - 10.1002/cam4.72448
UR - https://doi.org/10.1002/cam4.72448
AB - Precision oncology is based on comprehensive molecular characterization of a patient's tumor. This is mostly realized by next‐generation sequencing panels or exome sequencing. Data on the value of genome sequencing from formalin‐fixed paraffin embedded (FFPE) material in a clinical setting is still scarce. In this pilot, we generated datasets of matched exome and genome sequencing of FFPE tumor samples from 15 cancer patients to benchmark quality metrics, clinical feasibility, and added value for a molecular tumor board. Despite the reduced sequencing depth, diagnostic detection of small nucleotide variations, copy number variations, and complex biomarkers was maintained in genome sequencing compared to exome sequencing with the exception of hard‐to‐sequence regions. Evaluation by the local molecular tumor board identified additional treatment recommendations with high priority in 20% (3/15) of patients and additional molecular markers to support existing treatment recommendations in another 20% (3/15) of patients. Our work underscores the diagnostic superiority of genome sequencing even for FFPE samples and therefore supports its integration into clinical practice.
SN - 2045-7634
ER -