Comprehensive Evaluation of a 1021-Gene Panel in FFPE and Liquid Biopsy for Analytical and Clinical Use

In the era of precision oncology, comprehensive molecular profiling is critical for guiding targeted and immunotherapy strategies. This study presents the analytical and clinical validation of a 1021-gene next-generation sequencing (NGS) panel, designed for use with both formalin-fixed paraffin-embedded (FFPE) tissue- and liquid-biopsy specimens. Analytical validation confirmed the assay's high sensitivity and specificity across variant types-including SNVs (Single Nucleotide Variations), indels, CNVs (Copy Number Variations), and fusions-down to a 0.5% variant allele frequency. The assay also accurately identified microsatellite instability (MSI) and tumor mutational burden (TMB), essential biomarkers for immunotherapy. Clinical validation was performed on over 1300 solid tumor samples from diverse histologies, revealing actionable alterations in over 50% of cases. The panel detected on-label treatment biomarkers in 12.57% of patients, increasing to 20.15% when immunotherapy markers were included. Additionally, the assay demonstrated strong concordance with orthogonal methods and was effective in detecting variants in plasma-derived circulating tumor DNA in 70% of evaluable cases. These findings support the robust performance and broad clinical applicability of the 1021-gene panel for comprehensive genomic profiling in both tissue and liquid biopsies, offering a valuable tool for personalized cancer treatment.

Authors

Institutions

Publication Details

Journal
International Journal of Molecular Sciences
Published
2025-06-20
DOI
https://doi.org/10.3390/ijms26135930
Citations
3
Primary Topic
Gene expression and cancer classification
Type
article
Field-Weighted Citation Impact
2.42
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Comprehensive Evaluation of a 1021-Gene Panel in FFPE and Liquid Biopsy for Analytical and Clinical Use

Georgios Kapetsis, Chrysiida Florou-Chatzigiannidou, Georgios Tsaousis, Konstantinos Botsolis et al.
3 citations
International Journal of Molecular Sciences
Gene expression and cancer classification
2.42
article

Comprehensive Evaluation of a 1021-Gene Panel in FFPE and Liquid Biopsy for Analytical and Clinical Use

Georgios Kapetsis, Chrysiida Florou-Chatzigiannidou, Georgios Tsaousis, Konstantinos Botsolis, Eirini Papadopoulou, Andreas Agathangelidis, Sualp Tansan, Ioannis Boukovinas, Cemil Bilir, Stella Maxouri, Stylianos Giassas, George Nasioulas, Mustafa Özdoğan, Angeliki Meintani, Αθανάσιος Παπαθανασίου, Şahin Laçin, Ioannis P. Trougakos, Tahsin Özatlı, Dimitrios C. Ziogas, Konstantinos Papazisis, Nikolaos Touroutoglou, Maria Theochari, Vasiliki Metaxa-Mariatou, Aikaterini Tsantikidi, Panagoula Κollia, Paraskevas Kosmidis, Dimitrios Grigoriadis, Jinga Dan Corneliu
article en
3 citations

Abstract

In the era of precision oncology, comprehensive molecular profiling is critical for guiding targeted and immunotherapy strategies. This study presents the analytical and clinical validation of a 1021-gene next-generation sequencing (NGS) panel, designed for use with both formalin-fixed paraffin-embedded (FFPE) tissue- and liquid-biopsy specimens. Analytical validation confirmed the assay's high sensitivity and specificity across variant types-including SNVs (Single Nucleotide Variations), indels, CNVs (Copy Number Variations), and fusions-down to a 0.5% variant allele frequency. The assay also accurately identified microsatellite instability (MSI) and tumor mutational burden (TMB), essential biomarkers for immunotherapy. Clinical validation was performed on over 1300 solid tumor samples from diverse histologies, revealing actionable alterations in over 50% of cases. The panel detected on-label treatment biomarkers in 12.57% of patients, increasing to 20.15% when immunotherapy markers were included. Additionally, the assay demonstrated strong concordance with orthogonal methods and was effective in detecting variants in plasma-derived circulating tumor DNA in 70% of evaluable cases. These findings support the robust performance and broad clinical applicability of the 1021-gene panel for comprehensive genomic profiling in both tissue and liquid biopsies, offering a valuable tool for personalized cancer treatment.

International Journal of Molecular SciencesVol. 26(13)
Sakarya University (TR), Koç University (TR), National and Kapodistrian University of Athens (GR), Interbalkan Medical Center (GR), LETO Maternity Hospital (GR), Laiko General Hospital of Athens (GR), Ippokrateio General Hospital of Thessaloniki (GR), Istinye University (TR), Hygeia Hospital (GR), Athens Medical Center (GR), Antalya IVF (TR), Polyclinic General Hospital (GR)
Good health and well-being
Openalex Percentile: Top 11%
Gene expression and cancer classification
2.42
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.