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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
ClinBioNGS: A Clinical Bioinformatics Pipeline for Integrated Analysis of Somatic Next-Generation Sequencing Cancer
Raúl Marín1,2,3,4, Ania Alay1,2, Maria Ajenjo-Bauza1,2
1Unit of Bioinformatics for Precision Oncology (UBOP), Institut Català d'Oncologia (ICO), L'Hospitalet de Llobregat, Barcelona, Spain.
Purpose:
Somatic next-generation sequencing (NGS) panels are widely used in precision oncology to detect clinically actionable genomic alterations. However, interpreting diverse DNA and RNA alterations remains challenging because of the complexity of tumor-only data and the limitations of current pipelines, which are often proprietary, noncustomizable, or lack visual reports to support clinical interpretation. We present ClinBioNGS, an open-source, panel-agnostic bioinformatics pipeline for the comprehensive analysis of somatic NGS cancer panels in both clinical and translational settings.
Materials And Methods:
ClinBioNGS is a modular, fully containerized workflow implemented in Nextflow. It supports integrated analysis of DNA and RNA data, including multicaller small variant detection, copy number alteration (CNA) profiling, gene fusion and splice variant identification, and evaluation of complex genomic biomarkers such as tumor mutational burden and microsatellite instability. Variants are annotated and prioritized using established clinical frameworks. The results are compiled in a self-contained interactive HTML report with dynamic tables and informative visualizations to facilitate clinical interpretation. Validation included SEQC2 reference data sets across six commercial panels, and benchmarking was performed on 2,024 clinical tumor samples analyzed with three commercial platforms.
Results:
ClinBioNGS achieved high accuracy in SEQC2 validation, with precision (0.987-1.000), recall (0.920-0.997), and F1 scores (0.956-0.999) across diverse panels. In a clinical benchmarking with real-world data, the pipeline demonstrated high concordance with commercial solutions for small variants (97%), CNAs (89%), and RNA alterations (94%), while also identifying additional high-confidence alterations missed by vendor pipelines.
Conclusion:
ClinBioNGS provides a robust, flexible, and transparent solution for standardized analysis of somatic NGS cancer panels. It supports reproducible, clinically oriented interpretation of genomic data and is freely available for noncommercial research-use only at GitHub.
Insights
ClinBioNGS is an open-source bioinformatics pipeline for analyzing somatic next-generation sequencing (NGS) cancer panels. It offers accurate, comprehensive DNA and RNA analysis with interactive reports for precision oncology.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Somatic next-generation sequencing (NGS) panels are crucial for precision oncology, but interpreting complex tumor DNA and RNA alterations is challenging.
- Current bioinformatics pipelines often lack transparency, customizability, and integrated visualization tools, hindering clinical interpretation.
Purpose of the Study:
- To introduce ClinBioNGS, an open-source, panel-agnostic bioinformatics pipeline for comprehensive somatic NGS cancer panel analysis.
- To provide a robust, flexible, and transparent solution for both clinical and translational research in oncology.
Main Methods:
- ClinBioNGS is a modular, containerized Nextflow workflow supporting integrated DNA and RNA analysis.
- It includes multicaller small variant detection, copy number alteration (CNA) profiling, gene fusion and splice variant identification, and complex biomarker evaluation (e.g., tumor mutational burden, microsatellite instability).
- Results are presented in an interactive HTML report with dynamic tables and visualizations, validated on SEQC2 data and benchmarked on 2,024 clinical samples.
Main Results:
- ClinBioNGS demonstrated high accuracy in validation, with precision, recall, and F1 scores exceeding 0.920 across diverse panels.
- Benchmarking showed high concordance with commercial pipelines for small variants (97%), CNAs (89%), and RNA alterations (94%).
- The pipeline identified additional high-confidence alterations missed by vendor solutions.
Conclusions:
- ClinBioNGS offers a standardized, reproducible, and transparent solution for analyzing somatic NGS cancer panels.
- It facilitates clinically oriented interpretation of genomic data.
- The pipeline is freely available for noncommercial research use.
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