ClinVAP: a reporting strategy from variants to therapeutic options

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Next-generation sequencing (NGS) is crucial for personalized oncology, driving the need for efficient somatic variant analysis.
• Current methods for processing large variant lists in cancer diagnosis and therapy often lack reproducibility, scalability, and interoperability.

Purpose of the Study:

• To develop an automated, robust, and reproducible pipeline for annotating, filtering, and prioritizing somatic single nucleotide variants (SNVs).
• To enhance clinical decision-making by augmenting variant data with clinical effect, driver gene status, and druggability information.

Main Methods:

• The Clinical Variant Annotation Pipeline (ClinVAP) was developed as a fully containerized, self-contained system.
• ClinVAP processes variants in variant call format (VCF), annotates them with clinical relevance, and prioritizes them based on biological and therapeutic significance.
• The pipeline is designed for maximum reproducibility and scalability, handling large-scale genomic datasets.

Main Results:

• ClinVAP successfully annotates, filters, and prioritizes somatic SNVs, providing clinically relevant information.
• The pipeline generates JSON-based reports for automated downstream analysis and can produce human-readable reports from user-defined templates.
• Containerization ensures high reproducibility and scalability for analyzing extensive cancer genomic data.

Conclusions:

• ClinVAP offers a significant advancement in the automated processing of somatic variants for clinical oncology.
• The pipeline improves the efficiency and reliability of variant interpretation, supporting personalized cancer therapy.
• ClinVAP's design promotes interoperability and scalability, addressing key limitations in existing variant analysis tools.