Clinical NGS Data Analysis
From variant calling to clinical interpretation using ACMG/AMP guidelines
Bridging Genomics and Patient Care
The integration of Next-Generation Sequencing (NGS) into clinical practice has opened new frontiers in personalized medicine. By sequencing a patient's DNA, clinicians can identify genetic variants responsible for inherited diseases, predict susceptibility to conditions like cancer, and tailor treatments for maximum efficacy.
However, the journey from raw sequencing data to an actionable clinical report is complex and requires specialized expertise. This involves navigating massive datasets, using sophisticated bioinformatics tools to call and annotate variants, and, most critically, interpreting their clinical significance based on established guidelines. Our workshop provides comprehensive, hands-on training to empower clinicians and scientists to confidently perform this analysis and translate genomic discoveries into tangible patient benefits.
Key Features & Benefits
Clinical Focus & ACMG Guidelines
Gain specialized training in clinical variant interpretation, learning to apply the official ACMG-AMP guidelines for pathogenicity.
Hands-On with Real Data
Work with real-world targeted gene panel and whole-exome sequencing data to develop practical, transferable analysis skills.
End-to-End Pipeline Development
Learn not just the tools, but how to integrate them into a complete analysis pipeline and manage your code on GitHub.
Comprehensive Resources
Receive all session recordings, presentations, and reference materials for ongoing review and professional development.
What You Will Learn
Module 1: Command-Line Foundations
- Linux Essentials: Master the command line, directory structures, and file manipulation—essential skills for bioinformatics.
- Shell Scripting Basics: Learn to automate repetitive tasks by writing simple scripts.
Module 2: The NGS Data Analysis Workflow
- Sequencing & Data Fundamentals: Understand sequencing basics, common file formats (FASTQ, BAM, VCF), and analysis tools.
- Data Processing: Perform quality control (QC), read alignment, and data visualization.
Module 3: From Sequence to Variants
- Variant Calling: Implement both germline and somatic variant calling pipelines using GATK best practices.
- Variant Quality Control: Learn to filter and assess the quality of your variant calls from the VCF file.
Module 4: Clinical Interpretation & Reporting
- Variant Annotation: Integrate data from key databases like NCBI RefSeq, dbSNP, ClinVar, and population databases (e.g., gnomAD).
- Variant Interpretation: Apply the official ACMG/AMP guidelines to classify variants by pathogenicity.
- Prioritization & Reporting: Develop strategies to prioritize variants for clinical reports.
Module 5: Developing Pipelines
- Integration of Tools: Learn how to combine various bioinformatics tools to create a cohesive variant analysis pipeline.
- Hosting on GitHub: Share and manage your pipelines effectively using GitHub.
Ready to Master Clinical NGS Data Analysis?
Join our comprehensive workshop and gain the skills needed to analyze and interpret NGS data for clinical applications.