Genomics for Precision Oncology
I Introduction
Workshop Info
Pre-work
1. Create a Franklin Account
2. Download and Install IGV (Integrative Genomics Viewer)
Class Photo
Schedule
Meet Your Faculty
Instructors
Teaching Assistants
Facilitator
Data and Compute Setup
II Modules
Module 1
Lecture
Module 2
Lecture
Lab (Part 1)
AWS and Unix Basics
Docker
Investigating Some Genomics File Formats and Metadata
Lab (Part 2) - Implementing the GATK Best Practices Workflow
FastQC Quality Control
Alignment/Short-Read Mapping with BWA-MEM
GATK Pre-Processing
Putting Everything Together
Viewing BAMs in IGV
Somatic Variant Calling with MuTect2
Variant Annotation with VEP
Answers to Guiding Questions
Module 3
Lecture
Lab: Clinical Variant Interpretation with Franklin
Learning Objectives
Lab Overview
Part 1: Account Creation and Platform Navigation
Creating Your Franklin Account
Platform Navigation: Understanding the Main Interface
Creating and Searching for Variants
Creating New Cases
Understanding Franklin’s Automated Classification Logic
Part 2: Exploring Variant Classification
Step 1: Searching for a Variant
Step 2: Understanding the Classification Workspace
Step 3: Reviewing Automatically Assigned ACMG Codes
Step 4: Deep Dive into Population Data (PM2 Example)
Step 5: Editing Evidence Strength
Step 6: Exploring Additional Evidence Categories
Part 3: Uploading and Classifying Your Case VCF (45 minutes)
Step 1: Download Your Case Data
Step 2: Create a New Case in Franklin
Part 4: Variant interpretation
Step 3: Navigating to Your Case
Step 4: Reviewing BRCA2 Variants in Your Case
Step 5: Adding Patient Phenotype Information
Step 6: Exploring Case-Level Quality Control and Variant Filtering
Step 7: Deep Dive into Variant Classification: BRCA2:c.1813dup
Reviewing the Franklin ACMG Classification
Exploring the Variant Assessment Tab
Exploring Associated Conditions
Using the Publications Tab
Gene Assessment Tab
Step 8: Finalizing Your Classification and Creating a Clinical Report
Part 5: Extension Exercise (Optional)
Summary
Module 4
Lecture
Lab - Case 3: STK11 Deletion in Peutz-Jeghers Syndrome
Learning Objectives
Background
Section 1: Installing the Integrative Genomics Viewer
Section 2: Acquiring Case Study Data Files
Section 3: Loading Data into IGV and Navigating to STK11
Section 4: Quality Assessment of the Suspected Deletion
Section 5: Clinical Interpretation of Copy Number Loss Using ClinGen Guidelines
Step 6: Calculating the Final Classification
Step 7: Clinical Recommendations and Validation
References
Lab - Microsatellite Instability Visualization
Learning Objectives
Lab Overview
Background: Understanding Microsatellite Instability
Part 1: Data Download from Jupyter Notebook
Part 2: Loading Data into IGV
Part 3: Visualizing Microsatellite Instability
Summary and Clinical Significance
Sponsors
Genomics for Precision Oncology 2025
Data and Compute Setup
Course data downloads
Coming soon!
Compute setup
Coming soon!