Genetics Course 1 - JunLab - Biomedical Genetics Section - BUSM

From Dhawal Priyadarshi

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First genetics course at Jun Lab (March 5, 2024)

Topic 1: VCF Handling and Pre-GWAS QC

Instructor: Donghe Li

Basic handling of VCF files
Generate toy data from WES real data:
VCF data format
How to prepare the data for GWAS analysis
Pre-GWAS QC
Basic Phenotype QC for analysis
Genotype QC steps for GWAS

Topic 2: Population Stratification and Principal Components in GWAS

Instructor: Congcong Zhu

Introduction to Population Stratification
Principal Component Analysis
Introduction to PCA
Data Pruning
PC calculation

Topic 3: GWAS and post-GWAS Analysis

Instructor: Ryan Dacey

Running GWAS
GENESIS script
Input example
Output example
Post GWAS Analysis
QQ Plot
Manhattan Plot
Annotation script
QQ Plot and Manhattan Plot scripts
Regional plots

Topic 4: Meta-analysis

Instructor: Samantha Clayton

Introduction to meta-analysis
Fixed effects model
Heterogeneity
Random effects model
Forest plot
Tools and scripts
METAL (Intro + Code)
METASOFT (Intro)

Topic 5: Polygenic Risk Scores

Instructor: Dhawal Priyadarshi

Introduction to PRS
What is PRS?
PRS datasets
Base data and target data
Quality checks
PRS calculation
Step 1- Clumping+Thresholding
Code run snippet and outputs
Step 2 - DOS1 dosage file creation
Code run snippet and outputs
Step 3 – PRS calculation formula
Code run snippet and outputs

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