introduction_to_gwas

Material for the Course “Introduction to genome-wide association studies (GWAS)”

Instructors: Filippo Biscarini, Oscar Gonzalez-Recio, Christian Werner

This course will introduce students, researchers and professionals to the steps needed to build an analysis pipeline for Genome-Wide Association Studies (GWAS). The course will describe all the necessary steps involved in a typical GWAS study, which will then be used to build a reusable and reproducible bioinformatics pipeline.

Each day the course will start at 14:00 and end at 20:00 (CET). As a general rule, we’ll have a longer break (30 minutes) at 16:00 and two shorter breaks (10-15 minutes) later on during the day (to be decided flexibly depending on the sessions).

Day 1

• Lecture 0 General Introduction / Overview of the Course [Filippo, Oscar, Christian]
  • [General Introduction]
  • [GWAS Workflow (short)]
• Lecture 1 GWAS Overview: Case Studies / Examples from Literature [Oscar]
  • [GWAS Overview]<!–(slides/1_GWAS_overview.pdf)
• Lecture 2 Introduction to GWAS: Linkage Disequilibrium and Linear Regression [Oscar]
  • [Introduction to GWAS]
• Lecture 3 - Basic Linux and the Shell [Christian]
  • [Linux and the Shell]
• Lab 1 - Practicalities and Set-up (Server, github repo, R, etc) and Description of Datasets [Christian]
  • [Description of Datasets]
  • [Unix Cheatsheet]
• [Course Manual]
• [GWAS Workflow]

Day 2

• Lab 2 (Demonstration) GWAS: Basic Models (Linear and Logistic Regression) [Oscar]
  • R code. Exercise on Simple Linear Regression
  • Rmarkdown Code. Exercise on Simple Logistic Regression
• Lecture 4 Data Types & Formats [Christian]
  • [Common Data Types and Formats]
• Lecture 5 Initial Data Analysis, Exploratory Data Analysis and Data Pre-Processing [Christian]
  • [IDA, EDA & Data Pre-Processing]
• Lab 3 EDA & IDA [Christian]
• Lab 4 Data Pre-Processing [Christian]
• Lecture 6 The Multiple Testing Issue [Oscar]
  • [Multiple Testing]
• Lecture 7 Statistical Power, Population Stratification and Experimental Design [Oscar]
  • [Statistical Power and Population Stratification]
  • R code. Exercise on statistical power

Day 3

• Lecture 8 Imputation of Missing Genotypes [Christian]
  • [Imputation]
• Lab 5 Imputation of Missing Genotypes using Beagle [Christian]
• Lecture 9 KNN Imputation
  • [KNN Imputation]
• Lab 6 (Demonstration) KNNI Imputation [Filippo]
  • knni_illustration.Rmd
  • data_for_KNNI_illustration
  • 02_knni.sh
  • hamming.R [support script]
  • knni.R [support script]
• Lab 7 GWAS: The Stand-Alone Script(s) for the Full Model [Filippo]
  • gwas_rrblup.R
  • gwas_statgengwas.R
  • gwas_sommer.R
• Lab 8 Revising the Steps involved in GWAS [Filippo]
  • [slides]
  • 1.get_data.sh
  • 2.step_filtering.sh
  • 3.step_imputation.sh
  • 4.gwas.sh
• Brief Intermission:
  • R code PCA & Population Structure
  • Imputed rice genotypes
• Lab 9 Introducing the Exercise [Filippo]
  • [Collaborative Exercise]
• Collaborative Exercise: let’s build our own GWAS workflow on new data [Filippo, Oscar, Christian]
  • Part 1: Individual/Group Break-Out Sessions to give it a try independetly
  • Part 2: Whole-Group Revision of the Exercise

Day 4

• Lecture 10 Bioinformatics Pipelines: a super-elementary Introduction [Filippo]
  • [A bioinformatics pipeline for GWAS]
• Lab 10 Building a Pipeline with Snakemake [Filippo]
• Lab 11 The GWAS pipeline for Continuous Phenotypes [Filippo]
  • Plug-In for Mean or KNN Imputation
  • The GWAS pipeline for Binary Phenotypes (Guided Exercise) [Filippo]
• Q&A on building Pipelines for GWAS [Filippo, Oscar, Christian]
• Lecture 11 A light Touch on Post-GWAS Analysis: Inferring Functionality [Oscar]
  • [slides]
  • R code. Exercise on R, and FUMA

Day 5

• Lecture 12 GWAS Model Extensions: [Filippo]
  • [12.1 GWAS Model Extensions_Dominance_and_other_genotype_Codifications]
  • [12.2 GWAS Model Extensions_Polyploids]
  • [12.3 GWAS Model Extensions_Trait_Types]
  • [12.4 GWAS Model Extensions_Multi-Trait-Locus, software]
  • [R code GWASpoly (vignette)]
  • R code GWAS for categorical Traits
  • R code GWAS for categorical Traits - Examples
  • R code GWAS for longitudinal Traits
  • [R code GWAS for multi-trait and multi-locus Models]
• Lecture 13 A Glimpse on ROH-based Alternative [Filippo, optional]
  • [ROH-based and Resampling Methods as alternative Approaches]
  • [Other gene actions]
• Kahoot Quiz on what we learned about GWAS! [Filippo, Oscar, Christian]
• Conclusions and Wrap-Up Discussion on GWAS [Filippo, Oscar, Christian]

Organization of the Code for the practical Sessions

1. preparatory_steps: download and prepare the data
2. preprocessing: filter the data
3. imputation: imputing missing genotypes
4. gwas: run the GWAS models
5. power_and_significance: designing GWAS experiments
6. steps: identifying the individual steps involved in a GWAS study
7. pipeline: assembling the individual steps into a bioinformatics pipeline for GWAS
8. collaborative exercise: trying out what we learnt on new data