GWAS
In the following tutorials, you will get an introduction to conducting genome-wide association studies (GWAS) from start to finish, with considerations for multi-ancestry and admixed populations, as well as insight into running case-case (CC) GWAS.
In the first video, Dr. Huang goes over the steps for conducting a GWAS using PLINK software. In the second video, Dr. Coleman discusses in detail the different QC steps (missingness, Hardy-Weinberg equilibrium, sex check, homozygosity or the inbreeding coefficient, relatedness, and ancestry) for GWAS, why they are necessary, and how your data might throw challenges at you. Next, Dr. Atkinson discusses running a GWAS in populations of admixed individuals, and introduces the Tractor software for conducting ancestry-aware GWAS using local ancestry tracts. In the fourth video, Dr. Genovese discusses genotype calling and imputation using the MOsaic CHromosomal Alterations (MoChA) pipeline. Next, Dr. Zhou gives an introduction to the Scalable and Accurate Implementation of Generalized Mixed Models (SAIGE) software, which is important for conducting GWAS in large-scale biobanks with imbalanced case-control ratios and/or samples that are related. Lastly, Dr. Peyrot gives an introduction to CC-GWAS software for running a case-case GWAS, comparing cases of two different disorders using summary statistics from each respective disorder's case-control analysis.
Genome-Wide Association Studies in PLINK
Title: Genome-wide Association Studies
Presenter(s): Hailiang Huang, PhD (Department of Medicine, Harvard Medical School)
Level: Intermediate
Length: 15:47
Link to video transcript here.
Link to tutorial GitHub and datasets.
Genotype QC
Title: How to run quality control on genome-wide genotyping data
Presenter(s): Jonathan Coleman, PhD (Social, Genetic, and Developmental Psychiatry Centre, King’s College London)
Level: Intermediate
Length: 16:19
Link to video transcript here.
Link to PGC RICOPILI pipeline.
Link to Coleman lab GitHub GWAS scripts.
Tractor: GWAS with Admixed Individuals
Title: Tractor: Enabling GWAS in admixed cohorts
Presenter(s): Elizabeth Atkinson, PhD (Department of Molecular and Human Genetics, Baylor College of Medicine)
Level: Intermediate
Length: 18:38
Link to video transcript here.
Link to tutorial GitHub and datasets.
Genotype Calling and Imputation with MoChA
Title: Genotype calling/imputation on the cloud: MoChA pipleine
Presenter(s): Giulio Genovese, PhD (Program in Medical and Population Genetics, Broad Institute of Harvard and MIT)
Level: Intermediate
Length: 15:13
Link to video transcript here.
Link to MoChA GitHub and Webpage.
SAIGE: Family-Based GWAS
Title: Genetic association studies in large-scale biobanks and cohorts
Presenter(s): Wei Zhou, PhD (Analytic and Translational Genetics Unit, The Broad Institute of Harvard and MIT)
Level: Intermediate
Length: 27:17
Link to video transcript here.
Link to GitHub and Wiki Tutorials for SAIGE and SAIGE-GENE.
CC-GWAS
Title: Tutorial to use CC-GWAS to identify loci with different allele frequency among cases of different disorders.
Presenter(s): Wouter Peyrot, MD, PhD (Department of Psychiatry, Amsterdam UMC)
Level: Intermediate
Length: 21:46
Link to video transcript here.