In the summer of 2021 our team designed and offered this (online) workshop to 17 senior high school students from the University of Toronto Schools (UTS) in Toronto, Ontario, Canada, selected based on their interests and readiness in statistics, genetics or computing. Throughout the 4.5-day workshop, the mornings were used for lectures, providing the necessary background in genetics and statistics. The afternoons were guided tutorials, providing hands-on experience.
To download all files, use Code > Download ZIP or command line git clone https://github.com/sugolov/GWAS-Workshop.git.
GWAS_Manual.pdf contains instructions for conducting the workshop. Gene expression data can be found in the Datasets directory. For downloading genotype data, please see The Center for Applied Genomics http://www.tcag.ca/tools/1000genomes.html, download below:
http://www.tcag.ca/documents/tools/omni25_indep.tar.gz: cleaned, independent samples from 1000 Genomes project
Directory containing gene expression data for selected 1000 Genomes populations.
Datasets/ERAP2_YRI_phenotypes.txt: YRI dataset required for tutorial.Datasets/ERAP2_CEU_phenotypes.txt: CEU dataset for independent analysis.Datasets/ERAP2_CEU_YRI_phenotypes.txt: YRI and CEU dataset for mixed population analysis.
Contains all scripts mentioned throughout the manual.
Guided walkthrough of the scripts.
- The detailed hands-on manual and the most updated version is Open Access by Anton Sugolov and Eric Emmenegger
- The lecture notes (1 set) in genetics by Dr. Andrew Paterson
- The lecture notes (5 subsets) in statistics by Dr. Lei Sun.
We perform three Genome-Wide Association Studies on endoplasmic reticulum aminopeptidase 2 gene expression data collected by the Illumina microarray of HapMap3 individuals, having significant overlap with 1000 Genomes Project individuals. The association tests are performed with 88 YRI (Yoruba in Nigeria) individuals and 102 CEU (Northern Europeans in Utah) from the 1KG project that pass quality control at the Centre for Applied Genomics. Analyses on the YRI, CEU, and combined CEU and YRI individuals are performed in order to demonstrate the intersection of statistics and genomics for interested students. The workshop focuses on using PLINK and R to perform association tests and to interpret their results. Statistical methods and considerations for genetic data, visualization and interpretation of large amounts of data, population stratification through principal component analysis, and reproducibility research are at the forefront of this workshop.
Please see the workshop manual for a complete bibliography, and below for relevant links.
https://www.internationalgenome.org/category/gene-expression/ https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-198/ https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-264/ http://tcag.ca/tools/1000genomes.html