This course is presented by the University of Colorado Denver in collaboration with the Vanderbilt Genetics Institute at Vanderbilt University Medical Center and the International Genetic Epidemiology Society. It is designed to provide students with the background and knowledge foundations necessary to conduct statistical analysis of genetic association study data. This course includes multiple lectures and evaluations on each of the topics: the history of genetics research presented by Dr. Nancy Cox, foundational concepts in population genetics presented by Dr. Bruce Weir, population structure in genetic association studies presented by Dr. Todd Edwards, quality control in genetic studies presented by Dr. Goncalo Abecasis, analysis of population-based case-control association studies presented by Dr. Celia Greenwood, and analysis of family-based studies presented by Dr. Joan Bailey-Wilson. Examples of concepts and reference literature are also provided in this 6-module course.
Taught by Dr. Nancy Cox, Vanderbilt University Medical Center. In this module you will better understand genetic epidemiology from its origins to how modern ‘omics is integrated into genetic epidemiology of complex traits. Coverage includes introduction of liability and threshold models, genetic regulation of gene expression, and transcriptome imputation.
Module 1 Introduction: What is Genetic Epidemiology?•1 minute
Origins of Genetic Epidemiology•8 minutes
Legacies of these Origins and Scientific Rigor•8 minutes
Liability and Threshold Models: Introduction•7 minutes
Testing and an Example•3 minutes
Genetic Regulation of Gene Expression•9 minutes
Introduction•4 minutes
Methods•9 minutes
Methods Continued and Extension•9 minutes
Pleiotropy•10 minutes
4 readings•Total 35 minutes
Acknowledgements and Instructors•10 minutes
Glossary•10 minutes
Get help and meet other learners. Join your Community!•5 minutes
References and Links•10 minutes
1 assignment•Total 45 minutes
Module 1 Summative Assessment•45 minutes
1 discussion prompt•Total 10 minutes
Module 1 Discussion Prompt•10 minutes
Introduction to Population Genetics: Models and Assumptions
Module 2•3 hours to complete
Module details
Taught by Dr. Bruce Weir, University of Washington. Methods and designs using genetic data are built upon the foundation of population genetics. In this module, you will learn these foundations, including the Hardy Weinberg principle, genetic drift, population structure, inbreeding, and linkage disequilibrium. These principles will be essential to subsequent modules in this course.
What's included
16 videos1 reading1 assignment1 discussion prompt
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16 videos•Total 115 minutes
Introduction to Population Genetics•1 minute
Hardy-Weinberg Equilibrium Definition and Implications•9 minutes
HWE Testing and P-Values•9 minutes
HWE Testing Power, QQ Plots, and Multiple Tests•5 minutes
HW Departures and Population Structure•8 minutes
Genetic Drift I•8 minutes
Genetic Drift II•8 minutes
Population Structure I•9 minutes
Population Structure II•8 minutes
Inbreeding and Relatedness I•9 minutes
Inbreeding and Relatedness II•8 minutes
Inbreeding and Relatedness III•8 minutes
Linkage Disquilibrium I•7 minutes
Linkage Disquilibrium II•6 minutes
Linkage Disquilibrium III•6 minutes
Linkage Disquilibrium IV•5 minutes
1 reading•Total 10 minutes
Related Articles•10 minutes
1 assignment•Total 60 minutes
Module 2 Summative Assessment•60 minutes
1 discussion prompt•Total 15 minutes
Module 2 Discussion Prompt•15 minutes
Population Structure and Genetic Association Studies
Module 3•3 hours to complete
Module details
Taught by Dr. Todd Edwards, Vanderbilt University Medical Center. Building from the introduction to population genetics, in this module you will learn processes that lead to genetic differences between populations, methods to characterize these differences, and how to conduct association studies in structured populations. In addition, you will be able to describe how admixture methods can be applied for association mapping.
Basic Quality Control in Genetic Data: Data Structure
Module 4•2 hours to complete
Module details
Taught by Dr. Gonçalo Abecasis, University of Michigan and Regeneron, Inc. Quality control is an important step for high throughput genotype data. In this module, you will learn a range of different approaches to identify and to deal with quality problems at different stages of the analysis. In addition, genotype imputation is introduced to infer genotypes at markers that were not typed in the study samples.
What's included
11 videos1 reading1 assignment1 discussion prompt
Show info about module content
11 videos•Total 60 minutes
Basic Quality Control in Genetic Data•1 minute
Motivation and Background•7 minutes
Introduction to Quality Control•7 minutes
QQplots: Part 1•5 minutes
QQplots: Part 2•5 minutes
Mendelian Inconsistency Checks•8 minutes
Population Structure: Part 1•5 minutes
Population Structure: Part 2•6 minutes
Genotype Imputation: Introduction•5 minutes
Genotype Imputation: The Details, Part 1•5 minutes
Genotype Imputation: The Details, Part 2•7 minutes
1 reading•Total 10 minutes
Optional Readings•10 minutes
1 assignment•Total 60 minutes
Module 4 Summative Assessment•60 minutes
1 discussion prompt•Total 10 minutes
Module 4 Discussion Prompt•10 minutes
Population-Based Association Studies
Module 5•3 hours to complete
Module details
Taught by Dr. Celia Greenwood, McGill University. Population based association studies have played an important role in mapping genes and genomic regions for complex traits by detecting association between alleles and a trait. In this module, you will learn basic measures of association, common modeling strategies, how to adjust for multiple testing and why, how to evaluate association results, and how to increase reproducibility of study results, including the use of meta-analysis and genetic imputation.
What's included
14 videos1 reading1 assignment1 discussion prompt
Show info about module content
14 videos•Total 71 minutes
Population-Based Association Studies•1 minute
Basic Measures: Part 1•5 minutes
Basic Measures: Part 2•8 minutes
Common Modeling Strategies: Part 1•6 minutes
Common Modeling Strategies: Part 2•5 minutes
Introduction to Multiple Testing: Part 1•5 minutes
Introduction to Multiple Testing: Part 2•6 minutes
Reproducibility: Part 1•5 minutes
Reproducibility: Part 2•6 minutes
Introduction to Genotype Imputation: Part 1•6 minutes
Introduction to Genotype Imputation: Part 2•3 minutes
Introduction to Meta-Analysis and Consortia: Part 1•5 minutes
Introduction to Meta-Analysis and Consortia: Part 2•4 minutes
Introduction to Meta-Analysis and Consortia: Part 3•5 minutes
1 reading•Total 10 minutes
Resources•10 minutes
1 assignment•Total 60 minutes
Module 5 Summative Assessment•60 minutes
1 discussion prompt•Total 15 minutes
Module 5 Discussion Prompt•15 minutes
Family-Based Designs
Module 6•3 hours to complete
Module details
Taught by Dr. Joan Bailey Wilson, National Human Genome Research Institute, National Institutes of Health. In this module, you will learn about the various ways in which family-based collections of genetic data are utilized in Genetic Epidemiology. This includes methods that provide support that a genetic component to a trait exists as well as to identify modes of inheritance consistent with a set of data. In addition, linkage methods, which identify large regions of the genome, and association methods, which identify a smaller set of variants, are covered to understand genetic factors affecting a trait.
What's included
18 videos1 reading1 assignment1 discussion prompt
Show info about module content
18 videos•Total 107 minutes
Family-Based Designs•1 minute
Overview•6 minutes
Familial Clustering•6 minutes
Twin Studies•7 minutes
Other Designs•8 minutes
Classical Methods•7 minutes
Modern Methods•3 minutes
Basics Part 1•7 minutes
Basics Part 2•6 minutes
Recombination and Mapping•7 minutes
Parametric Methods•8 minutes
Model-Free Methods•9 minutes
Overview Part 1•8 minutes
Overview Part 2•4 minutes
Types of Methods•5 minutes
Overview•3 minutes
Linkage•8 minutes
Association•3 minutes
1 reading•Total 10 minutes
References and Software•10 minutes
1 assignment•Total 60 minutes
Module 6 Summative Assessment•60 minutes
1 discussion prompt•Total 15 minutes
Module 6 Discussion Prompt•15 minutes
Instructors
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V
VG
5·
Reviewed on Feb 24, 2025
more current scenarios should have been introduced
A
AS
4·
Reviewed on May 19, 2025
For the quizzes, it would be nice if they were problem based questions, and we could use some of the equations to calculate for a final answer. Otherwise concepts were good.
J
JB
5·
Reviewed on Nov 27, 2022
Excellent introductory lectures. I learned alternative ways of presenting this material and corrected some details from self study.
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