Genetic Epidemiology Foundations

Todd Edwards +1 more instructor

Offered By

Genetic Epidemiology Foundations

University of Colorado System

About this Course

This course is designed to provide students with the foundation necessary to conduct statistical analysis of genetic association study data. This course includes topics such as quality control in genetic studies, population-based case-control association studies, genome-wide association studies, and foundational concepts in population genetics and the history of genetics research. Examples of concepts and reference literature are provided in this 6-module course.

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Intermediate Level

Approx. 17 hours to complete

English

Subtitles: English

Instructors

Todd Edwards

Ph.D.

245 Learners

1 Course

Stephanie A. Santorico

Ph.D.

245 Learners

1 Course

Shareable Certificate

Earn a Certificate upon completion

100% online

Start instantly and learn at your own schedule.

Flexible deadlines

Reset deadlines in accordance to your schedule.

Intermediate Level

Approx. 17 hours to complete

English

Subtitles: English

Offered by

University of Colorado System

The University of Colorado is a recognized leader in higher education on the national and global stage. We collaborate to meet the diverse needs of our students and communities. We promote innovation, encourage discovery and support the extension of knowledge in ways unique to the state of Colorado and beyond.

Syllabus - What you will learn from this course

Week

Week 1

2 hours to complete

What is Genetic Epidemiology? Historical Perspective and Introduction

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.

2 hours to complete

11 videos (Total 69 min), 2 readings, 1 quiz

11 videos

Course Introduction2m

Module 1 Introduction: What is Genetic Epidemiology?53s

Origins of Genetic Epidemiology8m

Legacies of these Origins and Scientific Rigor7m

Liability and Threshold Models: Introduction6m

Testing and an Example2m

Genetic Regulation of Gene Expression9m

Introduction3m

Methods8m

Methods Continued and Extension8m

Pleiotropy9m

2 readings

Glossary10m

References and Links10m

1 practice exercise

Module 1 Summative Assessment45m

Week

Week 2

3 hours to complete

Introduction to Population Genetics: Models and Assumptions

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.

3 hours to complete

16 videos (Total 115 min), 1 reading, 1 quiz

16 videos

Introduction to Population Genetics44s

Hardy-Weinberg Equilibrium Definition and Implications9m

HWE Testing and P-Values9m

HWE Testing Power, QQ Plots, and Multiple Tests5m

HW Departures and Population Structure8m

Genetic Drift I7m

Genetic Drift II7m

Population Structure I9m

Population Structure II7m

Inbreeding and Relatedness I9m

Inbreeding and Relatedness II8m

Inbreeding and Relatedness III7m

Linkage Disquilibrium I6m

Linkage Disquilibrium II6m

Linkage Disquilibrium III6m

Linkage Disquilibrium IV5m

1 reading

Week 3

3 hours to complete

Population Structure and Genetic Association Studies

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.

3 hours to complete

12 videos (Total 66 min), 2 readings, 1 quiz

12 videos

Population Structure1m

Definition of Population Structure and Brief Overview of Human History6m

Factors the Influence Population Structure and Genetic Drift7m

Natural Selection8m

Examples of Population Structure in Modern Humans8m

Pima Example4m

Statistical Methods I: Structured Association and Genomic Control5m

Statistical Methods II: Principal Components Analysis5m

Statistical Methods III: LD Score Regression3m

Statistical Methods IV: Principal Components4m

Statistical Methods V: Mixed Models3m

Statistical Methods VI: Admixture Mapping6m

2 readings

Resources Part 110m

Resources Part 210m

1 practice exercise

Module 3 Summative Assessment1h

Week

Week 4

2 hours to complete

Basic Quality Control in Genetic Data: Data Structure

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.

2 hours to complete

11 videos (Total 60 min), 1 reading, 1 quiz

11 videos

Basic Quality Control in Genetic Data1m

Motivation and Background6m

Introduction to Quality Control6m

QQplots: Part 14m

QQplots: Part 25m

Mendelian Inconsistency Checks7m

Population Structure: Part 14m

Population Structure: Part 25m

Genotype Imputation: Introduction5m

Genotype Imputation: The Details, Part 14m

Genotype Imputation: The Details, Part 27m

1 reading

Optional Readings10m

1 practice exercise

Module 4 Summative Assessment1h

Week

Week 5

3 hours to complete

Population-Based Association Studies

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.

3 hours to complete

14 videos (Total 71 min), 1 reading, 1 quiz

14 videos

Population-Based Association Studies1m

Basic Measures: Part 14m

Basic Measures: Part 27m

Common Modeling Strategies: Part 15m

Common Modeling Strategies: Part 25m

Introduction to Multiple Testing: Part 15m

Introduction to Multiple Testing: Part 26m

Reproducibility: Part 15m

Reproducibility: Part 26m

Introduction to Genotype Imputation: Part 15m

Introduction to Genotype Imputation: Part 23m

Introduction to Meta-Analysis and Consortia: Part 14m

Introduction to Meta-Analysis and Consortia: Part 24m

Introduction to Meta-Analysis and Consortia: Part 34m

1 reading

Resources10m

1 practice exercise

Module 5 Summative Assessment1h

Week

Week 6

3 hours to complete

Family-Based Designs

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.

3 hours to complete

18 videos (Total 107 min), 1 reading, 1 quiz

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Genetic Epidemiology Foundations

Genetic Epidemiology Foundations

About this Course