Statistical Genetics
This module serves as a foundation for later population and quantitative genetics modules, as well as fitting into the statistical analysis stream. It provides a unified treatment for the analysis of discrete genetic data, starting with estimates and sample variances of allele frequencies to illustrate genetic vs statistical sampling and Bayesian approaches.
Concepts are demonstrated with exercises in R. We will take a detailed look at Hardy-Weinberg and linkage disequilibrium, including the use of exact tests with mid-p-values and take a new look at X-chromosome Hardy-Weinberg testing.
We also consider how to characterize population structure using F-statistics, based on allelic matching within and between populations with individual inbreeding and relationship estimation as a special case.
Learning Objectives: After attending this module, participants will be able to:
- Estimate allele frequencies from genotype counts and to estimate within-population inbreeding coefficients.
- Determine sample sizes required to detect inbreeding and perform goodness-of-fit tests for Hardy-Weinberg equilibrium.
- Use open source software to perform exact tests for Hardy-Weinberg equilibrium.
- Predict kinship levels for pairs of individuals in pedigrees and know which software to use for particular applications.
- Calculate allele-matching proportions within and between populations in order to estimate population structure parameters.
- Evaluate population structure using open source software.
Course Dates
- Wed June 5, 1:30 p.m. – 5:00 p.m. EST
- Thu June 6, 8:30 a.m. – 5:00 p.m. EST
- Fri June 7, 8:30 a.m. – 5:00 p.m. EST
Instructors
- Bruce Weir
- Jérôme Goudet
Suggested Course Pairings
Population and Statistical Genetics Streams
- Module 5: Bayesian Statistics
- Module 13: Multivariate Analysis
- Module 16: Population Genetics
- Module 20: Molecular Evolution
Course Materials
Visit the Box here.
About the Instructors
Bruce Weir is Professor Emeritus of Biostatistics at the University of Washington, Seattle, and holds adjunct appointments at Massey, Otago and Auckland Universities in New Zealand. He was the founding Director of the Summer Institutes in Statistical Genetics for 28 years, and is a Fellow of the Royal Society, in recognition of his contributions to forensic genetic inference and statistical measurement of population structure. Learn more about Bruce’s work here.
Jérôme Goudet is Professor of Population Genetics in the Department of Ecology and Evolution at the University of Lausanne in Switzerland. The main focus of his group concerns understanding the interplay between population structure, trait architecture, and natural selection, using a combination of theory and field research studies. Learn more about Jérôme’s work here.