23rd Summer Institute in Statistical Genetics (SISG)

Module 5: Population Genetic Data Analysis

Session 2: Wed Jul 11 to Fri Jul 13

Module dates/times: Wednesday, July 11, 1:30-5 p.m.; Thursday, July 12, 8:30 a.m.-5 p.m., and Friday, July 13, 8:30 a.m.-5 p.m.

This module serves as a foundation for many of the later modules. It includes:

  • 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.
  • A detailed look at Hardy-Weinberg and linkage disequilibrium, including the use of exact tests with mid-p-values and a new look at X-chromosome Hardy-Weinberg testing.
  • A new characterization of population structure with F-statistics, based on allelic matching within and between populations with individual inbreeding and relationship estimation as a special case.

Analyses illustrated with applications to forensic science and association mapping, with particular reference to rare variants. Concepts illustrated with R exercises.

Jérôme Goudet is Associate Professor of Ecology and Evolution at the University of Lausanne, Switzer- land. His research concerns an understanding of the interplay of population structure, trait architecture, and selection. For this, he uses different approaches, from theory and the development of statistical tools to field observations. He recently published “apex: phylogenetics with multiple genes.” Molecular Ecology Resources 17:19-26, 2017. He developed the R package hierfstat.

Bruce Weir is Professor of Biostatistics and Director of the Institute for Public Health Genetics at the University of Washington. He develops statistical methodology for genetic data with an emphasis on allelic dependencies, population structure, disease associations and relationships, and the use of genetic data for human identification. His most recent publication is “Detection and quantification of inbreeding depression for complex traits from SNP data.” Proc. Natl. Acad. Sci. USA 114:8602-8607, 2017.

Goudet and Weir recently jointly published “A unified characterization of population structure and re- latedness.” Genetics 206:2085-2103, 2017. They are currently working on the 3rd Edition of “Genetic Data Analysis” published by Sinauer.

Access 2017 Course Materials (2018 materials will be uploaded to this page prior to the start of the module)