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

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 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.

Background reading: Holsinger, K. and B.S. Weir. 2009. Genetics in geographically structured populations: defining, estimating, and interpreting Fst. Nature Reviews Genetics 10:639--650. Weir, B.S. and C.C. Laurie. 2011. Statistical genetics in the genome era. Genetics Research 92:461--470.