BST227

Introduction to Statistical Genetics

Course Head: Martin Aryee

Teaching Assistants: Michele Zemplenyi & Kushal Dey

Overview

This course will provide an introduction to statistical methods for genetic studies. The emphasis of this course is on understanding basic concepts and methods and how they are applied in the analysis of population genetic data. The course starts out with an overview of methods for identifying disease-associated variants, and then goes on to cover approaches for interpreting the role of these variants in disease. A background in genetics is not necessary. The basic concepts of human and molecular genetics relevant to the course will be covered in class.

Schedule

Class: Monday & Wednesday 3:45PM - 5:15PM, Kresge 202B
Lab Sections: Sections begin the week of Nov 5th. You may choose which section you would like to attend each week. Though sections are optional, we encourage you to attend.

Instructor office hours: Mon 12:30PM - 1:30PM, Building 2 Room 421B
TA office hours:

Lectures

29-Oct Introduction and overview of genetic disease
31-Oct Mendel’s Laws and genetic models for disease
5-Nov Hardy Weinberg Equilibrium and recurrence risk ratios
7-Nov An overview of linkage and association
12-Nov Veteran’s Day - No class
14-Nov Introduction to GWAS
19-Nov Population Substructure

Thanksgiving break

26-Nov Analysis of rare variants and non-SNP variation
28-Nov Variant calling from high-throughput sequencing data
3-Dec Estimating Heritability from Family Data and from Genome Data
5-Dec Using the 3-dimensional organization of DNA to interpret variants
10-Dec Editing DNA to interpret variants
12-Dec Genetic association studies in cancer
17-Dec Epigenome-wide Association Studies (EWAS)
19-Dec Project presentations

Final Project

Final Project Instructions

Final Project Groups and Diseases

Report Example

Data for each group:

Team Fisher.zip

Team Franklin.zip

Team McClintock.zip

Team Mendel.zip

Team Morton.zip

Team Pearson.zip

Homeworks

Homework 1

Homework 2, Homework 2 markdown

Homework 3, Data files: genotype, phenotype, genome legend

Homework Solutions

Homework 1

Homework 2

Homework 3

Lab Sections