TABLE OF CONTENTS

1. Introduction
2. Generating LD Plots
3. Computing Haplotype Blocks
4. Comparing Multiple LD Plots
5. Haplotype Frequency Tables
6. Haplotype Association Tests
7. Large-Scale Haplotype Association Testing

Download entire tutorial in PDF format

Tutorial: LD and Haplotype Analysis

Updated November 2009

Level: Intermediate

Modules: HelixTree

This tutorial leads you through various LD and haplotype analyses in SVS 7. For demonstration purposes, a simulated dataset is used consisting of actual Affymetrix 500K genotypes from the four HapMap populations (Phase II) and a fake case/control status.

By completing this tutorial you will learn how to:

• Generate and compare multiple LD plots
• Automatically and manually define haplotype blocks
• Produce haplotype frequency tables
• Compare single marker and haplotype association results

IMPORTANT: This tutorial does not cover quality assurance and therefore no quality assurance steps have been performed on the data. As it may be appropriate to filter markers out of Hardy-Weinberg Equilibrium or with low call rates and minor allele frequencies, it is recommended that you perform such measures with your own data prior to performing LD and haplotype analysis.

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Requirements

To complete this tutorial you will need to download and unzip the following file, which includes several datasets.

Download	Files	Size	Description
	LD_and_Haplotype_Tutorial.zip	83 MB	Project containing 500K genotype/phenotype data and initial single marker association results.