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Haploview: Visualization and Analysis of SNP Genotype Data

Adapted from Genetic Variation (eds. Weiner et al.). CSHL Press, Cold Spring Harbor, NY, USA, 2007.

INTRODUCTION

Association studies involve accessing, parsing, generating, and analyzing large volumes of data, often carried out in many steps over many months. Large-scale surveys of genetic variation, such as the International HapMap Project, and rapidly increasing volumes of single-nucleotide polymorphism (SNP) genotyping data have created exciting opportunities for association studies. However, they have further exacerbated the difficulty of curating and analyzing such data. Haploview is a program developed in Mark Daly’s lab at the Broad Institute of MIT and Harvard, which is designed to bundle many everyday analysis tasks into one easy-to-use package. Haploview has several features that are useful throughout different phases of association studies. Several of these features are illustrated in this article by following a hypothetical association study from design to execution. Haploview is used to (1) analyze HapMap data and choose tag-SNPs, (2) evaluate the quality of disease genotype data, (3) test for association, and (4) evaluate a region for follow-up of a positive association.