Protocol

Browsing HapMap Data Using the Genome Browser

This protocol was adapted from "Using the HapMap Web Site," Chapter 6, in Genetic Variation (eds. Weiner et al.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2007.

INTRODUCTION

The primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human disease. Within the project, ~3.9 million distinct single-nucleotide polymorphisms (SNPs) have been genotyped in 270 individuals from four worldwide populations. The project data are available for unrestricted public use at the HapMap website. This site, which is the primary portal to genotype data produced by the project, offers bulk downloads of the data set, as well as interactive data browsing and analysis tools that are not available elsewhere. Research into the genetic contributions to a human disease commonly focuses on candidate genes identified from linkage and/or association studies, as well as from pathways suspected to be involved in a particular disease process. In studying candidate genes, a researcher will want to know whether there are any common SNPs in the immediate vicinity, what those SNPs’ alleles are, and the relative frequencies of the alleles in the population. The researcher will also be particularly interested in coding SNPs, whose alleles change the amino acid sequence of the gene product and therefore might represent functional variations. This protocol provides details on how to use the genome browser to navigate to and explore HapMap data for a gene or region of interest.