---
title: "International HapMap Project"
chunk: 1/2
source: "https://en.wikipedia.org/wiki/International_HapMap_Project"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T03:49:21.458141+00:00"
instance: "kb-cron"
---

The International HapMap Project is an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation. HapMap is used to find genetic variants affecting health, disease and responses to drugs and environmental factors. The information produced by the project is made freely available for research.
The International HapMap Project is a collaboration among researchers at academic centers, non-profit biomedical research groups and private companies in Canada, China (including Hong Kong), Japan, Nigeria, the United Kingdom, and the United States. It officially started with a meeting on October 27 to 29, 2002, and was expected to take about three years. It comprises three phases; the complete data obtained in Phase I were published on 27 October 2005. The analysis of the Phase II dataset was published in October 2007.  The Phase III dataset was released in spring 2009 and the publication presenting the final results published in September 2010.

== Background ==
Unlike with the rarer Mendelian diseases, combinations of different genes and the environment play a role in the development and progression of common diseases (such as diabetes, cancer, heart disease, stroke, depression, and asthma), or in the individual response to pharmacological agents. To find the genetic factors involved in these diseases, one could in principle do a genome-wide association study: obtain the complete genetic sequence of several individuals, some with the disease and some without, and then search for differences between the two sets of genomes. At the time, this approach was not feasible because of the cost of full genome sequencing. The HapMap project proposed a shortcut.
Although any two unrelated people share about 99.5% of their DNA sequence, their genomes differ at specific nucleotide locations. Such sites are known as single nucleotide polymorphisms (SNPs), and each of the possible resulting gene forms is called an allele. The HapMap project focuses only on common SNPs, those where each allele occurs in at least 1% of the population.
Each person has two copies of all chromosomes, except the sex chromosomes in males. For each SNP, the combination of alleles a person has is called a genotype. Genotyping refers to uncovering what genotype a person has at a particular site. The HapMap project chose a sample of 269 individuals and selected several million well-defined SNPs, genotyped the individuals for these SNPs, and published the results.
The alleles of nearby SNPs on a single chromosome are correlated. Specifically, if the allele of one SNP for a given individual is known, the alleles of nearby SNPs can often be predicted, a process known as genotype imputation. This is because each SNP arose in evolutionary history as a single point mutation, and was then passed down on the chromosome surrounded by other, earlier, point mutations. SNPs that are separated by a large distance on the chromosome are typically not very well correlated, because recombination occurs in each generation and mixes the allele sequences of the two chromosomes. A sequence of consecutive alleles on a particular chromosome is known as a haplotype.
To find the genetic factors involved in a particular disease, one can proceed as follows. First a certain region of interest in the genome is identified, possibly from earlier inheritance studies. In this region one locates a set of tag SNPs from the HapMap data; these are SNPs that are very well correlated with all the other SNPs in the region. Using these, genotype imputation can be used to determine (impute) the other SNPs and thus the entire haplotype with high confidence. Next, one determines the genotype for these tag SNPs in several individuals, some with the disease and some without. By comparing the two groups, one determines the likely locations and haplotypes that are involved in the disease.

== Samples used ==
Haplotypes are generally shared between populations, but their frequency can differ widely. Four populations were selected for inclusion in the HapMap: 30 adult-and-both-parents Yoruba trios from Ibadan, Nigeria (YRI), 30 trios of Utah residents of northern and western European ancestry (CEU), 44 unrelated Japanese individuals from Tokyo, Japan (JPT) and 45 unrelated Han Chinese individuals from Beijing, China (CHB). Although the haplotypes revealed from these populations should be useful for studying many other populations, parallel studies are currently examining the usefulness of including additional populations in the project.
All samples were collected through a community engagement process with appropriate informed consent. The community engagement process was designed to identify and attempt to respond to culturally specific concerns and give participating communities input into the informed consent and sample collection processes.
In phase III, 11 global ancestry groups have been assembled: ASW (African ancestry in Southwest USA); CEU (Utah residents with Northern and Western European ancestry from the CEPH collection); CHB (Han Chinese in Beijing, China); CHD (Chinese in Metropolitan Denver, Colorado); GIH (Gujarati Indians in Houston, Texas); JPT (Japanese in Tokyo, Japan); LWK (Luhya in Webuye, Kenya); MEX (Mexican ancestry in Los Angeles, California); MKK (Maasai in Kinyawa, Kenya); TSI (Tuscans in Italy); YRI (Yoruba in Ibadan, Nigeria).

Three combined panels have also been created, which allow better identification of SNPs in groups outside the nine homogenous samples: CEU+TSI (Combined panel of Utah residents with Northern and Western European ancestry from the CEPH collection and Tuscans in Italy); JPT+CHB (Combined panel of Japanese in Tokyo, Japan and Han Chinese in Beijing, China) and JPT+CHB+CHD (Combined panel of Japanese in Tokyo, Japan, Han Chinese in Beijing, China and Chinese in Metropolitan Denver, Colorado). CEU+TSI, for instance, is a better model of UK British individuals than is CEU alone.