---
title: "International HapMap Project"
chunk: 2/2
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"
---

== Scientific strategy ==
It was expensive in the 1990s to sequence patients' whole genomes. So the National Institutes of Health embraced the idea for a "shortcut", which was to look just at sites on the genome where many people have a variant DNA unit. The theory behind the shortcut was that, since the major diseases are common, so too would be the genetic variants that caused them. Natural selection keeps the human genome free of variants that damage health before children are grown, the theory held, but fails against variants that strike later in life, allowing them to become quite common (In 2002 the National Institutes of Health started a $138 million project called the HapMap to catalog the common variants in European, East Asian and African genomes).
For the Phase I, one common SNP was genotyped every 5,000 bases. Overall, more than one million SNPs were genotyped. The genotyping was carried out by 10 centres using five different genotyping technologies. Genotyping quality was assessed by using duplicate or related samples and by having periodic quality checks where centres had to genotype common sets of SNPs.
The Canadian team was led by Thomas J. Hudson at McGill University in Montreal and focused on chromosomes 2 and 4p. The Chinese team was led by Huanming Yang in Beijing and Shanghai, and Lap-Chee Tsui in Hong Kong and focused on chromosomes 3, 8p and 21. The Japanese team was led by Yusuke Nakamura at the University of Tokyo and focused on chromosomes 5, 11, 14, 15, 16, 17 and 19. The British team was led by David R. Bentley at the Sanger Institute and focused on chromosomes 1, 6, 10, 13 and 20. There were four United States' genotyping centres: a team led by Mark Chee and Arnold Oliphant at Illumina Inc. in San Diego (studying chromosomes 8q, 9, 18q, 22 and X), a team led by David Altshuler and Mark Daly at the Broad Institute in Cambridge, USA (chromosomes 4q, 7q, 18p, Y and mitochondrion), a team led by Richard Gibbs at the Baylor College of Medicine in Houston (chromosome 12), and a team led by Pui-Yan Kwok at the University of California, San Francisco (chromosome 7p).
To obtain enough SNPs to create the Map, the Consortium funded a large re-sequencing project to discover millions of additional SNPs. These were submitted to the public dbSNP database. As a result, by August 2006, the database included more than ten million SNPs, and more than 40% of them were known to be polymorphic. By comparison, at the start of the project, fewer than 3 million SNPs were identified, and no more than 10% of them were known to be polymorphic.
During Phase II, more than two million additional SNPs were genotyped throughout the genome by David R. Cox, Kelly A. Frazer and others at Perlegen Sciences and 500,000 by the company Affymetrix.

== Data access ==
All of the data generated by the project, including SNP frequencies, genotypes and haplotypes, were placed in the public domain and are available for download. The website was retired in 2016, however the original data is still available for download. The website used to contain a genome browser which allows to find SNPs in any region of interest, their allele frequencies and their association to nearby SNPs. A tool that can determine tag SNPs for a given region of interest was also provided. These data can also be directly accessed from the widely used Haploview program.

== Publications ==
International HapMap Consortium (2003). "The International HapMap Project" (PDF). Nature. 426 (6968): 789–796. Bibcode:2003Natur.426..789G. doi:10.1038/nature02168. hdl:2027.42/62838. PMID 14685227. S2CID 4387110.
International HapMap Consortium (2004). "Integrating ethics and science in the International HapMap Project". Nature Reviews Genetics. 5 (6): 467–475. doi:10.1038/nrg1351. PMC 2271136. PMID 15153999.
International HapMap Consortium (2005). "A haplotype map of the human genome". Nature. 437 (7063): 1299–1320. Bibcode:2005Natur.437.1299T. doi:10.1038/nature04226. PMC 1880871. PMID 16255080.
International HapMap Consortium (2007). "A second generation human haplotype map of over 3.1 million SNPs". Nature. 449 (7164): 851–861. Bibcode:2007Natur.449..851F. doi:10.1038/nature06258. PMC 2689609. PMID 17943122.
International HapMap 3 Consortium (2010). "Integrating common and rare genetic variation in diverse human populations". Nature. 467 (7311): 52–58. Bibcode:2010Natur.467...52T. doi:10.1038/nature09298. PMC 3173859. PMID 20811451.{{cite journal}}:  CS1 maint: numeric names: authors list (link)
Deloukas P, Bentley D (2004). "The HapMap project and its application to genetic studies of drug response". The Pharmacogenomics Journal. 4 (2): 88–90. doi:10.1038/sj.tpj.6500226. PMID 14676823.
Thorisson GA, Smith AV, Krishnan L, Stein LD (2005). "The International HapMap Project Web site". Genome Research. 15 (11): 1592–1593. doi:10.1101/gr.4413105. PMC 1310647. PMID 16251469.
Terwilliger JD, Hiekkalinna T (2006). "An utter refutation of the 'Fundamental Theorem of the HapMap'". European Journal of Human Genetics. 14 (4): 426–437. doi:10.1038/sj.ejhg.5201583. PMID 16479260.
Secko, David (2005). "Phase I of the HapMap Complete" Archived 2011-05-14 at the Wayback Machine. The Scientist

== See also ==
Genealogical DNA test
The 1000 Genomes Project
Population groups in biomedicine
Human Variome Project
Human genetic variation

== References ==

== External links ==
International HapMap Project (HapMap Homepage) Archived 2014-04-16 at the Wayback Machine
National Human Genome Research Institute (NHGRI) HapMap Page
Browsing HapMap Data Using the Genome Browser
The Mexican Genome Diversity Project