International HapMap Project
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| International HapMap Project | |
|---|---|
| Name | International HapMap Project |
| Formed | 2002 |
| Dissolved | 2009 |
| Headquarters | Hinxton, Cambridge |
| Participants | Wellcome Trust Sanger Institute; National Institutes of Health; RIKEN; Centre National de la Recherche Scientifique; University of Tokyo; Beijing Genomics Institute; National Human Genome Research Institute; Perlegen Sciences; Coriell Institute for Medical Research |
International HapMap Project The International HapMap Project was a multinational collaboration to create a haplotype map of the human genome, designed to accelerate Human Genome Project follow-on studies, facilitate Genome-wide association studys, and enable pharmaceutical and clinical research into complex traits. Launched by consortia including the Wellcome Trust, the National Institutes of Health, and the Japan Science and Technology Agency, the initiative brought together sequencing centers and population cohorts from sites such as the Sanger Institute, the Beijing Genomics Institute, and the Perlegen Sciences facility. The project produced publicly accessible resources leveraged by investigators in projects like the 1000 Genomes Project and the International Cancer Genome Consortium.
Background and objectives
The project emerged after milestones achieved by the Human Genome Project and early work at the Sanger Centre and Celera Genomics, with objectives articulated by agencies including the Wellcome Trust and the National Human Genome Research Institute. Its primary goal was to catalogue common patterns of human genetic variation—specifically single-nucleotide polymorphisms—across diverse populations sampled from locations such as Yoruba people, Han Chinese, and Japanese cohorts, and the European (CEU) Utah population collection. Organizers aimed to provide a resource for mapping susceptibility loci discovered in studies led by principal investigators in academia and industry, including investigators affiliated with the Broad Institute and the University of Oxford.
Methods and data collection
Sampling employed cell lines and DNA panels derived from repositories such as the Coriell Institute for Medical Research and population studies coordinated with institutions like the Centre for Human Genetics (Belgium). Genotyping used high-throughput platforms developed by groups at Perlegen Sciences, the Sanger Institute, and the Wellcome Trust Sanger Institute, integrating technologies influenced by platforms from Applied Biosystems and Illumina. Quality control pipelines built on algorithms from research groups at the National Center for Biotechnology Information and the European Bioinformatics Institute assessed linkage disequilibrium and recombination hotspots, informed by theoretical work from population geneticists affiliated with Stanford University, Harvard University, and the Massachusetts Institute of Technology. Data sharing policies reflected norms advanced by the Bermuda Principles proponents and stewardship models practiced by the European Molecular Biology Laboratory and the National Institutes of Health.
Findings and results
The HapMap catalogs quantified patterns of linkage disequilibrium and identified common haplotypes spanning megabase regions, enabling tagSNP strategies used in association scans by investigators at the Wellcome Trust Case Control Consortium and multiple academic centers such as the University of Cambridge and University of Tokyo. Results showed population-specific allele frequencies highlighted in analyses by teams from the Yale School of Public Health, the University of Chicago, and the Karolinska Institutet. The project characterized recombination hotspots and implicated the role of proteins later studied by groups at the Cold Spring Harbor Laboratory and the Max Planck Institute for Evolutionary Anthropology, and supported mapping efforts that informed consortia such as the Global Alliance for Genomics and Health.
Impact on genetics and medicine
HapMap resources enabled the rapid expansion of Genome-wide association studys that implicated loci associated with diseases investigated by researchers at the National Cancer Institute, the Centers for Disease Control and Prevention, and the Mayo Clinic. Pharmaceutical research teams at companies influenced by collaborations with the Wellcome Trust and the Bill & Melinda Gates Foundation used HapMap tagging strategies in target validation pipelines and pharmacogenomics projects run at the US Food and Drug Administration and academic medical centers including Johns Hopkins University and Stanford University School of Medicine. The database underpinned translational work in complex traits pursued by the International HapMap Consortium investigators and informed clinical genomics initiatives like those at the Broad Institute and the Scripps Research Institute.
Criticism and ethical considerations
Scholars and advocacy groups including those connected with the Nuffield Council on Bioethics, the Presidential Commission for the Study of Bioethical Issues, and community representatives from indigenous and population cohorts raised concerns about consent models, benefit sharing, and the adequacy of privacy protections practiced at repositories such as the Coriell Institute. Debates referenced precedents from controversies involving the Human Genome Diversity Project and regulatory responses by institutions including the European Commission and national ethics committees at the Ministry of Health, Labour and Welfare (Japan). Critics also highlighted limitations in representing global diversity, prompting engagement from research networks like the H3Africa Consortium and funders such as the Wellcome Trust and the National Institutes of Health.
Successor projects and legacy
HapMap catalyzed successor efforts including the 1000 Genomes Project, the H3Africa Project, and population sequencing initiatives at the Chinese Academy of Sciences and the Genome Canada program. Its technical and policy precedents influenced data-sharing frameworks used by the Global Alliance for Genomics and Health and infrastructure at the European Genome-phenome Archive and the Database of Genotypes and Phenotypes. Legacy outputs—public genotype panels, tagSNP catalogs, and analytical methods—remain cited in work by investigators at the Broad Institute, the University of Washington, the Wellcome Trust Sanger Institute, and clinical translation programs at the National Institutes of Health Clinical Center.