International HapMap Project

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The aim of the International HapMap Project is to map the haplotypes of the human genome . This HapMap is intended to describe the patterns of genetic variation in humans.

The project is a collaboration between academic researchers, non-commercial biomedical research groups and companies in Japan , the UK , Canada , China , Nigeria and the USA .

It is believed that the HapMap is a key component in the identification of genes, especially those that affect human health or the response to environmental stimuli and drugs. The results of the project will be made available to researchers worldwide.

The International HapMap Project officially began with a conference on March 27-29. October 2002 and was planned for a period of three years. It consists of two phases; Phase I results were published on October 27, 2005. Completion of the work will enable a wide variety of work, for example the Japanese working groups will examine 300,000 people to identify the haplotypes for 47 diseases. The British working groups, on the other hand, want to try genotyping patients with diabetes mellitus , bipolar disorder , rheumatoid arthritis , heart disease and other common diseases.

Importance of studying genetic variation

Most common diseases such as diabetes, cancer , strokes , depression and asthma are influenced by a large number of genes and environmental factors. Although people differ from each other by only about 0.1% of their DNA , this variation affects the risk of illness and the effectiveness of drugs. Exploring this variation therefore offers a way to understand the complex causes of human disease.

To do this, researchers compare a group of sick people with a group of non-sick people. Those chromosome regions in which the groups differ in the haplotype frequency could contain genes that influence the disease. Theoretically, researchers could genotype the entire genetic deviations of one base pair each (the so-called single nucleotide polymorphisms , SNP). However, given the current state of the art, these methods are too costly. The HapMap aims to identify the much smaller number of special marker SNPs with which a large part of the genetic variation patterns can be extracted.

Examined peoples

Most common haplotypes occur in all human peoples, but not with the same frequency. For this reason it is necessary to collect data from several groups to identify the marking SNPs. Pilot projects found a sufficient spread of the haplotype frequencies in samples from Nigeria ( Yoruba ), Japan, China and the United States to justify a restriction of the HapMap tests to these population groups. A parallel project examines the haplotypes of other colonies in order to assess the usefulness of a more detailed investigation for the HapMap.

The DNA samples for the HapMap come from a total of 270 people: 30 pairs of parents with adult children from the Yoruba in Ibadan (Nigeria) and from the USA, as well as 45 unrelated people each from Tokyo (Japan) and Beijing (China). With this selection it should be possible to identify all haplotypes that occur with at least 5% frequency.

Ethical issues

The project raises a number of ethical questions. However, the samples are collected in such a way that a geographical assignment is possible, but the donor himself cannot be identified. In this way, the haplotype frequency of individual colonies can also be recorded and compared between them. This creates the risk of stigmatization or discrimination if a particular cluster of disease-promoting haplotypes can be assigned to a specific ethnic origin.

Scientific strategy

To develop the HapMap, at least one million SNPs from the human genome are genotyped. At the beginning of the project there were around 2.8 million SNPs in the public database dbSNP . However, many chromosome areas had only a few SNPs, some of which occurred too rarely to be really meaningful. Another 2.8 million were identified by September 2003.

Genotyping is carried out through ten centers in Canada, China, Japan, Great Britain and the USA. Each center examines certain chromosomes. Five different genotyping techniques are used for this purpose. The initial HapMap is intended to provide a map of 600,000 SNPs evenly distributed over the genome, which corresponds to a density of about one SNP per 5,000 base pairs. Other SNPs are typed to define the haplotypes. The quality of the typing is guaranteed by mutual checking of identical samples.

Access to the data and copyright

The research results are made available to the scientific public in the public domain .

The new SNPs, samples for genotyping and the frequency of SNP alleles , genotypes and haplotypes will be published shortly after identification. As soon as the SNPs have been typed sufficiently to define associated regions, the haplotypes, genotypes and marker SNPs they comprise will be made available to the public without restrictions. Until this point in time, the individual genotype data is available under a minimal data protection guideline, which mainly ensures controlled disclosure and non-restriction of access for others.

Suspension of the homepage and follow-up project

The official homepage of the HapMap project was maintained by the National Center for Biotechnology Information (NCBI) of the USA. The institute stopped maintaining the data in June 2016, as the website and the data have been accessed less and less since 2011. NCBI refers instead to the 1000 Genome Project , which can be viewed as the successor.

Web links

Individual evidence

  1. ↑ "NCBI retiring HapMap resource" . Retrieved on February 23, 2018.
  2. ↑ Buchanan CC, Torstenson ES, Bush WS, Ritchie MD .: "A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data." In: "J Am Med Inform Assoc.", March-April 2012, Edition 19, No. 2, pp. 289-294, doi: 10.1136 / amiajnl-2011-000652 .