Mapping A Road To Understanding Human Health
The quest to track down genes involved in health and disease and our response to treatments is a long and difficult challenge. Today (18th December 2003), in the journal Nature, the International HapMap Consortium, to which The Wellcome Trust is a major contributor, describes important new tools it will produce to enhance our use of the human genome sequence and to fast-track that quest.
Our individual predisposition to disease and our response to medicines are, in part, encoded within our DNA, in the differences (called single-nucleotide polymorphisms, or SNPs) scattered through our genetic sequence. However, we tend to share regions of SNPs with others, and these regions can be mapped onto the reference genome sequence, one-third of which was produced at the Wellcome Trust Sanger Institute.
Importantly, many regions can be ‘tagged’ by identifying SNPs that are characteristic of the region. The HapMap Project will define those all-important ‘tag’ SNPs in multiple populations and the regions of the genome where they are located.
As a result of the HapMap Project, researchers will not have to search through the 10,000,000 SNPs that occur in the human genome, but instead will be able to use the map developed by the Project to obtain as much information using a massively reduced number of SNPs, about 500,000.
“The Wellcome Trust’s funding strategy is about improvement of human health. The HapMap is a very important development following on from the Human Genome Project. It will help researchers to find genes contributing to some of our most important diseases, such as diabetes, heart disease and cancer. It will also help us to understand the variations between our individual responses to drug treatments.”
Dr Mark Walport Director of the Wellcome Trust
In order to maximize the likelihood of identifying most variation and to identify ‘tag’ SNPs that are broadly representative of all humans, the HapMap Project will use DNA samples from 270 individuals from populations of Yorubans in Nigeria, Japanese, Han Chinese and US residents with ancestry from northern and western Europe. Patterns of variation will be extracted from study of the SNPs present in each of these individuals. Those patterns will provide a basis on which to find the tag SNPs that most efficiently describe the patterns; these tag SNPs are the major resource of the Project.
In the UK, the Project is funded principally by the Wellcome Trust through The Wellcome Trust Sanger Institute near Cambridge and The Wellcome Trust Centre for Human Genetics in Oxford. In addition the Department of Statistics at the University of Oxford leads one of the analysis groups. In all, Trust-funded research will contribute towards 40% of the research effort.
“The HapMap will be applicable to many medical conditions that have a genetic component, especially our common diseases. It is vital that such a resource is readily available. It will be the index of human variation for many years to come.
“The groups contributing to this international Project will release the data and the resulting map of variation as a freely available public resource. In that way, we anticipate maximum medical benefit will accrue in the most rapid fashion.”
Dr David Bentley Head of Genetics at the Wellcome Trust Sanger Institute
The HapMap Project is an international collaboration involving researchers in Canada, China, Japan, Nigeria, UK and USA. The results generated will be applicable to all human populations, and will be valuable to researchers around the world.
The US$120M Project was officially announced in October 2002 and is expected to take three years to complete.
Since the announcement of the Project, samples have been obtained and substantial amounts of variation data have already been released. Preliminary analyses of these data support the validity and usefulness of the HapMap.
Today’s publication in Nature describes in detail the project’s scientific goals and methods.
More information
- A good analogy for the HapMap is to a bus timetable. People who regularly travel to work by bus will tend to catch the same bus each morning. So if we can identify a couple of people as being ‘tag passengers’ of that bus, then we can predict that their fellow travellers will also be on the same bus. The haplotype region is analogous to the bus: the tag SNPs to our chosen passengers, which provide information on the rest of the SNPs in that region. Of course, sometimes our tag passengers will travel on an earlier or later bus or not go to work and the prediction will not hold. But most often it will. SNPs in regions tend to be inherited together and thus ‘tag SNPs’ can in general predict most of the other variations present in those regions.
Scientifically, a haplotype map is a statistical prediction of which variations in DNA sequence tend to be inherited together. The basic data are catalogues of sequence variations (called SNPs, for single nucleotide polymorphisms) in individuals: the list of variations that one individual possesses is called a genotype. Collections of genotype data can be analysed to predict regions of the DNA sequence that tend to be inherited together; this Project will find those that are common in human populations. A catalogue of such regions is a haplotype map. Using the map and variation data, sets of SNPs can be identified that ‘tag’ any particular region – that are predictive for the other variations in that region. By using this markedly reduced set of tag SNPs, researchers need examine a smaller set of SNPs in the search for genes of medical importance.
- UK centres are at:
- The Wellcome Trust Sanger Institute
(Dr David Bentley: DNA sequence and genotyping); - The Wellcome Trust Centre for Human Genetics, Oxford
(Dr Lon Cardon: analysis) and - The University of Oxford Department of Statistics
(Professor Peter Donnelly: analysis).
- The Wellcome Trust Sanger Institute
- The official website for the HapMap Project is http://www.hapmap.org/
- The Project was announced officially on 27 October 2002: see release at http://genome.gov/10005336
- Participating groups and their contributions are listed at: http://www.hapmap.org/groups.html
The Wellcome Trust and Its Founder
The Wellcome Trust is the most diverse biomedical research charity in the world, spending about £450 million every year both in the UK and internationally to support and promote research that will improve the health of humans and animals. The Trust was established under the will of Sir Henry Wellcome, and is funded from a private endowment, which is managed with long-term stability and growth in mind.
