SNP Consortium and International HapMap Project

The Wellcome Trust has supported two global partnerships that are characterising variation in the human genome: the SNP Consortium and the International HapMap Project. They are providing valuable research tools, particularly useful to scientists searching for genes predisposing to common complex diseases such as diabetes and asthma.

Humans are genetically very similar. The most common differences are changes in single letters of the DNA code - single nucleotide polymorphisms or SNPs ('snips'). SNPs occur about one every 1000 nucleotides.

Although many SNPs have no impact, some can alter our sensitivity to drugs or our susceptibility to diseases. It is therefore important to identify where SNPs occur and what their biological effects are.

Also, because they are distributed fairly evenly through the genome, they are excellent genetic markers - sequence 'landmarks' in the genome, used to create genetic maps.

SNP Consortium

The Wellcome Trust contributed £9 million to the SNP Consortium - a £30 million collaboration involving the Wellcome Trust, leading academic centres and 13 pharmaceutical and technological companies.

The Consortium identified and mapped 1.5 million SNPs, which have been made publicly available to researchers over the internet.

The SNP Consortium is a not-for-profit organisation based in the USA.

International HapMap Project

The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the UK and the USA. It aims to map the patterns of common SNP variation across the globe.

Whereas the SNP Consortium focused on individual SNPs, the HapMap Project is looking at combinations of SNPs that are inherited together, known as haplotypes.

As there are so many SNPs in the human genome, it would aid research if a subset (those characteristic of a particular haplotype) could be used in genetic analyses. The project might simplify the search for genes associated with diseases by as much as 20-fold.

However, although most SNPs are found in all human populations, the patterns of SNP variants differ around the world. By sampling DNA from several populations, the HapMap Project is creating a more detailed, global view of SNPs and their grouping into haplotypes.

Hence, as well as identifying SNPs that are always diagnostic of particular haplotypes, the project will also provide a much clearer picture of variation within the genome.

The resulting haplotype map will again be made freely available to researchers.

Collaborators on the International HapMap Project include researchers at the Wellcome Trust Sanger Institute and Professor Lon Cardon, a Wellcome Principal Research Fellow at the Wellcome Trust Centre for Human Genetics, University of Oxford.