1000 Genomes Project publishes comprehensive map of human genetic variation

The 1000 Genomes Project, an international public-private consortium, has published the most comprehensive map so far of human genetic variations, estimated to contain approximately 95 per cent of the genetic variation of any person on Earth.

The £76 million project was launched in 2008 with three pilot projects to develop, evaluate and compare strategies for producing a catalogue of genetic variations, is funded by a number of research foundations and national governments.

“The pilot studies of the 1000 Genomes Project laid a critical foundation for studying human genetic variation,” Richard Durbin from the UK’s Wellcome Trust Sanger Institute, co-Chair of the consortium. “These proof-of-principle studies are enabling consortium scientists to create a comprehensive, publicly available map of genetic variation that will ultimately collect the sequences of 2,500 people from multiple populations worldwide, underpinning future genetics research.”

Genetic variation between individuals can be as small as a single base being replaced - known as a single nucleotide polymorphism (SNP) - or as large as whole sections of a chromosome being duplicated or relocated to another place in the genome. Some of these variations are common in the population and some are rare.

The 1000 Genomes Project’s aim is to provide a comprehensive public resource that supports researchers aiming to study all types of genetic variation that might cause human disease.

“By making data from the Project freely available to the research community, it is already impacting research for both rare and common diseases," said David Altshuler, Deputy Director of the Broad Institute of Harvard and MIT, and a co-chair of the Project. “Biotech companies have developed genotyping products to test common variants for a role in disease. Every published study using next-generation sequencing to find rare disease mutations, and those in cancer, used Project data to filter out variants that might obscure their results.”

The Project has studied populations with European, west African and east Asian ancestry. Nine centres sequenced the whole genomes of 179 people and the protein-coding genes of 697 people. Each region was sequenced several times, so that more than 4.5 terabases (4.5 trillion base letters) of DNA sequence were collected.

The resulting map of human genetic variation includes about 15 million SNPs, 1 million short insertion/deletion changes, and more than 20,000 structural variations. Many of the genetic variants had previously been identified, but more than half are new. The Project's database contains more than 95 per cent of the currently measurable variants found in any individual, and continuing work will eventually identify more than 99 per cent of human variants.

With the completion of the pilot phase, the 1000 Genomes Project has moved into full-scale studies in which 2,500 samples from 27 populations will be studied over the next two years.