1000 Genomes Project launched

A very exciting announcement:

An international research consortium today announced the 1000 Genomes Project, an ambitious effort that will involve sequencing the genomes of at least a thousand people from around the world to create the most detailed and medically useful picture to date of human genetic variation. The project will receive major support from the Wellcome Trust Sanger Institute in Hinxton, England, the Beijing Genomics Institute, Shenzhen (BGI Shenzhen) in China and the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH).

They won't be sequencing 1,000 complete genomes immediately. Instead, the project will first move through a "pilot phase" in three parts:

1. Complete genome sequencing for six individuals (two families, each of two parents and a child) at very high coverage;
2. Complete genome sequencing of 180 people at much lower coverage; and
3. Finally, the sequencing of the protein-coding portions of 1,000 genes in 1,000 people.

That's still a massive amount of sequencing work:

At 6 trillion DNA bases, the 1000 Genomes Project will generate 60-fold more sequence data over its three-year course than have been deposited into public DNA databases over the past 25 years,” said Gil McVean, Ph.D., of the University of Oxford in England, one of the co-chairs of the consortium’s analysis group. “In fact, when up and running at full speed, this project will generate more sequence in two days than was added to public databases for all of the past year.”

This project will immediately add significantly to our understanding of human genetic variation, by increasing the detection of less common genetic variants only present in a small proportion of people. It will also help to refine sequencing techniques, bringing affordable personal genome sequences closer to reality. And importantly, all of the information generated by the project will be freely available online.

So who are they sequencing? Don't bother volunteering your own DNA - the project will be using the same anonymous DNA samples that are being used for the HapMap project (which looked at millions of common variations throughout their genome, but didn't sequence their DNA). That's great for two reasons: firstly, it will allow us to determine exactly how much genetic variation is captured by the genotyping approach used by the HapMap project; and secondly, we will be getting a picture of gene sequence diversity from populations around the world:

Among the populations whose DNA will be sequenced in the 1000 Genomes Project are: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States.

Exactly how the project will proceed after the pilot phase is still unclear (that's the point of the pilot phase!), but in an email to Nature writer Erika Check, NHGRI project director Lisa Brooks says:

The exact final project design will depend on the data from the 3 pilots...but we expect that in the full project about 1000 samples will be lightly (2X) sequenced across the entire genome, and these 1000 samples plus possibly additional samples would be sequenced more in the gene regions.

I really can't emphasise enough how much this project will alter the field of human genetics - like the Human Genome Project itself, and the HapMap project after that, this project will have truly profound implications for research into human variation and disease.


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