NEW YORK, Oct. 29 - The US National Institutes of Health today officially announced a $100 million, 3-year international effort to build a complete haplotype map of the human genome.
Hap-map backers, most prominently the National Human Genome Research Institute's Francis Collins, say this effort to identify common patterns of SNPs will catapult research in complex genetic diseases and drug responses into a new and much more sophisticated era. By eliminating the need to scan whole segments of the genome for individual genetic variations, the map will provide a shortcut in the process of linking SNPs to disease.
But the hap map also has critics who charge that this large-scale project is a poor use of resources. Geneticists have not been able to prove that complex diseases are caused by common mutations, they point out, so the hap map may prove to be only marginally useful in clinical work. Some who are more hostile to the project assert the hap map is merely a cynical effort to keep federal research dollars flowing into the country's big sequencing centers.
Undoubtedly, it's an effort on a grand scale. The Whitehead Institute's David Altschuler, who was one of the first to hypothesize that SNPs could be found in recognizable patterns, has won one of the NHGRI's hap-map grants to define hap blocks over 24 percent of the human genome. The institute will develop 370,000 SNP-genotyping assays and perform roughly 71 million MALDI-TOF genotypes, according to the grant abstract.
NHGRI also is funding Baylor to work with ParAllele Biosciences to map one-third of the genome with a multiplexed method capable of assaying up to 1,000 SNPs at one time; and Illumina has won an NHGRI hap grant to apply its bead-based array platform to large-scale genotyping. The company plans to generate about 74 million genotypes and develop assays for about 400,000 SNPs.
Human blood samples for the hap map will come from roughly 200 to 400 volunteers in Nigeria, Japan, China, and the United States. The Coriell Institute for Medical Research in Camden, NJ, will process and store the samples, which will be analyzed by the consortium's 15 members at universities, institutes, and private companies in the UK, Canada, the US, and China. All data will be public.
The projects' public funders include the Wellcome Trust; Genome Canada; Genome Quebec; the Chinese Academy of Sciences, in Beijing; the Japanese science ministry; and the US National Institutes of Health, which has already pledged $40 million. The SNP Consortium will coordinate private funding.
Click here for more information about the hap map.