WASHINGTON - An international group of scientists said it will spend $100 million in the next three years to develop a "haplotype map," which is expected to make it easier, faster and even cheaper to identify genes that predispose people to diseases.
The HapMap Project, led by the National Institutes of Health, kicked off here Tuesday when a consortium of scientists and researchers met with the media to announce an ambitious plan to create the next-generation map of the human genome.
In collaboration with U.S. researchers, representatives from the UK, Japan, Canada and China will work on the project that involves collecting blood samples from 200 to 400 people from four large, geographically distinct populations. They are the Yorubas in Nigeria, the Japanese, the Han Chinese and U.S. residents with ancestry from Northern and Western Europe. The selection was based on the theory that all humans descended from a common set of ancestors who lived in Africa 100,000 years ago.
"This work will produce a resource that has no medical information attached to it. It simply lays out the landscape of how variations are organized in the human genome without any information of what that variation means medically," Francis Collins, director of the NIH's National Human Genome Research Institute, told reporters. "It will be up to the user of this resource to design carefully controlled studies and then apply this to try and understand the heredity factors."
He said the HapMap will serve as a tool to better understand the contribution that genes make in conditions such as cancer, diabetes and mental illness. Collins, a leader in the private-public partnership to sequence the human genome, said in that project researchers determined the order of the 3 billion A's, T's, C's and G's that make up the genome.
Scientists believe the human genome is divided into haplotypes (ancestral segments of chromosomes), with the entire human population containing only three to five common varieties at each location in the genome, according to a press statement released by the Whitehead Institute in Cambridge, Mass., a participant in the HapMap Project. Most genetic differences are in single-letter variations, referred to as single nucleotide polymorphisms, or SNPs.
In certain regions of the chromosomes, SNPs were inherited in an orderly set or "haplotype" block with little genetic shuffling.
Since each block comes only in a few common patterns, the search for genes underlying common diseases can be simplified to test the three to five different versions of a given region of a chromosome, the Whitehead Institute said.
According to the NIH, for any given disease, researchers could use the HapMap tag SNPs to compare the haplotype patterns of a group of people known to have the disease to a group of people without the disease. If a study finds a certain haplotype more often in those with the disease, researchers could zero in on that genomic region in their search for the specific genetic variant.
Collins said when the work it complete, it will be placed in the public domain. "Some would argue that it would be better if one nation did the work, but we don't think that would be right."
U.S. researchers are poised to analyze about 31 percent of the genome using NIH funding. Organizations participating include the Whitehead Institute, Baylor College of Medicine in Houston, the University of California at San Francisco and Johns Hopkins School of Medicine in Baltimore.
Illumina Corp., of San Diego, in conjunction with the Wellcome Trust Sanger Institute and the Wellcome Trust Centre for Human Genetics at Oxford University, said in a prepared statement that it expects to map the common haplotypes in 15 percent of the human genome as part of the project.
The Baylor research will be conducted using technology developed by ParAllele BioScience, a year-old company located in South San Francisco. The technology, known as Molecular Inversion Probe, will allow SNPs to be screened in a single laboratory reaction with a single molecular probe per marker.
Riken and the University of Tokyo, funded by the Japanese Ministry of Education, Culture, Sports, Science and Technology, will analyze 25 percent of the genome. The Wellcome Trust Sanger Institute, funded by the Wellcome Trust, of London, will analyze 24 percent; McGill University, funded by Genome Canada, of Ottawa, and Genome Quebec, of Montreal, will analyze 10 percent; and Beijing Genomics Institute and the China HapMap Consortium, funded by the Chinese Ministry of Science and Technology, the Chinese Academy of Sciences and the Natural Science Foundation of China, will analyze 10 percent.
The SNP Consortium, of Deerfield, Ill., will coordinate private funding.