Scientific Strategy
For the Phase I, one common SNP was genotyped every 5,000 bases. Overall, more than one million SNPs were genotyped. The genotyping was carried out by 10 centres using five different genotyping technologies. Genotyping quality was assessed by using duplicate or related samples and by having periodic quality checks where centres had to genotype common sets of SNPs.
The Canadian team was led by Thomas J. Hudson at McGill University in Montreal and focused on chromosomes 2 and 4p. The Chinese team was led by Huanming Yang with centres in Beijing, Shanghai and Hong Kong and focused on chromosomes 3, 8p and 21. The Japanese team was led by Yusuke Nakamura at the University of Tokyo and focused on chromosomes 5, 11, 14, 15, 16, 17 and 19. The British team was led by David R. Bentley at the Sanger Institute and focused on chromosomes 1, 6, 10, 13 and 20. There were four United States' genotyping centres: a team led by Mark Chee and Arnold Oliphant at Illumina Inc. in San Diego (studying chromosomes 8q, 9, 18q, 22 and X), a team led by David Altshuler at the Broad Institute in Cambridge, USA (chromosomes 4q, 7q, 18p, Y and mitochondrion), a team led by Richard A. Gibbs at the Baylor College of Medicine in Houston (chromosome 12), and a team led by Pui-Yan Kwok at the University of California, San Francisco (chromosome 7p).
To obtain enough SNPs to create the Map, the Consortium had to fund a large re-sequencing project to discover millions of additional SNPs. These were submitted to the public dbSNP database. As a result, by August 2006, the database included more than ten million SNPs, and more than 40% of them were known to be polymorphic. By comparison, at the start of the project, fewer than 3 million SNPs were identified, and no more than 10% of them were known to be polymorphic.
During Phase II, more than two million additional SNPs have been genotyped throughout the genome by the company Perlegen Sciences and 500,000 by the company Affymetrix.
Read more about this topic: International HapMap Project
Famous quotes containing the words scientific and/or strategy:
“What happened at Hiroshima was not only that a scientific breakthrough ... had occurred and that a great part of the population of a city had been burned to death, but that the problem of the relation of the triumphs of modern science to the human purposes of man had been explicitly defined.”
—Archibald MacLeish (1892–1982)
“Our strategy in going after this army is very simple. First we are going to cut it off, and then we are going to kill it.”
—Colin Powell (b. 1937)