Editing International HapMap Project (section)

== Scientific strategy ==
It was expensive in the 1990s to sequence patients’ whole genomes. So the [[National Institutes of Health]] embraced the idea for a "shortcut", which was to look just at sites on the genome where many people have a variant DNA unit. The theory behind the shortcut was that, since the major diseases are common, so too would be the genetic variants that caused them. [[Natural selection]] keeps the human genome free of variants that damage health before children are grown, the theory held, but fails against variants that strike later in life, allowing them to become quite common (In 2002 the [[National Institutes of Health]] started a $138 million project called the [[HapMap]] to catalog the common variants in European, East Asian and African genomes).<ref name=naid>{{cite journal | vauthors = Naidoo N, Pawitan Y, Soong R, Cooper DN, Ku CS | title = Human genetics and genomics a decade after the release of the draft sequence of the human genome | journal = Human Genomics | volume = 5 | issue = 6 | pages = 577–622 | date = October 2011 | pmid = 22155605 | pmc = 3525251 | doi = 10.1186/1479-7364-5-6-577 | doi-access = free }}</ref>

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]] in [[Beijing]] and [[Shanghai]], and [[Lap-Chee Tsui]] in [[Hong Kong]] and focused on chromosomes 3, 8p and 21. The Japanese team was led by [[Yusuke Nakamura (geneticist)|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 (company)|Illumina Inc.]] in [[San Diego]] (studying chromosomes 8q, 9, 18q, 22 and X), a team led by [[David Altshuler (physician)|David Altshuler]] and [[Mark Daly (scientist)|Mark Daly]] at the [[Broad Institute]] in [[Cambridge, Massachusetts|Cambridge, USA]] (chromosomes 4q, 7q, 18p, Y and [[mitochondrion]]), a team led by [[Richard Gibbs (biologist)|Richard 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 funded 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 [[Polymorphism (biology)#Genetic polymorphism|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 were genotyped throughout the genome by David R. Cox, [[Kelly A. Frazer]] and others at [[Perlegen Sciences]] and 500,000 by the company [[Affymetrix]].