Perlegen promotes improved HapMap

With considerable help from Affymetrix offshoot Perlegen Sciences, the International HapMap Consortium has announced it will build a more detailed map of human genomic variation than originally anticipated.

The consortium has already reached its stated goal of charting 1 million single nucleotide markers of human variation, based on analysis of 270 DNA samples from a spectrum of human populations, six months ahead of schedule. Now, with an additional US$3.3 million in public/private funding, the consortium aims to build a 'Phase II' map that is five times denser, incorporating a further 4.6 million single nucleotide polymorphisms (SNPs) from public databases.

The resulting map density will be increased from one marker every 3000 bases to one every 600 bases. The additional $3.3 million funding comes from sources including the Wellcome Trust; Genome Canada/Genome Quebec, Bristol-Myers Squibb, and Pfizer.

"This will help us create a far more powerful HapMap than we ever imagined," said Francis Collins, director of the National Human Genome Research Institute. "The payoff will be a better understanding of the genetic risk factors underlying a wide range of diseases and conditions."

"We are excited by the opportunity to apply our technology to all publicly available SNPs," said Perlegen's VP of genomics, Kelly Frazer. "This effort is so important that Perlegen is willing to contribute some of its own resources to make this possible."

The first phase of the HapMap Project has allowed scientists to make important analyses of the human genome that were not possible with just the human DNA sequence, and the International HapMap Consortium plans to publish its comprehensive analysis of this data later this year. Researchers around the globe can quickly access the HapMap data through free public databases, such as the HapMap Data Coordination Centre, the NIH-funded National Centre for Biotechnology Information's dbSNP, and the JSNP Database in Japan.