Haplotype team unveil goals
common variations of the human genome have given more details of
the rationale behind the effort, known as the HapMap project, in
the journal Nature (18 December).
As part of the effort, the team will obtain and identify genetic variations in DNA samples from 270 people in Nigeria, Japan, China and the US. They will analyse the DNA sequences to determine the most common patterns of genetic variations in populations. Once finished, the HapMap will provide a freely available catalogue of common patterns, or haplotypes.
"What we learn from the HapMap project will simplify and accelerate efforts to identify genes associated with common chronic diseases," commented Aravinda Chakravarti, professor and director of the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University in the US.
"This project is intense from a DNA analysis perspective, but it's going to make the next round of studies much easier to do," he said.
The power of haplotypes is that they offer a way of using the identity of a few key nucleotides in a given region of DNA to infer the rest of the sequence, which might be tens of thousands of nucleotides in length. So instead of having to sequence each person's genome, future studies could merely identify variants in key positions (and thus determine a person's haplotype) and extrapolate the entire sequence.
The Nature article describes the entire HapMap process, from working with communities to identify participants and collect samples to choosing which DNA variants to look for and how to analyse the data to create the actual map. 10 groups around the world will genotype the samples.
Ninety samples from the Yoruba people in Ibadan, Nigeria, will be analysed, along with 90 from people of Northern and Western European ancestry living in Utah. While the Nigerian and US samples will be from 30 "trios" - sets of parents and an adult child - 45 samples from Japanese and 45 from Han Chinese will be from unrelated people.
Chakravarti, who plans to use the data from the HapMap to determine the genetic underpinnings of heart disease, diabetes and psychiatric illness, received funds from the National Institutes of Health last year to participate in the international project as one of two computer analysis centres in the US.
