'HapMap' scientists provide detailed plans

December 18, 2003

The international team of scientists working to determine the most common variations of the human genome report the details of their plans, known as the "HapMap" project, in the Dec. 18 issue of Nature.

The team will obtain and identify genetic variations in DNA samples from 270 people in Nigeria, Japan, China and the United States. Scientists at Johns Hopkins are one of two U.S. groups who will analyze the DNA sequences to determine the most common patterns of genetic variations in populations. Once finished, the HapMap will provide a freely available catalog 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," says Aravinda Chakravarti, Ph.D., professor and director of the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins. "This project is intense from a DNA analysis perspective, but it's going to make the next round of studies much easier to do."

The power of haplotypes is that they offer a way of using the identity of a few key genetic building blocks in a given region of DNA to infer the rest of the sequence -- possibly tens of thousands of building blocks long. 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 instantly know nearly the entire sequence, the scientists say.

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 analyze the data to create the actual map. Ten groups around the world will genotype the samples, determining which of the four "letters" of DNA's language are at given positions along the genome.

Ninety samples from the Yoruba people in Ibadan, Nigeria, will be analyzed, along with 90 from people of Northern and Western European ancestry living in Utah. While the Nigerian and U.S. samples will be from 30 "trios" -- sets of parents and an adult child -- 45 samples from Japanese and 45 samples from Han Chinese will be from unrelated people.

Chakravarti, who plans to use the freely available products of the HapMap to determine the genetic underpinnings of heart disease, diabetes and psychiatric illness, received funds from the NIH last year to participate in the international project as one of two computer analysis centers in the United States. The other analysis group is at the Center for Genome Research at the Whitehead Institute in Cambridge, Mass.

"Analyzing the sequence information from all these samples is going to require new mathematical and computing methods," says Chakravarti. "So while the sequences and genotypes are being figured out, we are hard at work developing new ways to analyze the data so we can be confident in the map we end up creating. Anything less isn't enough."

Chakravarti, David Cutler, Carl Kashuk and Peter Chen of the McKusick-Nathans Institute are co-authors of the report, along with the many other members of the International HapMap Consortium. Chakravarti and Hopkins geneticist David Valle were members of the initial National Institutes of Health planning group on Populations and Ethical, Legal and Social Issues. The Johns Hopkins HapMap effort is funded by the National Institutes of Health.
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