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Genome-wide survey provides support for building haplotype map

Most of the genetic variation in the human genome is organized into large, neat units called haplotype blocks that are remarkably similar across population groups and may prove powerful in tracking disease-causing genes in the population, researchers reported in the May 24 issue of Science.

In the first broad-based survey of its kind, scientists found that each block contains a set of single-letter genetic variations that are inherited together as a unit, with little genetic shuffling and only three to five common varieties observed in the human population. Surprisingly, the pattern of genetic variation observed in humans is much simpler in its architecture than that of a common fruit fly, which has long served as a model for human biology.

The findings, by scientists at the Whitehead Institute/MIT Center for Genome Research and Massachusetts General Hospital, add impetus for building a so-called haplotype map of the human genome. Such a HapMap is expected to make it easier, faster and cheaper to find variations in human genes that influence an individual's susceptibilities to common illnesses such as cancer and diabetes.

Scientists have long known that most human genetic variation is in the form of single-letter DNA differences between individuals called nucleotide polymorphisms, or SNPs. But until recently, the prospect of searching through the 10 million common SNPs in the human genome to find disease genes seemed a daunting task.

Last year, studies began to show that in certain regions of the chromosomes, SNPs were inherited in an orderly fashion--as a set, or haplotype block. Further, each block comes only in a few common patterns, indicating that the search for genes underlying common diseases would require testing only three to five different versions of a given region of a chromosome.

If this were the case for the entire genome, a haplotype map would make finding disease genes a more manageable task. Instead of searching through a giant haystack of 10 million common SNPs across the genome, scientists would be searching through bundles of 10,000 to 50,000 DNA letters each, with each bundle coming in fewer than five patterns.

But until now, scientists lacked definitive evidence that the entire genome was organized as haplotype blocks, and how these patterns might vary across different population groups.

"This study is the first to broadly sample the entire genome and to compare the haplotype patterns across population samples from Africa, Asia and Europe," said senior author David Altshuler, of the Whitehead Genome Center, Massachusetts General Hospital and Harvard Medical School.

Professor of Biology Eric Lander, founder and director of the Whitehead Institute/MIT Center for Genome Research, is a coauthor of the study.

A version of this article appeared in MIT Tech Talk on June 12, 2002.

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