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SNP survey finds surprising similarity in humans worldwide
Edward R. Winstead


A new study shows that humans are even more genetically similar than previously thought. The evidence comes from one of the largest comparisons of DNA to date: Scientists surveyed single nucleotide polymorphisms, or SNPs, on human chromosome 21 for each of 20 ethnically diverse individuals. They found essentially the same patterns of SNPs on each chromosome, regardless of whether the donor was African, Asian, or Caucasian.

Detail of haplotype patterns for 20 independent globally diverse chromosomes. View larger

David R. Cox, of Perlegen Sciences in Santa Clara, California, and colleagues scanned 20 copies of chromosome 21 using high-density microarrays. In all, they found nearly 36,000 SNPs in the samples. Using the scan data, they identified groups of related SNPs, or haplotypes. Most of these structures turned up on all the chromosomes. Only eight percent of the haplotypes were specific to a particular ethnic group.

"It is remarkable that such a large fraction of globally diverse chromosomes are represented by such limited haplotype diversity," the researchers write in Science. Three common haplotypes accounted for 80 percent of the genetic diversity among the samples. This means that, for any region of the chromosome, the most common haplotype was found in 50 percent of individuals, the second most common in 25 percent of individuals, and the third most common in 12.5 percent of individuals.

The discovery that chromosome 21 is less structurally diverse than expected is potentially good news. It may make it easier for researchers to identify disease genes in diverse populations. Knowing the arrangement of common SNPs throughout the genome is critical to the success of genetic association studies. These studies identify genetic mutations related to disease by comparing the DNA of healthy individuals to that of individuals with a disease.

The new study "marks a dramatic shift in strategic thinking," writes Pui-Yan Kwok, of Washington University School of Medicine in St. Louis, in an accompanying commentary. Traditionally, researchers have looked at a limited set of DNA markers in genetic association studies. "Now," he writes, "one can aspire to analyze all of the unique DNA sequences in the genome simultaneously."

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Kwok, P.-Y. Genetic association by whole-genome analysis? Science 294, 1669-1670 (November 23, 2001).
Patil, N. et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719-1723 (November 23, 2001).

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