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SNP chips used to study cancer progression
By Bijal P. Trivedi

Genomic instability—losing pieces of chromosomes—is common during cancer progression. Now researchers are using a new type of DNA chip to study which regions are lost, and when. The expectation is that this knowledge will help them determine how various cancers progress and identify which genes accelerate the disease.

The new chip screens 600 Single Nucleotide Polymorphisms (SNPs) from all over the genome for loss of genetic material.

Researchers at the Fred Hutchinson Cancer Research Center in Seattle tested the SNP chip by comparing SNPs in normal cells, abnormal precancerous cells, and cancerous cells from patients with esophageal cancer or its precursor, Barrett's syndrome. The report appears in the September issue of Genome Research.

The SNPs serve as frequent genetic markers along the chromosome.

"Because we begin seeing patients at a pre-cancerous stage, we hope that we can identify which patterns of gene loss go on to cancer," says Patricia Galipeau, of Fred Hutchinson.

The results from the SNP chip were consistent with results from experiments using microsatellite genetic markers to search for DNA loss. The advantage of the chip over conventional genotyping methods is that it requires smaller DNA samples and is much faster.

A similar study using SNPs was undertaken by scientists at the Whitehead Institute for Biomedical Research in Cambridge and the Dana-Farber Cancer Institute in Boston to detect loss of DNA in small-cell lung carcinomas. Their report is published in the September issue of Nature Biotechnology.

Eventually, gene chips could be used to screen patients for risk of disease. Once more is known about the steps leading to particular cancers, the chips may also be used to predict the onset and prognosis of disease.

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Mei, R. et al. Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res 10, 1126-1137 (August 2000).
Lindblad-Toh, Kerstin. et al. Loss of heterozygosity analysis of small-cell lung carcinomas using single -nucleotide polymorphism arrays. Nat Biotechnol 18, 1001-1005 (September 2000).

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