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New analysis promises to speed application of human genome draft

A small team of scientists has dramatically improved "gene chip" technology, for the first time making it a practical method for rapidly determining the sequence of genetic building blocks. The advance, likely to speed the search for disease-related genetic changes, is reported in the November issue of the journal Genome Research.

The gene chips, or microarrays, are dotted with a microscopic grid of hundreds of thousands of tiny segments of DNA determined by the Human Genome Project. These segments, fixed in known spots on the chip, find their matches in a sample of DNA. The better the match, the more likely the known DNA sequence reflects the unknown sample sequence, explains the team from Johns Hopkins School of Medicine and a biotechnology company, Affymetrix, Inc.

A new analysis method lets the team identify and focus on the chips' more reliable information. "Until now, ways to analyze the chips were unable to distinguish highly accurate data from less reliable information," says lead author David Cutler, Ph.D., a research associate in the McKusick-Nathans Institute of Genetic Medicine at The Johns Hopkins University School of Medicine.

"We need the chips to be very accurate because variation in the human genome is relatively rare," adds Michael Zwick, Ph.D., John Wasmuth postdoctoral fellow in the McKusick-Nathans Institute of Genetic Medicine. "We've taken advantage of the fact that individual features, individual points, can be very reliable. Our analysis technique identifies them."

Previously, the only way to figure out the order of building blocks, or bases, in genetic material was to use machines known as DNA sequencers, which is still the only way to obtain the first genome of a species. Microarrays had been useful to study gene activity but not gene sequence, says Cutler.

"We took the most logical, straightforward approach we could to help us determine which of the microarray sequences to pay attention
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Contact: Joanna Downer
jdowner1@jhmi.edu
410-614-5105
Johns Hopkins Medical Institutions
14-Nov-2001


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