Dean A. Haycock
Special To BioWorld Today
Affymetrix Inc.'s GeneChip technology may have been DreamChiptechnology six years ago. But with publication of two papers inNature Genetics and one in Nature Biotechnology, the GeneChip ison its way to becoming a widespread, simple and practical methodfor analyzing genes and their expression.
The reports show how DNA chip technology can be used to detectdisease genes and other mutations, to identify natural gene variationsin populations and to track the expression of genes at different timesduring development. (A paper last July in Nature Medicinedemonstrated the application of GeneChip technology for studyingmutations in HIV protease genes, and a paper in Science last monthdemonstrated the technology'susefulness for resequencing the complete mitochondrial genome.)
"These papers demonstrate the breadth of the technology and ourability to export the technology," Rob Lipshutz, director of corporatedevelopment at Affymetrix, told BioWorld Today.
Much of the GeneChip-based research described in two of the paperswas conducted far from Affymetrix labs, in Santa Clara, Calif. "Alarge part of the work took place at Stanford and the National Centerfor Human Genome Research. It was done in close collaboration withour people here, but it shows the technology is out there," Lipshutzsaid.
GeneChip technology is a fusion of techniques used in thesemiconductor industry and in the molecular genetics laboratory.First, light shown through a "mask" is used to prepare specificregions of a 1.6 square cm glass slide for binding a nucleoside whichincludes a "protecting" group. This "protecting group" is removed,again by exposure to light, and a second nucleoside is allowed tobind to the first on the chip's surface. Cycle after cycle of this processproduces short chains of nucleotides called oligonucleotides attachedto the surface of the chip. In fewer than 80 chemical steps, thisphotolithographic-oligonucleotide synthesizing process can make anycombination or set of "20mers" _ oligonucleotides 20 nucleotideslong.
Scientists screen samples of DNA and RNA labeled with fluorescentdyes by passing them over the surface of the custom-designed chips.Genetic material in the experimental samples that recognizes andbinds to genetic material on the chips is detected by a scanner thatmeasures the fluorescent signal.
In the first study reported in the December Nature Genetics,Affymetrix scientists teamed up with researchers from the NationalCenter for Human Genome Research at the National Institutes ofHealth to diagnose mutations for the breast and ovarian cancer geneBRCA1 in patient samples. The promising results _ they accuratelydiagnosed 14 or 15 patients with known mutations and detected eightsingle nucleotide polymorphisms, or variations in the gene _ suggestthat DNA chip-based assays may provide a fast, cost-efficient, high-volume screening system in the future. The paper, "Detection ofheterozygous mutations in BRCA1 using high densityoligonucleotide arrays and two-color fluorescence analysis" wasauthored by Joseph Hacia, et al. Hacia is a post-doctoral fellow at theCenter for Human Genome Research.
Detectors To Pinpoint Predefined Sequence Tags
In the same issue of Nature Genetics, Daniel Shoemaker and co-authors of "Quantitative phenotypic analysis of yeast deletionmutants using a highly parallel molecular bar coding strategy"illustrate a second novel use of the technology. They show thatGeneChips can be used as "tag detectors" to detect predefinedsequence tags used to mark gene deletions in yeast.
"Our project was based on how to use Affymetrix technology to setup a system to allow all 6,000 genes to be studied. The Affymetrixchip is a key component in that equation," said Shoemaker, agraduate student in Ron Davis' lab at Stanford University.
A collaboration of Affymetrix scientists, led by senior scientist DavidLockhart, and researchers from Genetics Institute, in Cambridge,Mass., demonstrates the usefulness of GeneChip technology forstudying the expression of genes. The authors conclude that themethod is capable of simultaneously monitoring tens of thousands ofgenes in parallel experiments. The sensitivity of the technique isenough to allow detection of RNAs present at a frequency of1:300,000. The results are described in "Expression monitoring byhybridization to high-density olignonucleotide arrays," by DavidLockhart, et al., in the December issue of Nature Biotechnology.
While Affymetrix is exploring cancer screening applications withOncorMed Inc., of Gaithersburg, Md., it is continuing its DNA chiptechnology collaborations with Merck & Co. Inc., of WhitehouseStation, N.J., Hoffman-La Roche, of Basel, Switzerland, and IncytePharmaceuticals Inc., of Palo Alto, Calif., on gene expressionmonitoring. The company also is looking at broad resequencingapplications with Glaxo-Wellcome plc, of Middlesex, U.K.
Genetic Mapping Chip Development Underway
On the academic side, the company is working on gene mapping withEric Lander of the Whitehead Institute at the Massachusetts Instituteof Technology, in Cambridge.
"One of the goals is to develop applications for discoveringpolymorphisms that will allow us to create a new `mapping chip' thatcan be used for genetic mapping," Lipshutz said.
Affymetrix plans to increase the amount of information encoded onits chips the same way the computer industry increased the amount ofmemory on silicon chips during its early years.
"We are following the same path," Lipshutz said.
Lockhart, for instance, now is working on monitoring the expressionsof 6,500 genes on four chips. The company plans to move thosegenes onto a single chip, and at the same time produce a set of four orfive chips that can be used to monitor 40,000 or 50,000 genes.
Within six months the company could be producing chips with400,000 gene probes on them, up from today's 65,000 probes perchip.
"That increase allows them to look at more genes, more sequences,more polymorphisms," Lipshutz said. n
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