Gene+Chip

Gene Chips**, otherwise known as **microarrays**, are small squares of glass about the size of postage stamps, in which are embedded microscopic spots of DNA of varying lengths. The information contained in these chips are gathered by allowing DNA probes to bind with complementary RNA from specially prepared tissue samples, forming single strands of probes. These strands are then melded into glass with technology similar to that of the making of computer chips. The information on the chips are scanned and analyzed by a specialized computer, and can be used to identify which genes are present in the tissue sample, as well as their level of genetic expression.
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The development of gene chips has allowed researchers to scan thousands of genes simultaneously, and to determine specifically which genes are being “expressed”, or directing protein synthesis within the body. Before the development of the gene chip, this was a tedious and lengthy process that could take years; now, actively expressed genes can be identified within months, or even weeks. The data gathered from these chips are often used to combat diseases; this is done by collecting the genes of patients and non-patients alike, and comparing their genetic data in order to distinguish which combinations of actively expressed genes are more prevalent in patients than in non-patients. This process was used to isolate the genetic signature of a particular form of breast cancer, so that patients, as well as those with the potential of contracting breast cancer, could undergo more intensive screening, and begin taking extra precautions. During the epidemic of SARS, gene chips were also a crucial key in identifying the viruses responsible for the spreading of the disease. Furthermore, besides collecting information of just the human genome, gene chips are widely used for the research of animal diseases as well.

A gene chip containing information from the human genome.

__Identifying Life Threatening Blood Infection__
Right now there's no rapid way to diagnose sepsis, a fast-moving blood infection that is a leading cause of death in hospital intensive care units. The illness can cause death within days. Doctors have to make quick decisions in order to stop its lethal spread, and patients suspected of sepsis are usually prescribed power antibiotics before lab tests can even confirm the diagnosis. This has led to the inappropriate treatment of many patients.

New research now suggests that doctors one day could quickly distinguish sepsis from widespread non-infectious inflammation based on genetic profiles of patients' blood. The molecular profiles measure differences in patterns of gene expression that are unique to sepsis vs. non-infectious inflammation.

Currently, a diagnosis of sepsis or non-infectious systemic inflammation is made by sending cultures of patients' blood, sputum, or urine to the laboratory for analysis, which can take several days. Gene chips could cut the typical time needed for diagnosis to eight hours or less, says J. Perren Cobb, MD, director of Washington University's Center for Critical Illness and Health Engineering and a surgeon at Barnes-Jewish Hospital.

In a new research, Cobb and his colleagues mimicked sickness in four groups of mice: each of three groups had a varying severity of sepsis and a fourth had systemic non-infectious inflammation. Using gene chips, they created molecular profiles based on the abundance of messenger RNA expressed in immune cells taken from the blood of the sick mice. These profiles were compared with profiles from the blood of control mice.

Cobb's current studies are focused on narrowing the number of genetic markers in patients to make it practical to develop a bedside test to screen for signs of infection. He is also exploring whether gene chips can identify the specific type of invading organism in the blood samples. Early findings suggest that the technology detects differences in molecular profiles based on the type of pathogen involved.

__Speeding up H5N1 Diagnosis__
Quite recently, scientists have found an inexpensive “gene chip” test that s able to identify a variety of influenza A viruses, including H5N1. Researchers examined the test's ability to identify 24 H5N1 viral isolates and distinguish them from seven non-H5N1 isolates. They found that the "MChip" provided complete information about virus type and subtype for 21 of the 24 H5N1 isolates and gave no false-positives. The samples were collected between 2003 and 2006 from people and animals in places as widely separated as Vietnam, Nigeria, Indonesia, and Kazakhstan. Six of the human isolates were taken from an Indonesian family in which human-to-human transmission was suspected.

The MChip could enable more scientists and physicians, possibly even those working in remote places, to more quickly test for H5N1 and to accurately identify the specific strain and its features. This would greatly increase the ability for scientists to learn more about the viruses causing illnesses and take the best steps to respond. The MChip displays results as a pattern of fluorescent spots that are automatically interpreted by artificial neural network software designed to eliminate human error. The software component will make the test easier to use in the field. If approved by the FDA, the MChip system could be in great demand in a flu pandemic

__Forensic Uses__
Analysts of the __microarray array technology__ are currently forecasting that within the next 5 years Nanogen may have the ability to use a __DNA or Gene chip__ at a crime scene in order to replace existing blood and evidence tests. In order to do this, Nanogen has been working on a portable DNA chip system, with which we could analyze blood, urine, semen, hair, and skin without the cumbersome task of taking the evidence to the laboratory. The current methods can take up to 3 days, and often are a major obstacle in the way of convicting suspects.


 * Nanogen**: A company that provides human molecular diagnostic products to research, clinical laboratory, and point-of-care markets in North America, Europe and Asia. The company offers NanoChip Molecular Biology Workstation, an automated, multipurpose instrument primarily used for DNA-based analyses; and the NanoChip Cartridge, which provides a tool for the identification and analysis of biological test samples containing charged molecules.



-**Montanna Cheng**

Sites Used: http://equisearch.com/horses_care/health/anatomy/genechip_021606/ http://www.usatoday.com/tech/news/techinnovations/2003-04-07-gene-chip_x.htm <-- good article about the development and spread of gene chips and their use. http://www.physorg.com/news85760216.html (Gene Chip and Sepsis) http://www.cidrap.umn.edu/cidrap/content/influenza/panflu/news/nov1506mchip.html (Gene Chip and H5N1 Diagnosis) http://courses.washington.edu/newtech/GeneChip2.pdf (Overview of the many different Gene Chips and Forensic Use)

Other sites on this topic: http://researchnews.osu.edu/archive/genechip.htm