Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Study: ’homemade’ gene expression technology unreliable

31.05.2005


OHSU scientist participates in study supporting wider use of commercial microarrays



Technology for analyzing gene expression must be standardized among laboratories and across platforms around the world to support this age of human genome exploration, an Oregon Health & Science University researcher says.

Otherwise, scientists using DNA microarrays, also known as gene chips, risk having their research results called into question, said Peter Spencer, Ph.D., professor of neurology in the OHSU School of Medicine.


Spencer, director of the OHSU Center for Research on Occupational and Environmental Toxicology, co-authored with several OHSU colleagues one of three articles about microarrays appearing this month in the journal Nature Methods. They show that geographically separated multi-investigator teams adopting common commercial, rather than homemade, microarray platforms and common sets of procedures are able to generate comparable data.

"The important point of the three papers is that with contemporary microarray platforms, we have a relatively reliable method with which to assess gene expression, we can do so reproducibly within an individual laboratory, and we can be confident that a similar result would be obtained if the experiment is repeated elsewhere," Spencer said.

Gene chips contain tens of thousands of tiny droplets containing a cell’s whole gene sequences that are laid out on a single microscope slide by fast-moving robotic machines. Scientists determine how the expression of individual genes is turned up or down by placing copies of DNA or RNA molecules labeled with fluorescent dyes on the slide, and examining whether the molecules that bind to a particular gene light up when viewed with a special scanner.

By interrogating thousands of genes at once, scientists can quickly pinpoint genes affected by drugs being tested to treat heart disease, mental illness, infectious diseases and cancer. In the past, researchers were only able to analyze a few genes at once, and they were often uncertain whether these were of greatest importance.

Spencer’s group is using the technology in two National Institute of Environmental Health Sciences (NIEHS) centers led by CROET – one with Oregon State University and the Battelle-run Pacific Northwest National Laboratory focuses on mechanisms underlying Superfund chemicals with neurotoxic properties; the other with the OHSU School of Medicine’s Department of Pediatrics focuses on neurotoxicogenomics and child health.

Srinivasa Nagalla, M.D., associate professor of pediatrics, and cell and developmental biology, OHSU School of Medicine, led the initial bioinformatics research that supported the Nature Methods publication.

"The gene chip is a revolution in technology that is hoped rapidly to advance understanding of biological mechanisms and methods to assess the actions and effects of drugs and chemicals," said Spencer, who estimates there are "hundreds, if not thousands" of laboratories around the country using DNA microarrays.

Microarray platforms came into widespread use about five years ago. Pioneers in the field constructed their own gene chips, but these have now been replaced by much more reliable commercial platforms that generate highly reproducible data. One of these is used by CROET and another by OHSU’s West Campus microarray resource facility.

"It’s possible to buy a robot which will take some copies of RNA on a small pin and then write that on a glass slide repetitively until one can build up hundreds of thousands of different spots on this glass array," Spencer said.

But as commercial platforms improved over time, many laboratory or "home-built" platforms have not, he said. "The fruits of the research done on some of the early homemade and early commercial platforms have entered the literature, but the platforms were not reliable because they did not produce reproducible results."

Spencer co-authored the Nature Methods study, titled "Standardizing Global Gene Expression Analysis Between Laboratories and Across Platforms," as part of the Toxicogenomics Research Consortium, a group led by the NIEHS whose members study how the genome is involved in responses to environmental stressors and toxicants.

The three-year, NIEHS-funded study compared a lab-built spotted long oligonucleotide microarray, and a commercially produced long oligonucleotide microarray. The two types were represented among 12 microarray platforms used by seven consortium laboratories, all of which generated data from two standard RNA expression samples, one derived from mouse livers and the other taken from tissues of several mouse organs.

According to the study, reproducibility between platforms and across laboratories was generally poor, but reproducibility between laboratories dramatically increased to acceptable levels when a commercial microarray was used with standardized protocols for labeling the RNA, processing the microarrays, acquiring data and other elements.

"The bottom line is that if you use commercial platforms, you get very good interlaboratory consistency and correlation of data," Spencer said. "We’ve now entered a new era in which we can move forward confident that we have reliable platforms."

And this is particularly important as scientists delve deeper into the genomes of humans and other animal species in their quest to find cures for a variety of diseases.

"Human genome mapping has made the production of these microarrays possible," Spencer said. "Our interest is in how environmental factors – drugs, pollutants, workplace substances, natural toxins, food chemicals, fragrance raw materials, other factors – impact or interact with the genome to produce disease. That’s the big task before us."

Jonathan Modie | EurekAlert!
Further information:
http://www.ohsu.edu

More articles from Studies and Analyses:

nachricht Win-win strategies for climate and food security
02.10.2017 | International Institute for Applied Systems Analysis (IIASA)

nachricht The personality factor: How to foster the sharing of research data
06.09.2017 | ZBW – Leibniz-Informationszentrum Wirtschaft

All articles from Studies and Analyses >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Neutron star merger directly observed for the first time

University of Maryland researchers contribute to historic detection of gravitational waves and light created by event

On August 17, 2017, at 12:41:04 UTC, scientists made the first direct observation of a merger between two neutron stars--the dense, collapsed cores that remain...

Im Focus: Breaking: the first light from two neutron stars merging

Seven new papers describe the first-ever detection of light from a gravitational wave source. The event, caused by two neutron stars colliding and merging together, was dubbed GW170817 because it sent ripples through space-time that reached Earth on 2017 August 17. Around the world, hundreds of excited astronomers mobilized quickly and were able to observe the event using numerous telescopes, providing a wealth of new data.

Previous detections of gravitational waves have all involved the merger of two black holes, a feat that won the 2017 Nobel Prize in Physics earlier this month....

Im Focus: Smart sensors for efficient processes

Material defects in end products can quickly result in failures in many areas of industry, and have a massive impact on the safe use of their products. This is why, in the field of quality assurance, intelligent, nondestructive sensor systems play a key role. They allow testing components and parts in a rapid and cost-efficient manner without destroying the actual product or changing its surface. Experts from the Fraunhofer IZFP in Saarbrücken will be presenting two exhibits at the Blechexpo in Stuttgart from 7–10 November 2017 that allow fast, reliable, and automated characterization of materials and detection of defects (Hall 5, Booth 5306).

When quality testing uses time-consuming destructive test methods, it can result in enormous costs due to damaging or destroying the products. And given that...

Im Focus: Cold molecules on collision course

Using a new cooling technique MPQ scientists succeed at observing collisions in a dense beam of cold and slow dipolar molecules.

How do chemical reactions proceed at extremely low temperatures? The answer requires the investigation of molecular samples that are cold, dense, and slow at...

Im Focus: Shrinking the proton again!

Scientists from the Max Planck Institute of Quantum Optics, using high precision laser spectroscopy of atomic hydrogen, confirm the surprisingly small value of the proton radius determined from muonic hydrogen.

It was one of the breakthroughs of the year 2010: Laser spectroscopy of muonic hydrogen resulted in a value for the proton charge radius that was significantly...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ASEAN Member States discuss the future role of renewable energy

17.10.2017 | Event News

World Health Summit 2017: International experts set the course for the future of Global Health

10.10.2017 | Event News

Climate Engineering Conference 2017 Opens in Berlin

10.10.2017 | Event News

 
Latest News

Terahertz spectroscopy goes nano

20.10.2017 | Information Technology

Strange but true: Turning a material upside down can sometimes make it softer

20.10.2017 | Materials Sciences

NRL clarifies valley polarization for electronic and optoelectronic technologies

20.10.2017 | Interdisciplinary Research

VideoLinks
B2B-VideoLinks
More VideoLinks >>>