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 Rutgers-led innovation could spur faster, cheaper, nano-based manufacturing
14.02.2018 | Rutgers University

nachricht New study from the University of Halle: How climate change alters plant growth
12.01.2018 | Martin-Luther-Universität Halle-Wittenberg

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: In best circles: First integrated circuit from self-assembled polymer

For the first time, a team of researchers at the Max-Planck Institute (MPI) for Polymer Research in Mainz, Germany, has succeeded in making an integrated circuit (IC) from just a monolayer of a semiconducting polymer via a bottom-up, self-assembly approach.

In the self-assembly process, the semiconducting polymer arranges itself into an ordered monolayer in a transistor. The transistors are binary switches used...

Im Focus: Demonstration of a single molecule piezoelectric effect

Breakthrough provides a new concept of the design of molecular motors, sensors and electricity generators at nanoscale

Researchers from the Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague), Institute of Physics of the CAS (IP CAS) and Palacký University...

Im Focus: Hybrid optics bring color imaging using ultrathin metalenses into focus

For photographers and scientists, lenses are lifesavers. They reflect and refract light, making possible the imaging systems that drive discovery through the microscope and preserve history through cameras.

But today's glass-based lenses are bulky and resist miniaturization. Next-generation technologies, such as ultrathin cameras or tiny microscopes, require...

Im Focus: Stem cell divisions in the adult brain seen for the first time

Scientists from the University of Zurich have succeeded for the first time in tracking individual stem cells and their neuronal progeny over months within the intact adult brain. This study sheds light on how new neurons are produced throughout life.

The generation of new nerve cells was once thought to taper off at the end of embryonic development. However, recent research has shown that the adult brain...

Im Focus: Interference as a new method for cooling quantum devices

Theoretical physicists propose to use negative interference to control heat flow in quantum devices. Study published in Physical Review Letters

Quantum computer parts are sensitive and need to be cooled to very low temperatures. Their tiny size makes them particularly susceptible to a temperature...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

2nd International Conference on High Temperature Shape Memory Alloys (HTSMAs)

15.02.2018 | Event News

Aachen DC Grid Summit 2018

13.02.2018 | Event News

How Global Climate Policy Can Learn from the Energy Transition

12.02.2018 | Event News

 
Latest News

Researchers invent tiny, light-powered wires to modulate brain's electrical signals

21.02.2018 | Life Sciences

The “Holy Grail” of peptide chemistry: Making peptide active agents available orally

21.02.2018 | Life Sciences

Atomic structure of ultrasound material not what anyone expected

21.02.2018 | Materials Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>