Scientists are employing similar technology used to ensure emails arrive to your inbox intact to make the analysis of genes more sensitive and comprehensive in the quest to better understand disease.

The research centers on DNA microarray analysis, a multimillion-dollar industry used to identify gene activation in living things. Using a procedure based on a “check-sum” Internet protocol, researchers have found a way to verify the data points generated by a DNA microarray. A DNA microarray is a small chip that can monitor the turning on and off of as many as 30,000 different genes.

Check-sum IP has been used for about two decades to ensure emails don’t become garbled as they move from one computer to another.

The work by Ziv Bar-Joseph, assistant professor of computer science and biological sciences at CarnegieMellonUniversity in Pittsburgh, was done in collaboration with experts at The Hebrew University in Jerusalem. The results were published in the December issue of the journal Nature Biotechnology.

Static Snapshots

"While DNA microarrays are very powerful, they present a sampling problem… [they] only take static snapshots of gene activity over time," said Dr. Bar-Joseph.

This means that time-series DNA microanalysis data, which is commonly used to follow medically important microbiological changes such as study cell division and immune system responses, can miss gene activation that occurs between snapshots.

“Our protocol will offer greater overall sensitivity in detecting the expression of any gene, even if a gene turns on when no microarray sampling takes place,” added Dr. Bar-Joseph.

And this, he says, could “vastly” improve medical research by opening the door to new and more accurate models of the cell division cycle and therefore, to new targets for cancer drugs.

Binary Code

The principle behind the invention is to think of “on” and “off” genes as the 0’s and 1’s into which computers convert email messages. Using this analogy, a gene’s activation between microarray samples is rather like a digit of email binary code inadvertently flipping to the opposite value during transmission.

A “check sum” protocol does exactly what its name implies: it adds up all the 0’s and 1’s in a message and uses this to compare the message sent to the message received.

So if a set of DNA microanalysis data points have a lower “check sum” result than the previous set, the technology alerts scientists to the fact that they have missed a gene’s activation.

“So far I’ve had discussions with Affymetrix on this and other technologies we’re developing,” Dr. Bar-Joseph told RedHerring.com. "We are very excited about introducing this versatile, powerful method to the research community.”

The research was funded by a National Science Foundation CAREER award, the Pittsburgh Life Sciences Greenhouse, and the Pennsylvania Department of Health through the Tobacco Settlement Fund.