DNA diagnostic technique provides sharper tool for cancer detection

A DNA diagnostic technique developed by Laboratory scientists is expected to provide a valuable new tool to improve cancer diagnosis.
The advance is described in a paper published this month in the journal Proceedings of the National Academy of Sciences.

With this discovery, researchers can detect mutations in individual cancer cells by specific identification and by making numerous copies of the DNA in the genes important for cancer progression in each cell.

In addition to its use in cancer diagnosis, the Livermore technique could also be employed to genetically screen plants for agricultural uses, to genetically evaluate birth defects, and for applications in basic cell research, LLNL biomedical scientist Jim Tucker said. Another possible use would be a more rapid determination of whether a person has been exposed to radiation.

Livermore biomedical scientist Allen Christian is the paper’s lead author. Other authors are Melissa Pattee, Christina Attix, Beth Reed, Karen Sorensen and Tucker. All six are biomedical scientists in the Laboratory’s Biology and Biotechnology Research Program.

"Until now, there hasn’t been any way of doing DNA testing inside cells with the level of resolution that we have been able to achieve," Tucker said.
"Previous DNA testing techniques couldn’t easily, or on a routine basis, tell us which molecular changes were present in tumor cells. Now we have the basic techniques to develop tools to improve cancer diagnosis and cancer therapy," Tucker added.

The Lab scientists have succeeded in applying a technique to the study of cells and tissue that was originally used to evaluate isolated DNA. A patent is pending for their work and at least one company has already expressed interest in licensing the technology. Previously, the best resolution for detecting genetic abnormalities inside a single cell was a flawed or missing region of about 1,000 DNA base pairs long, out of the approximately 6.6 billion base pairs in every human cell. The process to find these abnormalities usually took several days.

Now, with the Lab advance, researchers can locate a single flawed DNA base pair within a cell, Tucker said. And the process can be done within a couple of hours.

"This technique could greatly speed efforts to measure the effectiveness of treatments in killing tumors and would improve the ability of physicians to individualize cancer treatments," Tucker said.

For example, when doctors try a particular cancer therapy, they can now evaluate its effectiveness much more rapidly, allowing alternative therapies to be considered earlier in the treatment process.

"The technique can be used to monitor the effectiveness of treatments to see how much of the tumor remains," he said.

Another major application of the technology, according to the Livermore scientist, could be in the area of improving agricultural crops. "Companies are always trying to make better strains of rice, corn, carrots or even Douglas fir trees, but until now they have lacked the rapid DNA diagnostic tests they’ve needed," Tucker explained.

In his view, the Lab technique will assist scientists in rapidly identifying which strains of a plant, tree or vegetable have the desired genetic characteristics.
In basic cellular research, the advance could prove useful for determining the genetic composition of bacterial, plant and human cells. The Lab scientists’ research expands upon a diagnostic technique known as rolling circle amplification. In this procedure, researchers take a designed sequence of DNA and bring the ends of the DNA together onto a target molecule to be studied.

The two ends of the DNA sequence are joined together to form a circle. Next, an enzyme is used to make a long DNA strand comprised of hundreds or thousands of linear copies of the circular DNA sequence that are joined together.

What LLNL’s biomedical scientists have done is to extend the use of the rolling circle amplification technique — which had been used in isolated DNA — to cells and tissue.

The scientists developed a way to eliminate one of the two strands in the double helix of DNA, so that more maneuverability is provided for the enzyme to make copies of the DNA.