Using a Digital Array from Fluidigm (www.fluidigm.com) – researchers at the renowned Fred Hutchinson Cancer Research Center (Seattle, WA, USA) have developed a method that allows for the early detection of a common mechanism of resistance on drug treatment for chronic myeloid leukemia. The researchers were able to detect a specific point mutation, which is associated with acquired resistance to the drugs Gleevec (imatinib mesylate), Sprycel (dasatinib), and Tasigna (nilotinib), as much as 100 days earlier than standard tests used in clinical practice today. In the future, this strategy could allow doctors to identify early relapse with this mutation (as well as others) and consider changing to alternatives earlier in treatment than they can now.

The work of Vivian Oehler, M.D. and Jerald Radich, M.D. of the Fred Hutchinson Cancer Research Center was disclosed a recent issue of Nature Magazine’s journal – Leukemia. In the letter, Dr. Oehler describes how she uses a Fluidigm integrated fluidic circuit (called a digital array). “Using this method, we can detect just a few mutated molecules in the background of as many as 100,000 molecules. It is a little like looking for a needle-in-a-haystack by first dividing the haystack into many smaller haystacks, which makes it easier to find the needle,” explained Dr. Oehler. The Fluidigm Digital Array uses nanoscale channels, valves and pumps to partition samples into up to 9,180 chambers prior to PCR.

As a result of this partitioning, a mixture containing one molecule of T3151 ABL in 100,000 molecules of unmutated ABL is separated into 1000 independent chambers. “The chamber containing the single mutant molecule now only contains approximately 100 molecules of unmutated ABL,” explained Ramesh Ramakrishnan, Ph.D., Fluidigm’s Director of Molecular Biology. “This 1000-fold increase in relative concentration theoretically allows for a 1000-fold improvement in the detection sensitivity of PCR reactions.”

The most common method used in clinical practice today is direct nucleotide sequencing. This method requires at least a 20 percent concentration of mutated molecules to be present in order to detect them. The problem with this method is that by the time mutations are usually detected, a relapse has already occurred. “With this new method we hope to move up the window of detection. In our studies we specifically looked at the T315I mutation first as currently all tyrosine kinase inhibitors are resistant to it, but we have designed assays for other mutations associated with poor prognosis as well,” said Dr. Oehler.

Fluidigm develops, manufactures and markets proprietary Integrated Fluidic Circuit (IFC) systems that significantly improve productivity in life science research. Fluidigm’s IFCs enable the simultaneous performance of thousands of sophisticated biochemical measurements in extremely minute volumes. These “integrated circuits for biology” are made possible by miniaturizing and integrating liquid handling components on a single microfabricated device. Fluidigm’s IFC systems, consisting of instrumentation, software and single-use IFCs, increase throughput, decrease costs and enhance sensitivity compared to conventional laboratory systems. Fluidigm products have not been cleared or approved by the Food and Drug Administration for use as a diagnostic and are only available for research use.