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Agilent Technologies Offers First FFPE Kit for Oligo CGH Microarrays

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Agilent Technologies Inc. and Kreatech Biotechnology BV have announced the availability of labeling kits that, for the first time, enable oligo microarray comparative genomic hybridization (CGH) analysis of DNA from formalin-fixed paraffin-embedded (FFPE) tissue samples.

The method is based on Kreatech’s Universal Linkage System (ULS) technology, a non-enzymatic direct labeling methodology that has been optimized for Agilent oligo CGH microarrays. Enzymatic labeling can introduce bias while further reducing DNA fragment size. This new labeling technology also features a simple, single-tube protocol, enabling a reduced cost per experiment.

“One of the key advantages of our ULS labeling technology is that it eliminates the bias often found with enzymatic labeling methods, so one can label DNA of any fragment size,” said Dimitri Pappaioannou, senior product manager at Kreatech.

“This makes it especially suited for FFPE DNA samples. We have been working closely with Agilent on the development, optimization and validation of the ULS technology on the Agilent oligo aCGH platform, and we are very excited about the results. Through Agilent we are now able to provide researchers with a solution for FFPE samples that were inaccessible in the past,” Pappaioannou continued.

“Now researchers can harness the high resolution, genome-wide copy number change profiling capabilities of the Agilent aCGH platform using FFPE samples,” stated Dione Bailey, Agilent CGH product manager.

“Given the rapid adoption of CGH versus classical techniques such as spectral karyotyping, FISH, and BAC arrays, we anticipate the release of this kit will further expand this growing marke,” Bailey said.

This method addresses an unmet need of clinical researchers. There are an estimated 400 million FFPE-preserved samples in tissue banks worldwide, and the DNA in these samples has been considered too degraded to use in microarray analysis techniques such as aCGH, a powerful method for studying DNA copy number variation in cancers and genetic disorders.

As an example, according to the National Cancer Institute’s Web site, the Department of Pathology and Laboratory Medicine at the University of Pennsylvania has approximately 600,000 paraffin-embedded tissue samples that date back to the 1940s. As a result, this labeling capability would allow more comprehensive retrospective analysis from sample biobanks and clinical repositories at a large number of cancer centers.

“Our comparison data showed that the new Agilent non-enzymatic labeling kit is superior to standard Klenow-based DNA labeling protocol,” said Lynda Chin, M.D., Dana-Farber Cancer Institute.

“The improved signal achieved with this non-enzymatic labeling technique was more apparent when working with modestly degraded genomic DNA extracted from formalin-fixed paraffin-embedded samples.” Chin added.

“The Agilent DNA extraction protocol combined with non-enzymatic labeling gave good results from our FFPE samples,” said Chris Jones, Ph.D. in the Pediatric Molecular Pathology Department of the Institute of Cancer Research in Sutton, U.K.

“We have a large number of FFPE samples across many tumor types that have been previously inaccessible. As an initial priority we have a series of approximately 90 clinical samples from which data can now be retrieved using this new extraction and labeling approach.”