Fluidigm and the Ludwig Institute for Cancer Research Join Forces to Measure Expression of 900 Genes in 96 Samples in One Week
12 Jun 2008Fluidigm today announced that the Sãn Paulo Branch of the international Ludwig Institute for Cancer Research (LICR) used the company’s BioMark™ System to conduct a large scale analysis characterizing the whole human “surfaceome” (the set of genes encoding cell surface proteins) in what was for them record time. The experiment compressed months of work for the LICR team into just one week at Fluidigm’s South San Francisco lab.
"I came to Fluidigm for one week with the goal of analyzing the expression of 900 genes in 96 samples. At first, I thought the task was impossible… but it turned out achievable using integrated fluidic circuits. Wow!” said Julia Pinheiro Chagas da Cunha, PhD., of LICR’s branch in Sãn Paulo, Brazil. “Fluidigm’s dynamic arrays are really impressive. With less than 100 micrograms of RNA and in a few hours, it was possible to get good data, making it feasible to analyze gene expression in small amounts of tissue, like biopsies. "
The LICR team used tumor needle biopsies of colon, lung, prostate and breast samples (as well as control samples) to conduct its experiments. Using Fluidigm’s new 96.96 dynamic arrays, Dr. da Cunha was able to process 55,000 data points in a day with just four hours of “hands-on” labor.
Gajus Worthington, Fluidigm’s President and CEO, noted that the Ludwig Institute of Cancer Research’s work currently uses the company’s 48.48 dynamic arrays. “But, with our newly introduced 96.96 dynamic arrays, all this gene expression work could now be completed faster, or four times as many samples can be finished in the same week at even lower cost.”
With the availability of the human genome sequence, as well as a large amount of data on expressed genes in cancer, the LICR is conducting several studies attempting to characterize genes differentially expressed in cancer. Sandro J. de Souza, Ph.D., of the Ludwig Institute said, “We have performed a large-scale analysis aimed to characterize the whole human “surfaceome,” integrated gene expression data into a “surfaceome” knowledge base, identified gene candidates to be differentially expressed in glioblastoma and colon tumors and want to validate some of these candidates using a large-scale qPCR strategy. Fluidigm’s 96.96 dynamic arrays will play a critical role in the qPCR phase of our research.”
Fluidigm’s new BioMark™ 96.96 Dynamic Array is capable of performing 9,216 simultaneous real-time PCR experiments running gold-standard TaqMan® assays in nanoliter quantities. This new generation of integrated fluidic circuit enables life science researchers to achieve new levels of cost and logistical efficiency and flexibility, as well as enhanced levels of profiling from miniscule amounts of sample.
When comparing Fluidigm’s new 96.96 Dynamic Arrays to industry-standard 384-well systems using 10 uL reaction volumes, the 96.96 provides significant improvements in productivity and efficiency.
24-fold higher throughput: one 96.96 Dynamic Array gives 9,216 parallel data points, the equivalent of twenty-four 384-microwell plates.
192-fold less master mix: 240 microliters compared to 46,080 microliters for 9,216 reactions.
A 96-fold decrease in setup complexity: the 96.96 Dynamic Array requires only 192 pipetting steps per 9,216 reactions compared to 18,432 pipetting steps for an equivalent number of microwell plate experiments.
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