Progenika has applied its proprietary Sendage Pharmacogenomics Platform to successfully develop and market DNAchips such as LIPOchip, BLOODchip and PHARMAchip . A series of new DNAchips are also under development or in the late-stages of clinical validation.
The Sendagene Pharmacogenomics Platform has allowed the scientists and engineers at Progenika to optimize each step in the development and production of Progenika’s DNAchips. This optimization has been applied to all processes from the design of the DNAchip through to their manufacture, and to the production of the algorithms and software required to analyse the data obtained in order to produce a user-friendly tool.
The target sequence always lies in the centre of the oligonucleotides in order to maximize the specificity of hybridization. Oligonucleotides are specific to the normal or the mutant allele.
Several replicates of each oligonucleotide probe are spotted onto glass slides using a robot, along with oligonucleotides that serve as positive and negative controls of hybridization.
Normal DNA is used to control the quality of the process in terms of the hybridization signal, background signal, specificity, sensitivity, reproducibility of each replicate probe (coefficient of variation).
Target DNA for hybridization is prepared in several independent amplification reactions, permitting the amplification of the exons to be analysed. Biotin is incorporated into the amplified products during the amplification process. The biotinylated amplicons are hybridized to the array in an automatic hybridization station and they are subsequently stained with a fluorophore conjugated streptavidin.
Data analysis and genotyping software
After scanning and quantifying the hybridization signals from the arrays, the export file from the scanner is processed by Progenika’s own proprietary genotyping software. The results are available in a matter of seconds and can be communicated immediately to the supervising physician.
The specificity and sensitivity of the DNAchips are tested with more than ten control DNA samples per mutation. The overall specificity and sensitivity coefficients obtained for all the mutations tested reach 99.7% and 99.9%, respectively.
The coefficient of variation for the replicates of each oligonucleotide is under 15% for any given DNAchip.
International multicentre clinical trials are carried out in order to demonstrate the clinical application of each Progenika DNAchip. Clinically-typed anonymous samples from more than 1000 subjects are tested with each Progenika DNAchip, in order to demonstrate the clinical accuracy of the assay.
Mutations that are not currently identified by the microarrays are continuously being introduced into the assay.
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