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The BioPrime® Total FFPE Genomic Labeling System is a complete genomic DNA labeling kit designed for use in array comparative genomic hybridization applications (aCGH) using formalin fixed paraffin embedded (FFPE) samples. 

  • Improved call rates and less channel bias with enhanced Alex Fluor® 3 and 5 dye formulation for FFPE samples in aCGH experiments
  • Representative results from FFPE samples using enzymatic RPA method
  • Eliminate complicated volume-reduction steps with Purelink® purification included
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Improved call rates and reduced channel bias with FFPE samples

This complete, all-inclusive aCGH labeling kit is optimized to work across a wider range of sample input material with no need for pre-amplification. Highly concentrated exo-Klenow fragment in a component limited reaction allow for consistent, robust DNA yields of genomic FFPE DNA input. Optimized dye labeled nucleotide mix with new dNTP linkers, novel, application-specific Alexa Fluor® 3 and 5 dyes, and improved buffer chemistry reduce labeling variation and increase signal to noise in aCGH. Excitation and emission spectra of Alexa Fluor® 3 and 5 dyes are suited for conventional two color scanners with no need to change settings.

Representative results using enzymatic RPA method

With a random prime amplification (RPA) method, using labeling mixes specifically formulated for FFPE samples, BioPrime® Total FFPE Genomic Labeling System generates high yields of labeled DNA which is most representative of the starting sample. Increased call accuracy is achieved with higher yields of labeled material on the array, giving you more accurate calls in your aCGH experiments.

Eliminate complicated volume-reduction steps

BioPrime® Total FFPE Genomic Labeling System is supplied with Purelink™ purification which allows low elution, eliminating the need for complicated volume-reduction steps. The Purelink™ purification also reduces background due to dye bleed-through found in other purification systems.

Comparing PureLink™ (Invitrogen) and Microcon (Agilent) indicates that the majority of the free nucleotides are removed with PureLink™ purification.  In addition PureLink™ also produces more higher molecular weight reaction products.  The labeling data (not shown) further indicated that there is no purification bias for labeled and unlabeled nucleotides, as the DOL was not effected by two purification methods.

Figure 1.  TBE Urea Gel of aCGH Labeling Kinetics. 
Reaction products were separated by electrophoresis in 6% TBE-Urea gels and visualized on a Typhoon scanner/imager (Applied Biosystems) using the fluorescein channel (MW markers) and Cy/AF channels (labeling reaction products).  

Lane 1: Purelink™ Normal     Lane 3: Microcon® Normal
Lane 2: Purelink™ MCF7       Lane 4: Microcon® MCF7
Lane 7: Purelink™ Normal     Lane 9: Microcon® Normal
Lane 8: Purelink™ MCF7       Lane 10: Microcon® MCF7
Lane 5&6: BioVentures fluorescein labeled Map Marker