Array Comparative Genomic Hybridization

Array based comparative genomic hybridization (array CGH) has emerged as a powerful tool for detecting gene copy number variants implicated in many disease states. Simple, robust genomic DNA labeling reagents and removal of free dye and nucleotides are two of the most critical components determining array CGH experiment’s performance. Suboptimal labeling and purification can lead to lower signals, channel bias, and greater variation, decreasing your ability to make accurate calls from array data. BioPrime® Total array CGH kits:

  • Improve array CGH call rates and reduce channel bias with optimized Alexa Fluor® 3 and Alexa Fluor® 5 dye formulation
  • Generate higher DNA yields and improved signal-to-background ratios on arrays for more accurate data interpretation
  • Eliminate complicated volume-reduction steps with PureLink™ purification included

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Purification column change

We are making changes to the purification columns contained the BioPrime® Array CGH Genomic Labeling System kit.

BioPrime® Total array CGH reagent systems

BioPrime® Total for Agilent® array CGH

The BioPrime® Total for Agilent® array CGH system is a complete genomic DNA labeling kit for use in array comparative genomic hybridization applications on the Agilent® array CGH platform. Master mix formulation includes restriction enzymes Alu I and Rsa I.

  • Optimized and validated for the Agilent® array CGH workflow, arrays, and scanners

 

 

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The BioPrime® Total FFPE Genomic Labeling System

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

 

  • Get representative results from FFPE samples using enzymatic RPA method

 

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BioPrime® Total Genomic Labeling System

The BioPrime® Total Genomic Labeling System reduces labeling variability and increases signal to noise ratios on arrays, by using an optimized dye-labeled nucleotide mix with novel, Alexa Fluor® 3 and Alexa Fluor® 5 dyes, improved dNTP linkers, and new buffer chemistry.

  • Simplify the workflow and reduce steps with a master mix formulation for oligo and BAC aCGH experiments

 

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Reagent Selection FAQs

Which BioPrime® is right for me?
The BioPrime® Total array CGH reagents offer various configurations to allow for optimal performance on arrays based on premier enzymes, primers, dyes and purification systems.  For 2 color array CGH and ChIP on Chip experiments Invitrogen recommends the BioPrime® Total Genomic Labeling system.  The BioPrime® Total Genomic Labeling system allows for the lowest starting input material, includes application optimized dye labeled nucleotides with Alexa Fluor® 3 and Alexa Fluor® 5 dyes, and is the simplest, easiest to use kit in the product family.  For researchers favoring other dyes, BioPrime® aCGH Genomic Labeling systems are available without dyes and can be used with your dye of preference to offer superior yield and total dye incorporation due to higher performance enzymes and reagents from Invitrogen.  Both BioPrime® Total and BioPrime® array CGH kits have been successfully used with both oligo and BAC arrays from vendors such as:  Agilent, Perkin Elmer, Signature Genomics, Combimatrix Diagnostics, and BlueGnome. For microarray systems requiring biotin labeling the BioPrime® DNA Labeling system includes biotin labeled nucleotides in the kit and has been successfully used in both one and two color microarray experiments.  View the Genomic array CGH selection guide.

What are the differences between Alexa Fluor® 555, 647, 3 and 5 used in the kits?
Both lines of Alexa Fluor® dyes can be used on traditional 2 color scanners with excitation and emission wavelengths optimized for these scanners.  The Alexa Fluor® 3 and Alexa Fluor® 5 dye conjugated nucleotides have been optimized for DNA Microarray applications and are incorporated with the enzymes used in BioPrime® Total Genomic Labeling systems to provide excellent performance when dried down on arrays.

Why is random primed linear amplification (RPA) so important for these applications?
All of the BioPrime® Genomic Labeling systems are based on linear, random primed amplification methods – the best method to maintain accurate representation of copy number.  Other methods of amplification may provide inaccurate amplification of starting material which potentially invalidate array results.

Why is the selection of a Genomic Labeling kit so important?
The overall performance of your microarray experiment is driven by numerous factors including the microarray, amplification method, labeling method, hybridization solutions/conditions, blocking and wash methods, as well as performance of the associated hardware systems.  In order to achieve the highest confidence in your array results best in class components must be selected for each step.   Invitrogen’s BioPrime® Total and Cot-1 DNA® products are the proven labeling and blocking reagents to increase accuracy, sensitivity, and simplicity.