Copy Number Variation (CNV) with Real-Time PCR | Thermo Fisher Scientific

Applied Biosystems TaqMan Copy Number Assays combine TaqMan MGB probe chemistry with Applied Biosystems real-time PCR instruments to provide a method for obtaining specific, reproducible, and easy-to-interpret copy number results. This fast and simple method can be completed in hours rather than days. Use TaqMan Copy Number Assays to screen specific targets using a workflow that can be automated to process several hundred to thousands of samples in a single day. And because TaqMan Assays are the gold standard for accurate target quantitation, they are ideal for use in microarray follow-up studies.

The TaqMan Copy Number Assay family includes the following:

Predesigned TaqMan Copy Number Assays

Human: over 1.6 million predesigned assays available for genome-wide coverage
Mouse: over 180,000 predesigned assays available for gene exons
Common vector marker and reporter gene assays

Custom Plus TaqMan Copy Number Assays

Submit user-defined human or mouse genomic targets for custom assay design, including up-front bioinformatic sequence analysis and in silico QC

Custom TaqMan Copy Number Assays for other targets of interest

Submit any masked target sequences for assay design
Submit primer/probe pair sequences for assay synthesis
Does not include up-front bioinformatic sequence analysis or in silico QC

Human and mouse TaqMan Copy Number Reference Assays are also available.

A simple method for studying study copy number variation, TaqMan Copy Number Assays feature easy assay ordering and a simple workflow to enable quick results.

TaqMan Copy Number Assays Video Brochure ›

Experimental workflow (human and animal): Find the products you need for every step

For plant samples, please visit our Agrigenomics section.

Step 1Prepare Sample
Step 2Select Assays
Step 3Amplify DNA
Step 4Analyze Data

Isolate and purify genomic DNA.

Products for Step 1: Prepare Sample

DNA Isolation Kits
Kits for isolating DNA from blood, cells, tissues, plasmids, and more.

Select or design TaqMan probes for test assays. For human samples, select an RNase P or TERT reference assay. For mouse samples, select a Tfrc or Tert reference assay.

Predesigned TaqMan Copy Number Assays
Applied Biosystems TaqMan Copy Number Assays are designed for CNV analysis and include over 1.6 million human assays with genome-wide coverage. The mouse collection includes over 180,000 assays targeting gene exons. Assays for common vector marker and reporter genes are also available for transgenic studies.

Custom and Custom Plus TaqMan Copy Number Assays
Custom and Custom Plus TaqMan Copy Number Assays enable the generation of specific, reproducible, and easy-to-interpret copy number results. They are ideal for validation studies and large sample screens. Custom Plus Assays help define human or mouse genomic targets for custom assay design, and feature the same quality as predesigned copy number assays. Custom Plus Assays undergo thorough bioinformatic analysis, including SNP and repetitive sequence masking, as well as genome specificity checks. Custom TaqMan Copy Number Assays are not limited by species—they can be designed to any target sequence. Custom Assays do not, however, include up-front bioinformatic sequence analysis or in silico QC.

TaqMan Copy Number Reference Assays
Applied Biosystems TaqMan Copy Number Reference Assays are run with predesigned, Custom Plus, and Custom TaqMan Copy Number Assays in duplex real-time PCR reactions to detect and measure copy number variation in human and mouse genomes.

Prepare a reaction plate and amplify DNA using sequence-specific primers and a TaqMan probe on an Applied Biosystems real-time PCR system. Note: TaqMan Copy Number Assays (test assays) are run simultaneously with your choice of a TaqMan Copy Number Reference Assay.

Reagents & kits

TaqPath ProAmp Master Mixes*
Applied Biosystems TaqPath ProAmp Master Mixes are versatile master mixes developed for high-throughput genotyping and copy number variation protocols requiring accurate results from samples containing PCR inhibitors. TaqPath ProAmp Master Mix includes Applied Biosystems ROX passive reference dye for lower multiplexing of up to 3 targets.

TaqPath ProAmp Multiplex Master Mix*
TaqPath ProAmp Master Mixes are versatile master mixes developed for high-throughput genotyping and copy number variation protocols requiring accurate results from samples containing PCR inhibitors. TaqPath ProAmp Multiplex Master Mix includes Applied Biosystems MUSTANG PURPLE passive reference dye for higher multiplexing of up to 4 targets.

* General purpose reagents: TaqPath master mixes are general purpose reagents manufactured in an ISO 13485–certified facility and labeled "For Laboratory Use."

Instruments & accessories

ProFlex PCR System
The Applied Biosystems ProFlex PCR System combines the reliability and performance you’ve come to expect from Applied Biosystems thermal cyclers with the flexible configuration and control features that fit how you work today. Interchangeable block formats allow you to maximize your throughput or run independent experiments concurrently.

SimpliAmp Thermal Cycler
The Applied Biosystems SimpliAmp Thermal Cycler is an easy-to use, compact, and accurate thermal cycler designed to fit every lab’s essential PCR workflow. Innovations like a responsive color touch screen and Applied Biosystems VeriFlex temperature control technology enable simple, accurate optimization.

Using data analysis software, calculate the possible copy numbers for a set of samples in a run, provide confidence values for each copy number call, and remove any outliers in your data.

Software

CopyCaller Software
CopyCaller Software enables you to perform relative quantitation analysis of genomic DNA targets using the real-time PCR data from predesigned, Custom Plus, or Custom TaqMan Copy Number Assays. The software and associated copy number assays can be used to detect and measure copy number variation of specific sequences in the human and mouse genomes.

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Step 1 : Prepare Sample

Isolate and purify genomic DNA.

Products for Step 1: Prepare Sample

DNA Isolation Kits
Kits for isolating DNA from blood, cells, tissues, plasmids, and more.

Step 2 : Select Assays

Select or design TaqMan probes for test assays. For human samples, select an RNase P or TERT reference assay. For mouse samples, select a Tfrc or Tert reference assay.

Step 3 : Amplify DNA

Reagents & kits

* General purpose reagents: TaqPath master mixes are general purpose reagents manufactured in an ISO 13485–certified facility and labeled "For Laboratory Use."

Instruments & accessories

Step 4 : Analyze Data

Using data analysis software, calculate the possible copy numbers for a set of samples in a run, provide confidence values for each copy number call, and remove any outliers in your data.

Software

Download

Resources

Product Bulletins

TaqMan Copy Number Assays

Posters

Application Notes

Analysis of Copy Number Variation: Design Pipeline and Validation of TaqMan Copy Number Assays

Background References (Web)

Copy Number Variants and Common Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies PLoS Genet 2007; 3(10): e190. doi:10.1371/journal.pgen.0030190 Authors: Estivill X., et. al.
Detection of large-scale variation in the human genome Nature Genetics 2004; 36, 949 - 951 Authors: A John Iafrate, et. al.
Large-Scale Copy Number Polymorphism in the Human Genome Science 23 July 2004: Vol. 305. no. 5683, pp. 525 - 528 Authors: Jonathan Sebat, et. al.
Global variation in copy number in the human genome Nature 444, 444-454 (23 November 2006) Authors: Richard Redon, et. al.

Citations (Web)

Differential quantification of CYP2D6 gene copy number by four quantitative real-time PCR assays Pharmacogenetics and Genomics 2010, 20:451-454. Authors: Anuradha Ramamoorthy, et al.
Recurrent microdeletions at 15q11.2 and 16p13.11 predispose to idiopathic generalized epilepsies Brain. 2010; 133:23-32; doi:10.1093/brain/awp262 Authors: De Kovel, C. G., et. al.
Copy Number Variants of GSTM1 and GSTT1 in relation to lung cancer risk in a prospective cohort study. Ann Epidemiol. 2009; 19(8):546-52 Authors: Lam, T.K., et. al.
Sample degradation leads to false-positive copy number variation calls in multiplex real-time polymerase chain reaction assays Analytical Biochemistry. 2009 Mar 15;386(2):288-90. Authors: Cukier H.N., et. al.
Origins and functional impact of copy number variation in the human genome Nature advance online publication 7 October 2009 | doi:10.1038/nature08516; Received 14 August 2009; Accepted 21 September 2009; Published online 7 October 2009 Authors: Conrad D.F., et. al.
A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures Nature Genetics. 2008 Mar;40(3):322-8. Authors: Sharp A.J., et. al.
Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes The New England Journal of Medicine. 2008 Oct 16;359(16):1685-99. Authors: Mefford H.C., et. al.

For Research Use Only. Not for use in diagnostic procedures.

* General purpose reagents: TaqPath master mixes are general purpose reagents manufactured in an ISO 13485–certified facility and labeled "For Laboratory Use."