Copy Number Variation (CNV) with Real-Time PCR

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 with 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.

TaqMan® Copy Number Assays Video Brochure

The TaqMan® Copy Number Assay Product 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 genes assays
Custom Plus TaqMan® Copy Number Assays
- Submit user-defined human or mouse genomic targets for custom assay design including upfront 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 upfront bioinformatic sequence analysis or in silico QC

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

As the simplest method available to study copy number variation, the TaqMan® Copy Number Assays feature easy assay ordering and a simple workflow to enable quick results.

Experimental Workflow: Find the Products You Need for Every Step

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 assay. For human samples, select RNase P or TERT for reference assay. For mouse samples, select Tfrc or Tert for reference assay.

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

		Custom and Custom Plus TaqMan® Copy Number Assays Custom Plus TaqMan® Copy Number Assays and Custom 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 upfront bioinformatic sequence analysis or in silico QC. design assays

		TaqMan® Copy Number Reference Assays TaqMan® Copy Number Reference Assays are run with predesigned, Custom Plus, and Custom TaqMan® Copy Number Assays in a duplex real-time PCR reaction to detect and measure copy number variations in the human and mouse genomes. TaqMan® Copy Number Reference Assay, Human, RNase P, 750 Reactions TaqMan® Copy Number Reference Assay, Human, RNase P, 3000 Reactions TaqMan® Copy Number Reference Assay, Human, TERT, 750 Reactions TaqMan® Copy Number Reference Assay, Human, TERT, 3000 Reactions TaqMan® Copy Number Reference Assay, Mouse, Tfrc, 750 Reactions TaqMan® Copy Number Reference Assay, Mouse, Tfrc, 3,000 Reactions TaqMan® Copy Number Reference Assay, Mouse, Tert, 750 Reactions TaqMan® Copy Number Reference Assay, Mouse, Tert, 3,000 Reactions

Prepare reaction plate and amplify DNA using sequence specific primers and TaqMan® probe on an Applied Biosystems® Real-Time PCR System. Note: TaqMan® Copy Number Assays (test assay) are run simultaneously with the choice of TaqMan® Copy Number Reference Assays (reference assay).

Reagents & Kits

		TaqMan® Genotyping Master Mix Obtain unrivaled cluster resolution for unambiguous SNP allelic discrimination. Optimized for end-point fluorescence detection in genotyping applications. TaqMan® Genotyping Master Mix, Quick Reference Card TaqMan® Genotyping Master Mix Protocol TaqMan® Genotyping Master Mix, Mini-Pack (1mL) TaqMan® Genotyping Master Mix, 1-Pack (1 x 10 mL) TaqMan® Genotyping Master Mix, 1 Bulk Pack (1 x 50 mL) TaqMan® Genotyping Master Mix, 2-Pack (2 x 10 mL) TaqMan® Genotyping Master Mix, Multi-Bulk Pack (2 x 50 mL)
Instruments & Accessories

		StepOnePlus™ Real-Time PCR System The StepOnePlus™ Real-Time PCR System makes it simple and easy to get publication-ready high-quality real-time PCR results on day one. This remarkably simple 96 well, 4 color, real-time PCR system is designed with a user-friendly, yet powerful, interface for researchers of all experience levels. StepOnePlus™ Real-Time PCR System with Laptop StepOnePlus™ Real-Time PCR System with Tower StepOnePlus™ Real-Time PCR System StepOnePlus™ Real-Time PCR System, 1-year Extended Warranty StepOnePlus™ Real-Time PCR System, 3-year Extended Warranty

		StepOne™ Real-Time PCR System Applied Biosystems’ 48-well low-throughput real-time PCR instrument makes it simple and easy to get publication ready high quality data on day one. This remarkably simple real-time PCR system is designed with a user-friendly, yet powerful, interface for researchers new to real-time PCR. StepOnePlus™ Real-Time PCR System with Laptop StepOnePlus™ Real-Time PCR System with Tower StepOnePlus™ Real-Time PCR System StepOnePlus™ Real-Time PCR System, 1-year Extended Warranty StepOnePlus™ Real-Time PCR System, 3-year Extended Warranty

		7500 Fast Real-Time PCR System The 7500 Fast Real-Time PCR System offers maximum performance in the minimum time. Fully optimized for Fast cycling, the 7500 Fast delivers high-quality results in as little as 30 minutes. 7500 Fast Real-Time PCR System with Dell™ Notebook 7500 Fast Real-Time PCR System with Dell™Tower Tower Computer Kit for 7300/7500/7500 Fast Real-Time PCR Systems Notebook Computer Kit for 7300/7500/7500 Fast Real-Time PCR Systems 7500 Fast System Upgrade Kit 7500 Fast System SDS v1.4 21 CFR Part 11 Module High Resolution Melt (HRM) Software v2.0

		7500 Real-Time PCR System The 7500 Real-Time PCR System is a powerful platform for labs requiring superior performance and maximum dye versatility. This third generation platform features an innovative optical system that enhances sensitivity and lets you access a broader range of fluorophores. The variable excitation capability allows greater sensitivity for longer wavelength (red) dyes. 7500 Real-Time PCR System with Dell™ Notebook 7500 Real-Time PCR System with Dell™Tower Tower Computer Kit for 7300/7500/7500 Fast Real-Time PCR Systems Notebook Computer Kit for 7300/7500/7500 Fast Real-Time PCR Systems 7500 Fast System Upgrade Kit 7500 System SDS v1.4 21 CFR Part 11 Module


		7900HT Fast Real-Time PCR System The 7900HT Fast Real-Time PCR System combines 384-well plate compatibility with fully automated robotic loading—and now also offers optional Fast real-time PCR capability. Acknowledged as the gold standard in real-time PCR, the 7900HT system combined with TaqMan® Genomic Assays enables you to achieve unprecedented throughput and flexibility, allowing you to pursue projects beyond the scope of previous real-time instruments. ABI PRISM® 7900HT Sequence Detection System User's Manual 7900HT Fast Real-Time PCR System with 384-Well Block Module 7900HT Fast Real-Time PCR System with 384-Well Block Module and Automation Accessory 7900HT Fast Real-Time PCR System with Standard 96-Well Block Module 7900HT System Automation Accessory Upgrade 7900HT System Standard 96-Well Block Upgrade Kit 7900HT System Standard 384-Well Block Upgrade Kit 7900HT System Fast 96-Well Block Upgrade Kit 7900HT Fast Real-Time PCR System with Fast 96-Well Block Module 7900HT Fast Real-Time Service Upgrade 7900HT Fast Real-Time Service Upgrade with Computer

		ViiA™ 7 Real-Time PCR System The ViiA™ 7 Real-Time PCR System combines all the qPCR features you want in a single high performance instrument to optimize your productivity. With a simplified workflow, intuitive software, touch-screen interface, and one-button protocols for error minimization, this system offers exceptional reproducibility with minimal well-to-well and instrument-to-instrument variation. Full compatibility with any standard or Fast-cycling 384- or 96-well plates and TaqMan® Array Microfluidic Cards and Assays makes high-productivity real-time PCR accessible to any size lab. Applied Biosystems® ViiA™ 7 Real-Time PCR System with 384-Well Block Applied Biosystems® ViiA™ 7 Real-Time PCR System with TaqMan® Array Block Applied Biosystems® ViiA™ 7 Real-Time PCR System with 96-Well Fast Block Applied Biosystems® ViiA™ 7 Real-Time PCR System with 96-Well Block ViiA™ 7 System Automation Accessory Robot (100–240 V) 384-Well Block Upgrade Kit TaqMan® Array Upgrade Kit 96-Well Fast Block Upgrade Kit 96-Well Block Upgrade Kit HRM Software Module for ViiA™ 7 System 21 CFR Part 11 Software Module for ViiA™ 7 System

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 Assay experiments. 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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Literature

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 intended for any animal or human therapeutic or diagnostic use.