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nCounter® Copy Number Variation CodeSets

Precision, Accuracy and Reproducibility

nCounter CNV CodeSets provide superior accuracy and reproducibility for studies of all sizes. Achieve better results faster and with substantially less effort than with qPCR or arrays.

Product Highlights

  • Multiplex up to 800 target regions in a single reaction
  • Just 25-minutes of hands-on time per 12 samples
  • High accuracy for multiallelic CNVs
  • Compatible with DNA from FFPE

Simplified Workflow Delivers Gold-Standard Data, Faster

With the lowest hands-on time of any copy number variation (CNV) analysis platform, the nCounter Analysis System is ideal for studies in which large numbers of samples must be tested. Built on NanoString’s unique digital detection technology, nCounter CNV CodeSets provide superior accuracy and reproducibility for studies of all sizes. With nCounter CNV CodeSets, you can achieve better results, faster, and with substantially less effort than qPCR or arrays.

TECH NOTE: Analyzing FFPE Specimens with the nCounter CNV Assay

nCounter CNV and FFPE

For many decades, pathologists have preserved tissue samples as Formalin-Fixed, Paraffin-Embedded (FFPE) blocks. Archives of well characterized FFPE samples offer great potential for advancing biomedical research. However, the fixation and embedding process modifies and degrades nucleic acids, making genomic analysis challenging.

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High Quality Data Delivered in A Simple Workflow

The CNV CodeSet workflow requires the least hands-on time of any platform commonly used for CNV analysis. In less than 25 minutes you can set up 12 reactions with no technical replicates required. And it’s simple. Just fragment your DNA and set up the hybridization – the rest is automated.

Efficiently Screen 1000's Of Samples

With the nCounter Analysis System, completing large-scale, statistically powered CNV projects has never been easier. Whether you are performing cohort studies or screening cell lines, NanoString allows you to conduct your projects more efficiently than other technologies such as arrays and qPCR. The system’s multiplexing capacity makes the most of your DNA by allowing you to assay up to 800 loci in a single tube, with as little as 300ng of starting material. With nCounter CNV CodeSets you can screen hundreds of samples against hundreds of CNVs in a few days.

nCounter® CNV Specifications

  • Custom CNV Specs
  • Cancer CN Specs
  • CNV Kits
  • Ordering Info

Custom CNV Specifications

Description Specifications
Multiplexing capability Up to 800 regions of the human genome in each reaction
Recommended amount of starting material 300ng purified genomic DNA
Sample type supported Purified genomic DNA from blood and saliva
Reproducibility 99%
Number of copies detected 0 - 4, multiallelic
Synthetic ssDNA control spike titration correlation > 0.95
nCounter Prep Station throughput 12 samples < 2.5 hours
nCounter Digital Analyzer throughput 12 samples / 4 hours (up to 72 samples per day unattended running in continuous mode)
Controls 10 invariant genomic regions, and spike-in process controls

To receive a quote, please fill out the Request Information form.

Cancer CN Specifications

Description Specifications
Genomic regions analyzed in one reaction 87 genes commonly amplified or deleted in cancer (average 3 probes/region)
Recommended amount of starting material 300ng purified genomic DNA
Sample type supported Human genomic DNA from FFPE samples, fresh or frozen tissue, or cell lines
Reproducibility 99%
Number of copies detected 0 - 4, multiallelic
nCounter Prep Station throughput 12 samples < 2.5 hours
nCounter Digital Analyzer throughput 12 samples / 2.7 hours
Controls 54 invariant genomic regions, and spike-in process controls

To receive a quote, please fill out the Request Information form.

nCounter® CNV Kits

nCounter CNV Custom CodeSets
CNV Custom CodeSets provide the ultimate in flexibility and can be designed for specific genes, organisms, and hard-to-target sequences.

Product Data Sheet: nCounter CNV Custom CodeSets


nCounter Cancer CN Assay
Highly multiplexed assay that enables copy number quantification for 87 genes commonly amplified or deleted in cancer.

Product Data Sheet: nCounter v2 Cancer CN Assay


nCounter Human Karyotype Panel
The nCounter Human Karyotype Panel allows for the simultaneous measurement of all 24 human chromosomes, including 338 individual loci.

Product Data Sheet: nCounter Human Karyotype Panel


Ordering Information

Description Quantity / Use Part Number (P/N)
nCounter Custom CNV Assay*
(includes DNA Prep Kit with spike-in plasmid control)
Increments of 192 CNV-P1CS-XXX
nCounter Cancer CN Assay 12 assays
24 assays
48 assays
96 assays
CNV-CAN1-12
CNV-CAN1-24
CNV-CAN1-48
CNV-CAN1-96
nCounter Master Kit
(all reagents, sample cartridges, and consumables necessary for processing 192 assays)
192 assays NAA-AKIT-192
nCounter Analysis System
(includes the Prep Station and Digital Analyzer)
1 NCT-SYS-120
Additional nCounter Prep Station 1 NCT-PREP-120
Additional nCounter Digital Analyzer 1 NCT-DIGA-120

To receive a quote, please fill out the Request Information form.


Request Information | E-mail us: info@nanostring.com | Call us: 1 888 358 6266