ProNex® DNA QC Assay BioRad CFX96™

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Evaluate Quality and Quantity of gDNA from Degraded Samples

  • Human-specific, multiplexed probe-based qPCR assay with internal positive control
  • Detect 75bp, 150bp and 300bp human genomic DNA sequences
  • Evaluate your samples for amplifiability and predict downstream assay success

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Catalog number selected: NG1004

$ 1,181.00
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This product can be added to Helix

This product is available through the Promega Helix onsite stocking program. We offer numerous convenient solutions to meet your lab's needs.

Learn more about the Helix Collection »

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This product is available under our Catalog (FT) program - Learn More
ProNex® DNA QC Assay BioRad CFX96™
200 reactions
$ 1,181.00
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Qualify and Quantify Your Samples in a Single Reaction

The ProNex® DNA QC Assay evaluates the quality and quantity of genomic DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples or other potentially degraded DNA sources. It is a human-specific, multiplexed probe-based quantitative polymerase chain reaction (qPCR) assay that may also be used to evaluate the ratio of circulating cell-free DNA (ccfDNA) to higher molecular weight genomic DNA in plasma samples. The multiplex assay detects 75bp, 150bp and 300bp human genomic DNA sequences, and it includes an internal positive control (IPC) to test for false-negative results that may occur in the presence of PCR inhibitors.

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One Step Toward a Better NGS Workflow

Using the ProNex® DNA QC Assay to determine the amplifiability and quantity of your precious sample can save you time and money.

Comparison of Quantitation and Quality Control Features

Not all QC analysis is the same. Only the ProNex® DNA QC Assay includes everything you need, with minimal sample usage.

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Downstream Predictive Value for Degraded Samples

Due to the inherent variability of FFPE DNA quality, knowing the quantity of DNA alone is not reliably predictive of downstream assay success. The ProNex® DNA QC Assay allows you to determine the amount of amplifiable DNA in a sample. You can use the ProNex® DNA QC Assay to evaluate if a sample is suitable for downstream analysis using techniques such as next-generation sequencing (NGS) or droplet digital PCR (ddPCR).

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Four separate FFPE tumor tissue samples of varying age and fixation times from 4 different tissue types (breast, lung, colon and rectal) were purified with three different methods for a total of 31 extractions. Each DNA Sample was quantified using a single-target qPCR assay and normalized for 10ng input into the Swift Biosciences Accel-Amplicon™ 56G Oncology Panel. After sequencing, samples were retroactively processed with the ProNex® DNA QC Assay and a degradation ratio (75/300bp quantitation ratio) was calculated. Samples with high degradation ratios were clearly correlated with poor coverage uniformity of sequencing, enabling users of the DNA QC Assay to predict downstream performance.

Evaluate ccfDNA Samples for gDNA Contamination

Genomic DNA contamination of ccfDNA can mask low level mutations. You can use the ProNex® DNA QC Assay to measure gDNA contamination in ccfDNA, allowing you to assess sample quality and suitability for downstream processing.
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ccfDNA was extracted from a serum sample. DNA was quantified with the ProNex® DNA QC Assay, and the ratio of 75:300bp concentrations was measured. Low ratios (close to 1) indicate gDNA contamination, whereas ratios >10 indicate extremely clean ccfDNA. “Contaminated” indicates sample as extracted without cleanup. “Clean” sample was processed with the ProNex® Size-Selective DNA Purification system to perform a dual-sided size selection and removal of DNA greater than 300-400bp. The increase in 75:300bp ratio is a result of the removal of gDNA.
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To verify correlation of 75:300bp ratios generated by the ProNex® DNA QC Assay, samples shown in figure were run on the Agilent 2200 TapeStation System. The clean sample trace (teal) is equivalent to a high ratio on the ProNex® DNA QC Assay, whereas the contaminated sample trace (bronze) equates to a low ratio.

Process Your Data with the ProNex® DNA QC Assay Analysis Software

The ProNex® DNA QC Assay Analysis Software will process qPCR data generated with the ProNex® DNA QC Assay Kits. The software includes calculations and methods to define values for the following:

  • Standard Curves (acceptable r2 and slope values)
  • Sample quantity (based on the Standard Curves)
  • Sample quality (possible inhibition, contamination, or degradation)

The ProNex® DNA QC Assay Analysis Software can import results from the Applied Biosystems® 7500, 7500 Fast or QuantStudio™ 6 Flex Real-Time PCR Systems, and the BioRad CFX96 Touch™ Real-Time PCR Detection System.

 

Download Analysis Software
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Protocols

Complete Protocol

Specifications

You are viewing: NG1004 Change Configuration

What's in the box?

Item Part # Size Concentration Available Separately

ProNex® DNA QC Dilution Buffer

 NG101A 2 × 1.5ml

2X ProNex® DNA QC Master Mix

 NG121A 2 × 1.1ml

20X ProNex® DNA QC Primer-Probe-IPC Mix, BioRad CFX96™

 NG151A 1 × 220μl

ProNex® DNA QC gDNA Standard

 NG302A 1 × 150μl 50ng/μl

Nuclease-Free Water

 P119A 2 × 1,250μl View Product

SDS

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Certificate of Analysis

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Use Restrictions

For Research Use Only. Not for Use in Diagnostic Procedures.

Storage Conditions

BB

Patents and Disclaimers

Dye compounds in this product are sold under license from Biosearch Technologies, Inc., and protected by U.S. and worldwide patents either issued or in application. The license does not include rights for human IVD use.

Specifications

You are viewing: NG1005 Change Configuration

What's in the box?

Item Part # Size Concentration Available Separately

ProNex® DNA QC Dilution Buffer

 NG101A 8 × 1.5ml

2X ProNex® DNA QC Master Mix

 NG121A 8 × 1.1ml

20X ProNex® DNA QC Primer-Probe-IPC Mix, BioRad CFX96™

 NG151A 4 × 220μl

ProNex® DNA QC gDNA Standard

 NG302A 4 × 150μl 50ng/μl

Nuclease-Free Water

 P119A 8 × 1,250μl View Product

SDS

Search for SDS

Certificate of Analysis

Search by lot number

Use Restrictions

For Research Use Only. Not for Use in Diagnostic Procedures.

Storage Conditions

BB

Patents and Disclaimers

Dye compounds in this product are sold under license from Biosearch Technologies, Inc., and protected by U.S. and worldwide patents either issued or in application. The license does not include rights for human IVD use.

Resources

Articles

Citations

Posters

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Frequently Used With

ProNex® Size-Selective Purification System

Magnetic resin-based purification of dsDNA for NGS, PCR and general molecular biology applications.

NG2001, NG2002, NG2003

ReliaPrep™ FFPE gDNA Miniprep System

Fast, manual method for purifying DNA from FFPE tissue without using organic solvents.

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Maxwell® RSC DNA FFPE Kit

Extracts DNA from FFPE tissue samples using the Maxwell® RSC Instrument.

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Maxwell® RSC ccfDNA Plasma Kit

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