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PyroMark Q24 Advanced Software

Analysis software for upgrading PyroMark Q24 systems to PyroMark Q24 Advanced
  • Advanced technology, software, and chemistry for long sequence runs
  • Quantitative methylation analysis at consecutive CpG or CpN sites
  • Improved quantification of sequence variations at any sequence position
  • Easy and improved base calling functionality
  • Assay versatility on the same instrument and in the same run
PyroMark Q24 Advanced features improved Pyrosequencing technology to provide even better real-time sequence-based detection and quantification than before. PyroMark Q24 Advanced Software enables users to upgrade their existing PyroMark Q24 systems and take advantage of these new benefits and features. The software now has 4 analysis modes: AQ (allele quantification), SNP (genotyping), CpG (methylation at CpG or CpN sites), and SEQ (base-calling of unknown sequences).
Cat No./ID: 9022779
PyroMark Q24 Advanced Software
Analysis software for upgrading PyroMark Q24 systems
PyroMark Q24 Advanced Software is intended to be used only in combination with QIAGEN kits indicated for use with the PyroMark Q24 Advanced for the applications described in the kit handbooks. If PyroMark Q24 Advanced Software is used with other than QIAGEN kits, it is the users responsibility to validate the performance of such product combination for any particular application.

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Quantification of CpN methylation.
The new CpN mode of Pyromark Q24 Advanced enables methylation analysis of cytosine residues that are not part of CpG sites. Each of these positions can be selected individually. This example shows the analysis of a CpN site (CpA in this case) in the first position, followed by 2 classical CpG sites.
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Additional warning information.
PyroMark Q24 Advanced Software provides warning information in the event that a problem occurs during the run or the system detects an inconsistency with an assay in a particular well. Such warnings might relate to only to a certain position or be relevant for the whole run. The quality label for an affected well will change from blue to yellow, indicating check quality and that the assay might still be acceptable, or to red, indicating failed quality and that the assay has failed.
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Troubleshooting recommendations.
PyroMark Q24 Advanced Software also offers a Warning Info option. This new information window includes a brief description of each warning, along with recommendations on how to solve the issue for subsequent runs.
Performance
Quantification of CpN methylation
The new CpN mode of PyroMark Q24 Advanced now enables methylation analysis of cytosine residues that are not part of CpG sites. Analysis of CpN and CpG sites can be performed together in a single Pyrosequencing reaction. Each of these positions can be selected individually in the software during the run setup (see figure Quantification of CpN methylation).

Convenient and improved tools for run analysis
The PyroMark Q24 Advanced analysis software is user-friendly and intuitive, and now provides convenient and improved tools for run analysis. If a problem occurs during the run, or if the system detects an inconsistency with an assay, the software provides specific warning information for each individual well (see figure Additional warning information). A "Warning Info" button now gives access to additional information about the warning along with recommendations for troubleshooting and preventing its occurrence in subsequent assays (see figure Troubleshooting recommendations).

Longer Pyrosequencing runs and improved accuracy
PyroMark Q24 Advanced features improved chemistry and instrument operation algorithms that significantly increase the assay read length and accuracy of the base calling functionality, enabling easy analysis of long de novo sequencing runs. Assay read length was previously limited by background peaks and reduced light signals in the sequencing reaction. The updated chemistry and algorithms of PyroMark Q24 Advanced reduce these background peaks, thereby increasing read length and reliability. Depending on the sequence to be analyzed, highly accurate read lengths of 140 or more bases can be obtained in just a single PyroMark Q24 Advanced reaction (see figure Long de novo sequencing runs).

Improved methylation analysis at any position
PyroMark Q24 Advanced enables improved methylation quantification in long sequence runs at any sequence position. Previously, analysis of methylation sites further away from the sequencing primer could be uncertain, but now with longer read lengths and higher accuracy, methylation quantification is highly reliable throughout the entire sequencing run (see figure Analysis of 16 CpG sites in a long sequence run).

Improved sequencing accuracy in homopolymers
Bisulfite conversion in DNA methylation analysis leads to frequent poly T stretches in the nucleotide sequence, and analysis of CpG sites directly after such T homopolymers has previously been challenging due to uncertain quantification of the light signal at these sites. The increased accuracy of PyroMark Q24 Advanced enables reliable quantification of CpG methylation behind and even within a stretch of 8 T nucleotides (see figure Improved methylation quantification in homopolymers).

Analysis of mutations over long sequences
PyroMark Q24 Advanced also provides reliable quantification of multiple polymorphisms in a single assay. Since single nucleotide polymorphisms (SNPs) and other mutations are often not located close to one another, traditional Pyrosequencing chemistry usually requires separate assays for each mutation site to be analyzed. The new chemistry of PyroMark Q24 Advanced allows much longer runs, enabling reliable analysis of more than one mutation or SNP in the same run (see figure Quantitative mutation analysis in long sequence runs).
Principle
PyroMark Q24 Advanced Software enables users to upgrade their existing PyroMark Q24 systems and take advantage of the new benefits and features of PyroMark Q24 Advanced. The software is compatible with PyroMark Q24 instruments running firmware 3.0 or higher. Please refer to the Upgrade to PyroMark Q24 Advanced  resource in the "Resources" tab for upgrade instructions and details concerning compatibility.
Applications
Pyrosequencing is becoming increasingly important for research applications in a variety of disciplines. Whether examining drug-resistance development in pathogens, the role of epigenetic DNA methylation in gene expression regulation, genetic markers for specific phenotypes in livestock, or polymorphisms in forensic samples of mitochondrial DNA, the PyroMark Q24 Advanced enables powerful and versatile analysis of genetic and epigenetic variation. In addition, because Pyrosequencing integrates sequence detection and quantification, the enhanced analysis resolution can lead to new discoveries.

Product comparison
  PyroMark Q24 Advanced PyroMark Q24
Throughput 1–24 samples 1–24 samples
Running volume 25 µl 25 µl 
PCR requirements 5–10 µl
(~0.5–3 pmol of product)
5–10 µl
(~0.5–3 pmol of product)            
Read length (assay- and
sequence-dependent)
10–140 bp or more 10–80 bp
Application software PyroMark Q24 Advanced SW
(requires firmware 1.5.6903 or higher)
PyroMark Q24 SW 2.0
Software functionality SEQ (de novo sequencing)
CpG/CpN methylation
SNP
AQ
SQA (de novo sequencing)
CpG methylation
AQ/SNP 
 
Main applications Complex mutation analysis
Epigenetics (CpG and CpN analysis)
Resistance typing and microbial ID  
Mutation analysis
Resistance typing 
 
Compatible reagents PyroMark Q24 Advanced Reagents
PyroMark Q24 Advanced CpG Reagents  
PyroMark Q24 Gold Reagents 
Sensitivity 2% mutation
98% wt  
2% mutation
98% wt  
Important: PyroMark Q24 Software cannot be used with PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents. PyroMark Q24 Advanced Software cannot be used with PyroMark Gold Q24 Reagents. Using the incorrect reagent and software combination will result in incorrect reagent dispensations and lead to inaccurate results.

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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0003
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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0004
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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0005
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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0006
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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0007
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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0008
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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0009
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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0010
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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0011
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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0012
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Instrument methods file for use with PyroMark Q24 Advanced Software, PyroMark Q24 Advanced Reagents or PyroMark Q24 Advanced CpG Reagents, and PyroMark Q24 Cartridges marked with method 0013
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Files for upgrading existing PyroMark Q24 instruments to firmware 1.5.6903
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Operating Software (1)
Files for upgrading existing PyroMark Q24 instruments to firmware 1.5.6903
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Application Notes (1)
A Pyrosequencing method for the forensic identification of tissue source using QIAGEN’s PyroMark Q24 Advanced system.
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