Bio-Rad Sponsors New Version of MIQE qPCR App for Real-Time PCR and Digital PCR

Bio-Rad Laboratories, Inc. announced that it is sponsoring a new version of the MIQE qPCR app. Researchers can use the new version to validate their digital PCR (dPCR) experiments according to the recently published digital MIQE (dMIQE) guidelines (Huggett et al. 2013).

Professors Michael Pfaffl (TU Munich, Weihenstephan, Germany) and Afif Nour (LaSalle Beauvais, France) designed the original MIQE qPCR app to help researchers improve their real-time PCR (qPCR) assay protocols by making it easier to adopt a set of best practices described in an earlier publication: The MIQE guidelines: Minimum information for publication of quantitative real-time PCR experiments (Bustin et al. 2009). Progress bars in the app show the percentage of assay compliance as each item in the MIQE checklist is completed.

“We were pleased to find that the MIQE qPCR app encouraged our customers to follow the new MIQE guidelines,” said Jean-Pierre Dakkak, a laboratory equipment trading company manager.

“Researchers are really eager to learn how this app can make their life easier,” said Dr. Nour. “They report it instills confidence in the validity of every qPCR or dPCR project.”

The new updates include:

• Project-specific checklists — checklists remove unnecessary items; for example, reverse transcription items are irrelevant in DNA research
• Updated references — researchers can stay current with the latest MIQE and dMIQE literature and qPCR symposiums
• Easy export — users can save their projects and share them with colleagues

The MIQE qPCR app runs on the Apple iPhone, iPod touch, and iPad. It has been downloaded more than 6,500 times in 87 countries. To get your copy, visit http://bit.ly/MIQEapp.

Building a custom PCR assay that conforms to MIQE guidelines

If you’ve been following the news lately, you’ve likely heard about Bio-Rad’s new PrimePCR platform which provides scientists with commercial qPCR kits that are guaranteed to conform to the MIQE guidelines. If you haven’t heard about the PrimePCR platform then you can learn more by reading the article MIQE trouble free posted on the Canadian Biotechnologist.

Below we present you with a video tutorial on how you can use the PrimePCR platform to build a custom assay.

PrimePCR News Announcement

Bio-Rad Laboratories, Inc., recently announced the availability of its CFX Manager 3.0 software for real-time PCR data acquisition and analysis. By integrating with Bio-Rad’s new PrimePCR™ assays and panels, enhancing its user interface, and adding new data analysis tools, CFX Manager 3.0 now offers researchers a complete, user-friendly solution for gene expression analysis that covers everything from run setup to generating publication-quality figures.

Most real-time PCR system software involves numerous steps to get runs started and requires data export or Web upload for advanced data analysis. CFX Manager 3.0 combines streamlined run setup and sophisticated data analysis in one software package.

Key benefits of CFX Manager 3.0 include:

Quick run start: intuitive navigation, a new startup wizard, and a streamlined interface let users start collecting data with just a few clicks

Integrated PrimePCR workflow: fully integrated workflow for running and analyzing data files generated using PrimePCR assays

Guided gene expression analysis: guided plate setup wizard creates a gene expression analysis–compatible layout to assist users with experimental setup

Extraction of more information: data plotting options that are particularly well-suited for large data sets include volcano plots, clustergrams, heat maps, and scatter plots

CFX Manager 3.0 is compatible with the CFX96™, CFX96 Touch™, CFX Connect™, CFX384™, CFX384 Touch™, and MiniOpticon™ real-time PCR detection systems.

For further details about CFX Manager 3.0, please visit <a href="Bio-Rad Laboratories, Inc., today announced the availability of its CFX Manager 3.0 software for real-time PCR data acquisition and analysis. By integrating with Bio-Rad’s new PrimePCR™ assays and panels, enhancing its user interface, and adding new data analysis tools, CFX Manager 3.0 now offers researchers a complete, user-friendly solution for gene expression analysis that covers everything from run setup to generating publication-quality figures. Most real-time PCR system software involves numerous steps to get runs started and requires data export or Web upload for advanced data analysis. CFX Manager 3.0 combines streamlined run setup and sophisticated data analysis in one software package. Key benefits of CFX Manager 3.0 include: Quick run start: intuitive navigation, a new startup wizard, and a streamlined interface let users start collecting data with just a few clicks Integrated PrimePCR workflow: fully integrated workflow for running and analyzing data files generated using PrimePCR assays Guided gene expression analysis: guided plate setup wizard creates a gene expression analysis–compatible layout to assist users with experimental setup Extraction of more information: data plotting options that are particularly well-suited for large data sets include volcano plots, clustergrams, heat maps, and scatter plots CFX Manager 3.0 is compatible with the CFX96™, CFX96 Touch™, CFX Connect™, CFX384™, CFX384 Touch™, and MiniOpticon™ real-time PCR detection systems.

A novel approach for studying a large number of related gene targets in a single experiment

Pathway analysis has become an important application in life science research and drug development. Investigating how individual targets communicate and respond within complex molecular networks has helped elucidate how biological processes function at a cellular level. Academic institutions use network analysis to advance our fundamental understanding of molecular and cellular biology while pharmaceutical companies now apply pathway analysis to the development of next generation therapeutics. With the advent of genomics and personalized medicine, pathway-based analysis will become an even more valuable tool in aiding our understanding and ability to navigate signaling and disease networks. As the body of literature regarding these networks continues to rapidly increase, challenges such as assay design and therapeutics development can utilize this knowledge to increase the chance of success in research and development.

Read “Pathway Curation and Real-Time PCR Panel Design Strategy” to learn how Bio-Rad Laboratories’ pathway curation and ranking strategy ensures that the gene assays present on each real-time PCR pathway and collection panel are the most relevant for gene expression profiling based on differential expression studies and the frequency with which gene targets appear in the peer-reviewed literature.

A Sensitive Technique for Probing Small Differences in Copy Number Variation

Cytogenic studies over the past 50 years have hinted at the impact that copy number variations (CNVs) can have on phenotypic traits and disease susceptibility. Given the high incidence and clinical impact of CNVs, a precise, rapid and cost-effective method is needed for high-throughput validation of candidate CNV associations and for subsequent routing deployment in diagnostic settings. The predominant method used to validate CNVs in larger population is real-time or quantitative PCR (qPCR), which measures the relative rates of fluorescence increases during the exponential amplification of target and single-copy reference genes. The accuracy and precision of these measurements can be impacted by multiple factors including differences in amplification rates between the target and reference genes, variations in their amplification rates during qPCR, sampling error due to DNA concentration and analysis errors. Weaver et al. rigorously characterized these factors and found that systemic errors can be addressed by increasing the number of replicates to achieve the desired precision. however, the required number of replicates increases rapidly as finer discrimination is desired, with four replicates required to distinguish a twofold difference and up to 18 replicates to distinguish a 1.25-fold difference.

Read Digital PCR – Probing Copy Number Variations Using Bio-Rad’s QX100 Droplet Digital PCR System to learn more on how droplet digital PCR (ddPCR) can be used to determine small fold differences for higher-order CNV states.