Off to a good start: Designing NGS panels and dPCR assays for microbial applications
Microbiologists are using digital PCR (dPCR) and next-generation sequencing (NGS) to obtain a deeper understanding of microbial communities. But are you making the best use of these molecular methods? In “How to capture any microbial target with dPCR and NGS,” learn how to find or design effective dPCR assays and NGS panels for comprehensive analysis of diverse targets and challenging species – so your project gets off to a good start and an even better end.
You’re not alone. Every microbiologist has banged their head against the wall at some point this year, this month, this day. Microbial projects with dPCR and NGS are intriguing, but sometimes, they can also make you want to throw all your Eppis out the window, flush your data down the toilet and shut yourself in the -80°C freezer.
- How do you obtain assays for your specific microbial target?
- How do you tackle less-characterized species and complex communities?
- How do you avoid incomplete and imperfect data?
- How can you stop wasting resources on a tightening budget?
If you’re going to work smarter, you need to do so right from the start. This means finding or designing the right NGS or dPCR tools to support your research journey.
With the help of four QIAGEN experts, discover how to perfectly match your microbial project to effective dPCR assays and NGS panels.
Here’s a micro preview of what you’ll learn in the webinar.
- How to handle microbial diversity and less-characterized organisms – Even within the same species, genetic variations can complicate the design of reliable assays. For example, standard assays designed for E. coli might miss important pathogenic strains due to subtle genetic differences.
Customizable tools for dPCR and NGS help you target specific regions, strains or genetic variants. Use free online tools like GeneGlobe to find or design assays tailored to your microbial targets and ensure specificity even in the face of genetic diversity. GeneGlobe offers knowledge of intricate networks, plenty of pre-designed products and intuitive tools for creating custom assays and panels for bacterial, fungal or viral targets. - How to get more complete NGS data – Many NGS panels fall short when analyzing microbial genomes because they’re designed against one or a limited set of reference sequences. For example, for HepC, there are some genotypes of the same species that differ in genomic content by over 30%. If you design your panel against just one sequence, your panel will perform poorly against most HepC variants. For tuberculosis, there are lineages with entire genes that are absent from other lineages. If you don’t include most of these, you will have gaps in your genome. To fight these shortcomings, use ready-made hybrid-capture panels that have been designed against thousands of sequences at the same time to fully cover the diversity of a bacterial or viral genome. Or consider custom NGS panels to achieve comprehensive coverage against the targets you need. With custom panels, you also avoid wasting reads on irrelevant species or regions, making your sequencing more cost-efficient.
- How to get more precise dPCR data – You use digital PCR because you strive for maximal sensitivity, specificity and precision. However, closely related strains, off-target amplification and low-abundance targets in complex matrices can all get in the way of fine resolution and accuracy.
There are steps you can take to overcome these obstacles. Check if ready-made assays exist for your target of interest. On the GeneGlobe platform, you can find hundreds of lab-tested assays for applications in human disease, wastewater, food testing and many more. If no assay dedicated to your species exists, then avoid off-target amplification by creating your own dPCR assay. Benefit from unique design tools, such as those on the GeneGlobe platform, that use sophisticated algorithms to include off-target information and the chance to optimize sensitivity and specificity, even from closely related species.
Simply watch the webinar “How to capture any microbial target with dPCR and NGS” hosted by QIAGEN on 29 January and apply your learnings to your dPCR and NGS experiments for immediate improvements.
About the author of this blog:
QIAGEN is a long-term partner of FEMS and is a Bronze Sponsor of the FEMS MICRO 2025: Congress & Exhibition. They provide products and services that enable researchers to gain valuable insights from any biological sample – from basic research to clinical healthcare. They have kindly sponsored this FEMSmicroBlog post to help FEMS in its mission to support the microbiology community. If your company or organization would like to sponsor FEMS, please reach out to us to discuss how we can tailor our partnership.