Reaction Miniaturization - A Trend in Genomics

December 29, 2017 by Paul Berning Leave a Comment

Who is asking about reaction miniaturization?

When it comes to sample preparation for NGS and PCR, there is no bigger buzz word in the market right now than “Miniaturization”. Who is talking about it? What are the benefits?

My tenure at FORMULATRIX® has allowed me the privilege of interacting with many researchers. Our customers study everything from mice, to plant pollen, to my personal favorite, bacterial growth to track where individuals have traveled. In each individual project, scientists aim to understand the most specific details regarding their sample, which are the actual sequences of DNA and RNA from their target organisms.

What resources are available to my lab, if we wish to conserve reagents through reaction miniaturization?

These days, many companies offer reagents that can be used to prepare samples for NGS and PCR. There are almost too many to count! Commonly, reagent manufacturers will provide SOP’s that walk you through the steps required to begin developing a protocol for your experiment. Also, many vendors supply, and offer application support, for application specific hardware that allows for analysis of reactions prepared with their chemistry.

Basically, these experiments allow researchers to either quantify the abundance of target DNA/RNA molecules (qPCR) or to sequence the DNA/RNA present in a given sample (NGS). Sample preparation includes combining purified samples and various reagents at precise ratios. Hardware to facilitate this “sample preparation workflow” can usually not be obtained directly from reagent vendors. Companies like FORMULATRIX fill this market gap with instruments that assist researchers in processing or preparing their samples prior to analysis.

FORMULATRIX has worked hard to help researchers around the world learn how to perform sample preparation to effectively miniaturize reactions, and can now provide a wealth of support in the form of references, and even SOPs for quarter volume reactions. Since FORMULATRIX does not provide reagents, we have no problem helping our customers get 4x or even 12x as many reactions out of their reagent kits for a far reduced cost per sample.

What is “Reaction Miniaturization”?

Reaction Miniaturization: The reduction in scale of genomics reaction volumes in order to achieve cost savings. Often, there is a trade-off between data quality and reaction volume that must be characterized to elucidate the optimal reaction volume for a given experiment.

Although reducing the volumes of your reactions in genomics workflows can sound intimidating, it really does not have to be complicated. When looking at the SOP provided by the manufacturer of your reagents, simply divide their recommended volumes by 2, 4, or even 10 and dispense them at these volumes instead of the ones recommended. See the example below for the case of the SMART-Seq v4 cDNA Synthesis Kit from Takara Bio. Researchers utilizing this ¼ volume SOP are saving more than $2,000 per 96-well plate in their single-cell analysis workflow.

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Table 1. Miniaturized Reaction Volumes for Illumina Nextera XT Sample Preparation

If you are interested in reaction miniaturization for your single-cell analysis workflow, please reach out to me at paul.berning@formulatrix.com I can also provide a list of reference customers, an application note proving that the sequencing data is comparable between full and quarter volume reactions, and also various webinars of researchers describing their process and cost savings when moving to ¼ volume reactions. Working with other scientists can help you approach validation of miniaturized reactions in order to ensure that your reads and sequencing depth are sufficient to answer your specific biological questions.

Why doesn’t everyone miniaturize their reactions?

Good Question! Let’s look back at this math. As you can see, 1.25µL is listed in the experiment above. For some companies that sell equipment to support the “sample preparation workflow” transferring that low of a volume of liquid reproducibly can be a real issue. Keeping the ratios between samples and various reagents consistent through precise liquid handling is critical if you aim to compare data between samples. To help researchers dispense such low volumes precisely and with highly viscous reagents, FORMULATRIX offers the MANTIS® Liquid Handler and TEMPEST® Liquid Handler. These instruments utilize patented positive displacement technology to facilitate reaction miniaturization by dispensing volumes as low as 100nL at 3%CV’s and with only a 6µL dead volume. Nothing says quality and costs savings more than the previous sentence. I have heard researchers say that they do not run enough samples to miniaturize, or that they have too many to validate a new process. I assure you, wherever you are on this spectrum, a cost analysis can be very surprising. And of course, you can reach me for a cost analysis at any time. Happy Miniaturizing!

 

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About the Author

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Paul Berning joined FORMULATRIX as the Midwest Account Manager in August of 2016.  Prior to working at FORMULATRIX, Paul spent four years at Integrated DNA Technologies (IDT), where he worked directly with various liquid handling platforms.  Paul won employee of the year at IDT in 2015 for the method development and optimization of their liquid handlers. Paul has performed over 100 demonstrations of the MANTIS and TEMPEST Liqiud Handlers, helping researchers to refine their approach to genomic sample preparation along the way.

Posted in: Liquid Handling, Mantis

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