qPCR with Cambridge Consultants

Delivering rapid iteration, optimisation and scalability of a high quality qPCR workflow

Introduction

Cambridge Consultants is a world leader in disruptive innovation and technology-based consulting. Formed in 1960, it has delivered thousands of ground-breaking technology projects to clients all around the world in multiple industry sectors. Today it has over 800 staff globally across 6 sites and manages over 400 projects every year.

Cambridge Consultants started working with Synthace in 2016 as they recognised the need for a scalable, robust tool to streamline their lab operations. With such a high turnover of projects their labs need to be flexible and able to develop and execute robust new protocols quickly. Cambridge Consultants chose Synthace as Antha provides true end-to-end connectivity of devices and data to run protocols effectively, particularly complex multi-factorial experiments with many varying conditions. 



Rapid and Flexible Automation Workflow Development

One example where Antha has made a big impact is in the rapid and flexible development of liquid handling automation workflows with its library of standard elements.

The Standard Element Set provides the user with a number of liquid handling functionalities that would regularly be carried out in a lab during manually executed protocols. For example; aliquoting, serial diluting or mixing of liquids together into target labware. Through a visual user interface (UI) different experimental steps can be wired together into logical workflows.

Whilst Antha provides a high-level abstraction for the user with regards to programming liquid handling automation platforms it also provides the optional interface for optimising the resulting workflows with low level parameter control, for example, how a liquid should be handled (its liquid handling policy) or whether to use multichannel or single channel pipetting.

The Antha UI allows for the rapid prototyping of experimental workflows whilst supporting the flexibility required for downstream optimisation of a liquid handling workflow, all of which can be evaluated in silico prior to running any physical experiments in the lab.

The Cambridge Consultants team used the Antha software in conjunction with a Gilson Pipetmax automated liquid handling platform (Figure 1) to prototype and optimise the liquid handling automation of qPCR protocols for a specific client project with the Antha Standard Element Set (Figure 2).

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Figure 1. Laboratory set up. All automated experimental set ups were carried out on a Gilson Pipetmax housed in a sterility hood, alongside a Quant Studio 5 qPCR thermocycler, collectively controlled via the Antha software.

Figure 2. The Antha Workflow Editor. Antha provides a sand box environment, the Workflow Editor, for rapid liquid handling workflow development utilising the Standard Element Set.

An example Antha qPCR workflow developed to address Cambridge Consultants’ specific assay requirements, incorporating sample re-suspension, splitting of positive and negative control samples for storage and future re-use, serial dilution of qPCR standards, aliquoting of qPCR master mix and final qPCR reaction set up.

 

While this is a well-known technique, the Cambridge Consultants team had some specific needs, requiring the flexibility to rapidly iterate and optimise, that made it more challenging to develop this workflow through the vendor’s software platform. In particular:

  • Consistently high throughput to run many thousands of samples during the project.

  • Fast execution speed to process up to a thousand unique samples per day.

  • The ability to add custom sample handling steps upstream of qPCR reaction set up (Figure 2).

  • Robust sample traceability to manage the data and its provenance (Figure 3).

  • Excellent reproducibility to allow optimisation of underlying process (Figure 4).

  • Minimising execution costs given the scale of testing (reduced FTE time, Figure 6).

The results of the experiments (Figure 5) are used as part of formal acceptance testing therefore liquid handling reliability is essential (especially cross-contamination control) along with clear traceability where both the liquid handling platform and analytic device are under the control of a single software solution.

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Figure 3. Antha Sample Tracking. Samples can be tracked from provenance to end point reaction via the Plate Prep, Deck Layout or Execution Graph views. An example of the liquid handler deck layout for a qPCR run is demonstrated here.

Figure 4. Antha driven reaction reproducibility. Cycle threshold values generated from Antha automated (blue) and manual (red) qPCR reaction set up. The automated process gives statistically significant different results to the manual process (p < 0.05) for all non-blank replicates. The blank sample contains a starting solution common to Samples A-D retrieved from the processing site whilst the No Template Control was prepared with Nuclease free water only. Higher CT values for the no template control and a lower CT value for samples indicates the automated process provides better contamination control and can recover more DNA from the samples under test, overall giving improved sensitivity.

 
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 Results and Discussion

Manual vs. Automation

 

Manual approach

Initially, a traditional manual protocol was developed using 384 well plates, hand pipetting and direct user operation of the qPCR instrument (an Applied Biosystems QuantStudio 5). This approach quickly showed its limitations. For example,

  • Processing a 384 well plate takes a skilled molecular biologist up to 2 hours, limiting throughput to a few hundred samples a day.

  • Hand pipetting introduces variability in sample manipulation and the potential for process errors, particularly after long periods of work. Plates are typically only partially filled to avoid human error, but this impacts throughput.

  • Scaling requires training new users, which can take 2 or 3 practice runs before they are confident with a complex protocol. This also requires two people – the trainee and the trainer.

  • Sample processing time scales unpredictably with complex sample sets and replicates. The experimental design becomes limited by the ability of the human brain to organise it, not the optimal set up for throughput.

  • Data is only available locally on the qPCR instrument, making analysis and management laborious.

Antha approach

Antha software was deployed to automate the entire qPCR workflow. This included interpretation of a qPCR experimental design input, automated dilutions, plate setup and execution of analytical run (Figure 2) Synthace’s specialist team of forward-deployed engineers spent time with Cambridge Consultants’ scientists in their labs implementing a specialist workflow in Antha that would allow multiple qPCR experiments to be run at the push of a button.

Liquid handling actions were performed on a Gilson Pipetmax robotic platform situated inside a sterility hood with the qPCR run on the same Applied Biosystems QuantStudio 5 instrument as the manual workflow (Figure 1). Both devices were controlled by the Antha platform as part of a single workflow. Input materials to the workflow are provided in a non-standard format so custom plate designs were created in hardware and software to allow the liquid handler to operate directly on the input materials.

By using Antha, the Cambridge Consultants team made a step change in their productivity (Figure 6).

  • A complete 384-well plate can be processed in 2 hours with a hands-on time of only 25 minutes saving Cambridge Consultants nearly 2 hours of hands on time per run (and associated staff costs) and eliminating manual pipetting errors (Figure 6).

  • Data has full traceability from sample to result (Figure 3) and is available in the Cloud so can be accessed and analysed anywhere.

  • The performance of the protocol is improved, with less background contamination (a key requirement) and higher signals from samples (Figure 4).

  • The scientific team has high confidence in the data and is freed from the laborious and repetitive execution of protocols to focus on data analysis and experimental design.

  • With Antha, up to four 384 well plates of qPCR reactions can be prepared within a day providing robust results that allow confident process assessment and evaluation (Figure 5).

 

Experimental Results and ROI

Figure 5. Effect of process treatments on DNA concentration at process completion. Each process treatment shows absolute DNA quantification from 9 independent reactions each performed in triplicate across 5 test conditions. With controls (not shown) and standards the total number of experiments performed in this specific run was 162, 42% of total plate capacity. Similar runs are routinely performed in a 2-hour period, allowing a total throughput of up to 4 x 384 experiments in a working day. Data shows high process variability particularly for treatments B and C with ongoing work to resolve this. This variability is identified and can be attributed to the process given the underlying measurement process is robust and repeatable.

 

Figure 6. Comparison of operator hands-on time and time to data output for manual and automated processes. The hands-on time for the operator has reduced by 81% from 2hrs 15min to 25min per plate. Time to data output has also improved from 3hrs to 2hrs, a 50% increase in throughput.

 

Conclusions

Using Antha has made a significant increase in productivity in the Cambridge Consultants lab. High-quality qPCR protocols can now be executed with a few button presses using a complex range of samples and replicates without extensive training and practice reducing operator hands on time by 81% (Figure 6).

This workflow is now scalable to allow extensive testing in realistic timelines, increasing throughput by 50%. The resulting data generated is highly reliable and reproducible whilst improving cross contamination control. With the Antha Standard Element Set rapid and flexible automated liquid handling protocols can be prototyped and optimised to provide bespoke automated workflow solutions over other more rigid automation solutions.

Achieving all of these key objectives was a critical step to support delivery of a successful project to a client of Cambridge Consultants.

Antha is a great platform that adds value to our customers, we can save time, increase the hands off time of a biological protocol and make it more repeatable; that’s really beneficial to clients who are paying us by the hour
— Matthew Jones PhD, Synthetic Biologist at Cambridge Consultants
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