From manual to automated workflows for RT-qPCR and NGS protocols


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"For the last couple of years, we've been Covid testing and have been very successful with the SPT Labtech liquid handlers."
Farruk Kabir | NGS Lab Manager | Aperture NextGen Laboratories

Aperture NextGen Laboratories is an FDA approved CLIA lab for interdisciplinary clinical testing and research. Over the course of the pandemic, the team of around 15 to 20 lab staff based in Plano, Texas, has been busy testing for SARS-CoV-2 and developing proprietary NGS protocols. Starting out with manual workflows, Aperture has since transitioned to largely automated setups thanks to SPT Labtech's liquid handling solutions for genomics.

We caught up with Farruk Kabir, PhD, the NGS Lab Manager at Aperture, to find out how the team has been getting on.

Making the move to automation

When Aperture first started using its RT-qPCR for testing saliva specimens, the protocol involved lots of time-consuming manual pipetting. Like many other CLIA labs seeking to improve productivity and save on reagent costs, Aperture was on the lookout for an automation and miniaturization solution.

Following an initial evaluation, Farruk validated Aperture's protocols for use with SPT Labtech's dragonfly® discovery, mosquito® HV, and mosquito® X1. The team had opted for the SPT Labtech solutions because of the benefits compared to competitor products, plus the added value for money, as Farruk explains:

"We chose the SPTL instruments mostly on their flexibility – they allow you to do sample pipetting in different ways, like column-by-column or cherry-picking with microliter-to-nanoliter dispensing – and based on pricing!"

Since the end of last year, when Aperture started automating its SARS-CoV-2 testing, the team has achieved full walk-away capabilities across much of the RT-qPCR workflow, as Farruk is very pleased to point out:

"Basically, we transitioned from our manual protocol – mostly human pipetting steps – to the SPT Labtech liquid handlers with a workflow that's now 80% automated."

The team uses the mosquito HV for sample pipetting and mixing the mastermixes. The mosquito X1 is used to do the cherry-picking for the controls, while the aliquoting of the mastermix is done with the dragonfly discovery.

The initial setup of this workflow went smoothly, and Farruk was able to validate the team's protocols quickly within a very short period. This included developing decontamination protocols to ensure the safety of everyone handling the instruments on a daily basis (for SARS-CoV-2 testing) and achieving compliance with regulatory requirements:

"It didn't take long to validate the automated workflows – we needed to comply with FDA regulatory instructions, like how to validate your assay when you automate, and also when you're miniaturizing."

The ROI for liquid handling automation

In Farruk's opinion, the move to automation has been a clear success:

"We are able to generate quality results rapidly, in a short period of time, and with precision, and can now implement any NGS workflow."

As the demand for Covid testing has started to slow in recent months, the team is now focusing more on the R&D side of Aperture's operations and has been using the SPT Labtech instruments successfully in its NGS workflows, including library prep and bead clean-ups. In this context, Farruk is very keen to carry out an ROI assessment, so the team can measure and demonstrate the increase in productivity and the resulting positive business impact of the move to automation:

"We've been trying to do an ROI evaluation – what's our efficiency over the last six months or so? We can do that, and it's definitely a good idea."

An assessment of the business case for automation is a valuable exercise for any lab, especially when you factor in the benefits of miniaturization:

"Like most other labs, we need to miniaturize because we like to cut the cost of reagents, and improve performance with larger batches and greater sample volumes, while also doing quality assurance."

In addition to reducing tangible costs, the move to automation generates many intangible benefits, such as accelerating and streamlining scientific collaboration. Farruk was glad to hear that the mosquito software offers a straightforward way of uploading CSV files for importing and exporting worklists. He was also interested in updating the team's mosquito software to the latest version, especially with a view to sharing protocols and collaborating with others inside Aperture and externally with other labs.

An excellent choice for CLIA labs

Asked if he would recommend SPT Labtech's mosquito and dragonfly discovery workflow combination to other labs, Farruk is emphatic: "Yes, definitely - I would!" Considering the instruments' ease-of-use and how they've improved Aperture's workflow, Farruk was more than happy to give an endorsement of SPT Labtech for other professionals in the field, particularly at other CLIA labs:

"If a CLIA lab is thinking about automation, saving money, or planning to miniaturize their protocol, then I would say it's a good choice!"

Want to know more about miniaturizing NGS protocols?

The mosquito and dragonfly combination – for highly accurate positive displacement pipetting and non-contact, nanoliter-to-milliliter dispensing – offers proven miniaturization workflows. If you'd like to see the successes other SPT Labtech customers have had miniaturizing over 40 popular NGS kits, take a look at our resources for DNA sequencing, RNA sequencing, qPCR/PCR setup, single-cell cDNA synthesis, sample and library bead clean-up, and much more: mosquito® & dragonfly® for genomics miniaturization