Advantages of Automating NGS Sample Prep

As any scientist who relies on next-generation sequencing (NGS) will tell you, the quality of sequencing results is greatly influenced by the quality of the NGS library that goes into the sequencer. The library is a pool of DNA fragments extracted from an original starting sample (e.g., cells, tissue, or liquid biopsy) that have been prepared for NGS using PCR to amplify the DNA fragments, adding appropriate adapters to the fragments’ ends. Optimizing this process, known as NGS sample preparation, is important for consistent and reproducible results.

Though it can be performed manually, NGS sample preparation benefits from automating some or all of this multi-step process. Indeed, some of the common challenges encountered during NGS sample preparation—inconsistencies, throughput bottlenecks, errors, high variability, and time-consuming tasks—can be reduced or eliminated by automating the workflow. “By removing the human element from the process and limiting total hands-on time, errors are reduced, the reproducibility of results is improved, [and the time to results can be accelerated],” says Andrew Hutchison, Associate Director of Product Management, Clinical Sequencing and Oncology at Thermo Fisher Scientific. “For example, the Ion Torrent Genexus Purification System integrates with the Genexus Integrated Sequencer to deliver a report in a single day, requiring only two user touchpoints.” This article discusses how automation of the workflow can help to address common challenges encountered during NGS sample preparation.

Reducing errors, increasing safety and throughput

With its numerous procedural and pipetting steps, the NGS sample prep workflow is rife with opportunities for error. “NGS sample preparation is a multi-day, tedious, and error-prone process,” says Cindy Perettie, Head of Molecular Labs, Customer Area at Roche Diagnostics. “Manual processing, even in experienced hands, results in high run-to-run variability and limited throughput.” Using automation, the reduction in run-to-run variability lends itself to more consistent overall sequencing results.

Automating NGS sample prep also helps to keep lab personnel safe. “Standard workflows are two to three days long and include many repetitive pipetting steps, which can be hard on the hands,” notes Markus Billeter, International Business Leader at Roche Sequencing Solutions. Automating the workflow can not only reduce the incidence of repetitive stress injuries, but it can also help to protect lab workers from exposure to dangerous materials that may be used during sample preparation. “Automation reduces the handling of hazardous chemicals and eliminates most pipetting steps and repetitive motions from lab staff, with some technologies requiring only 20 minutes of hands-on time,” says Hutchison. Freeing up human hands for less tedious endeavors, and increasing safety and efficiency, are only a few of the many ways that automation addresses NGS sample prep challenges.

Labs that process large numbers of samples will notice a valuable boost in throughput with automation. “In research labs, reproducibility, consistency, and walk-away time are considered valuable,” says Henry Shu, Senior Product Manager at Agilent Technologies. “We’ve also encountered lab automation users who use their instruments to advance their research by scaling up throughput to test multitudes of variables quickly, to identify target candidates, and optimize workflows.”

Automating the workflow can even increase scheduling flexibility for lab personnel. For instance, when performing NGS sample prep manually, scheduling long incubations and other workflow steps is harder with a typical 8-hour work shift, and researchers tend to have difficulty in processing more than 24 samples at a time, notes Perettie, because “it’s hard to keep track of movements within a plate.” Indeed, a completely automated workflow may continue processing samples throughout the weekend, allowing lab workers a day (or two) off.

Automation saves samples

Manual sample preparation is vulnerable to human errors that can compromise sample yields or even lead to cross contamination. “What happens during sample preparation can have a big impact downstream, such as for NGS results, especially when samples are processed in different batches or different shifts,” says Shu. “Automated lab instruments can bring greater consistency and reproducibility to the sample prep process across batches and users, increasing sample throughput while maintaining the quality of processed samples.”

Conserving starting sample material is a common challenge. For researchers who use rare or difficult-to-obtain samples, such as patient biopsy tissue or preserved historical samples, it can be difficult to obtain the amount of sample material required to produce NGS results. Automation reduces the risk that human errors could result in wasting sample material, and require re-starting the sample prep process to construct another library. “If specimen material is wasted because of a human error in the lab, that may lead to additional biopsies or hardship for the patient providing the sample, ultimately impacting their experience and slowing time to results,” says Hutchison.

Automation improves quality by facilitating QC checks

Automation can also improve the overall quality and consistency of NGS results, by automatically performing quality control (QC) and quantitation at multiple key points in the NGS sample prep workflow. Quantitation and QC checks during NGS sample preparation are already a recommended ingredient in high-quality sequencing results, and incorporating them into an automated workflow is a smart way to ensure they are performed consistently and regularly. “Automated sample prep solutions ensure stringent quality control checks throughout the process,” says Hutchison. “[For example,] the Genexus Purification System leverages Invitrogen Qubit quantitation technologies to determine if researchers have sufficient nucleic acid for the experiment.”

QC and quantitation are incorporated into a completely automated platform for NGS library prep offered by Roche Diagnostics. “Our AVENIO Edge System is a true walk-away solution that automates quantification, library preparation, target enrichment, and pooling,” says Perettie. “It standardizes QC by building these components into our system, and allows samples to be processed during nights and weekends.”

Any degree of automation that you can incorporate into your workflow is likely to help right away. The main benefits of automating your NGS sample prep workflow—namely, increased quality, throughput, and reliability—mean that you can have more confidence in your sequencing results.