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6 reasons to automate your sample preparation workflows

By 09.07.2022

Automated sample preparation has filled a gap that occurred when the volume of labs processing samples skyrocketed starting in 2020. But as the volume of samples requiring nucleic acid extraction and analysis grew, labor shortages occurred. Therefore, lab automated instruments able to reduce touch time and perform automated sample preparation like nucleic acid extraction, immunoprecipitation, sample transfer, and cell isolation were more necessary. Depending on the needs of individual labs, small to large scale systems were put in place to accommodate a variety of throughputs.

High-throughput molecular biology workflows have enabled a surge in diagnostic research development and therapeutics development. Crucial to these workflows is rapid, accurate, flexible, and scalable sample management, preparation, and processing. Across academic, non-profit, government research, and biotechnology sectors, sample collection and processing needs have significantly increased. Establishment of community-, city-, and county-wide molecular testing programs have become a necessity for respiratory research, such as SARS-CoV-2.1

Traditionally, many molecular biology and diagnostic research workflows were manual, placing a heavy burden on skilled personnel for efficient, reproducible, and rapid sample handling and extraction. But with a growing labor shortage in the biotechnology industry, the necessity to do larger-scale sample preparation with fewer skilled hands is increasing, putting a strain on many laboratories.2  In the modern lab, see below for the top six reasons to automate sample preparation workflows:

  1. More samples can be processed and analyzed in less time

When more samples can be processed and analyzed in less time, lab technicians can focus on the areas of their research that matter most. A large percentage of sample preparation and molecular biology workflows are time-consuming, laborious, and repetitive. In fact, many laboratories are in a position where skilled technicians process one type of sample or perform one protocol repeatedly. However, as sample numbers scale, inefficiencies emerge. Time spent on processing and extraction increases proportionally with the number of samples.

Thus, automating sample processing frees up skilled laborers to conduct insight-driven data analysis or to focus on more technically demanding experiments. For example, wastewater-based epidemiological programs rely on multi-step, repetitive cycles of sample concentration, nucleic acid extraction, and quantitative reverse transcription PCR (qRT-PCR).3

The implementation of liquid-handling robots to take on the lion’s share of this workflow decreases sample processing time by 20-fold: 96 raw sewage samples can be processed in 4.5 hours, with a significant reduction in handling times. on the other hand, automated genomic DNA, cell-free DNA, and RNA extraction workflows have reported between 50 and 75% less touch time than manual sample preparation.

 

  1. Lower margin for error using automated workflow

Automated sample preparation systems can avoid many known pre-analytical errors, thus, helping labs produce reliable and reproducible data. Consequently, they get rid of person-to-person variation in sample preparation, allowing standardization. With repetitive tasks, the risk of human error increases.4 In clinical research, most errors, including sample collection and processing, occur before analysis.5

Automate DNA, RNA and protein purification with Thermo Scientific KingFisher instrument

In a recent webinar, Dr. Suraj Patel, Emily Zeringer and Dr. Ketil Pedersen from Thermo Fisher R&D teams talk about the differences between manual and automated sample prep. Each technology or workflow has it’s own strengths and limitations.

  1. Improved safety of lab technicians

Certain sample types (i.e., blood, saliva, etc.) can contain infectious agents, putting laboratory personnel at risk when handling them directly.7 In addition, solvents and other harmful chemicals used in nucleic acid purification protocols can expose personnel to toxic materials. Therefore, using automated sample preparation systems physically separates laboratory personnel from these two sources of danger, mitigating the overall risk to the entire lab.

  1. Improved customization and optimization for research protocols

Method development and validation can require optimizing multiple steps within a protocol. Many automated systems make customization easy. In addition, the software enables you to create, modify, and store different protocols to suit your laboratory’s needs. More intuitive user interfaces help customization and fine-tuning protocols easy.

An important step is to vary specific parameters of a protocol in a methodical, controlled, and meticulous manner, keeping all other variables fixed. Given the point about human error and sample-to-sample variation above, an automated system can facilitate protocol optimization, enabling control over single variables.

  1. Automated purification instruments have broad applicability across biology

Labs can often work on a wide array of research projects. In other words, they have a need for processing different sample types and extraction methods. Automated purification instruments perform essential steps used in most microbiology research across the biosciences. In microbiome research, for instance, there is a microbial community in nearly every free-living or host-associated niche on the planet.8 Therefore, versatile extraction reagents and workflows are needed for a broad range of biomolecules (i.e., DNA, RNA, protein) and diverse sample types, from stool to soil samples.

Automated systems, such as the KingFisher, can accommodate various kits for nucleic acid extraction, immunoprecipitation, exosome isolation, and peptide mapping. It can also handle complex samples, including blood, saliva, mucus, seawater, soil, fecal matter, and fish scales.

  1. Sample preparation at scale requires lab instruments not laborers

Scaling up sample preparation may require increased staffing and space. And the high cost needed to support both. Automated instruments enable an out-of-the-box solution to increase sample processing capacity and scaling up. It also avoids the increased burden on staff that often comes with increased throughput.

Higher throughputs and more efficient personnel use can significantly reduce the cost per sample. Likewise, automated sample preparation instruments help reduce reagent costs by reducing experimental error and volume used for sample preparation.9

This video highlights the technology behind the KingFisher Apex. These are automated sample preparation instruments designed to scale up extracting and purification of DNA, RNA, Protein or cells from a wide range of sample types.

Select simple, powerful, automated sample preparation

Thermo Fisher Scientific has been at the forefront of developing automated instruments for sample transfer and purification. KingFisher instruments serve laboratories worldwide in their efforts to purify samples and prepare them for downstream applications such as qPCR, NGS, digital PCR, and mass spectrometry.

To learn more about the technologies behind automated extraction and analysis of nucleic acid, cells or proteins, you can read about KingFisher and MagMAX and how they use magnetic bead based separation.

This article is for Research Use Only. Not for use in diagnostic procedures.

References:

  1. Overview of Testing for SARS-CoV-2, the virus that causes COVID-19. CDC website: https://www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html. Published February 11, 2022. Accessed April 20, 2022.
  2. In the region’s booming biotech industry, workers are in short supply. Boston Globe website: https://www.bostonglobe.com/2022/01/30/business/regions-booming-biotech-industry-workers-are-short-supply/. Published January 30, 2022. Accessed April 20, 2022.
  3. Karthikeyan S, Ronquillo N, Belda-Ferre P, et al. High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County. mSystems. 2021;6(2):e00045-21. doi:10.1128/mSystems.00045-21
  4. Yeow J, Ng PK, Sin Tan K, Chin T, Yin Lim W. Effects of stress, repetition, fatigue and work environment on human error in manufacturing industries. J. Appl. Sci. 2014;14: 3464–3471. doi:10.3923/jas.2014.3464.3471
  5. Bonini P, Plebani M, Ceriotti F, Rubboli F. Errors in laboratory medicine. Clin Chem. 2002;48(5):691-698.
  6. Full high-throughput workflow with the KingFisher SpeciTRAX Sample Transfer System. Thermo Fisher Scientific website: https://assets.thermofisher.com/TFS-Assets/BID/Application-Notes/workflow-kingfisher-specitrax-sample-transfer-system-app-note.pdf. Published April 7, 2022. Accessed April 20, 2022.
  7. Burnett LC, Lunn G, Coico R. Biosafety: guidelines for working with pathogenic and infectious microorganisms. Curr Protoc Microbiol. 2009; Chapter 1(1):111-1A.1. doi:10.1002/9780471729259.mc01a01s13
  8. Thompson LR, Sanders JG, McDonald D, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551(7681):457-463. doi:10.1038/nature24621
  9. Zanatta L, Valori L, Cappelletto E, et al. Reagent and labor cost optimization through automation of fluorescence in situ hybridization (FISH) with the VP 2000: an Italian case study. J Lab Autom. 2015;20(1):25-31. doi:10.1177/2211068214558294

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