by Mahesh Kalikiri

The evolution of next-generation sequencing (NGS) technologies is driving the development of novel solutions in genomics testing, but the associated technical challenges are limiting the roll out of wide-spread, rapid sequencing. In this article, Mahesh Kalikiri, Eppendorf EMEA, explores how automated liquid handling platforms are reducing variability and increasing throughput in NGS workflows for clinical applications.

Clinical diagnostics is undergoing a fundamental shift, driven by the convergence of high-throughput genomics, precision medicine, and an ever-increasing global demand for rapid and reliable test results. Genomics laboratories are no longer operating at the scale of tens of samples per day, but often hundreds or thousands, requiring innovative solutions to increase capacity, whilst maintaining accuracy.

As clinical diagnostics have evolved, the limitations of manual workflows have become more apparent – the variability, throughput constraints and extended turnaround times of these approaches have a direct impact on clinical outcomes. Automated liquid handling systems have emerged as a critical solution, allowing laboratories to transition from labour-intensive processes to scalable, standardized and reproducible workflows.

Evolution of genomic testing in clinical diagnostics

Advances in next generation sequencing (NGS) technologies are accelerating the evolution of genomic testing, shifting from targeted, single-gene assays to comprehensive multigene panels and whole-genome or whole-exome analysis. NGS platforms are becoming increasingly more efficient, which reduces sequencing costs and physical space requirements while maximizing throughput and analytical capacity; this creates opportunities for decentralized testing centres and in-house genomics diagnostics.

In clinical practice, this move has had a profound impact. Instead of sequential testing strategies that could take weeks or months, clinicians can now access comprehensive genomic insights from a single assay in hours. However, as genomic testing has scaled, so too have the associated technical challenges. NGS workflows involve multiple highly sensitive steps, each requiring precision and consistency. Sample preparation represents a crucial step which is often reliant on manual labour and is therefore susceptible to human errors. Even the smallest variations introduced in sample preparation can lead to differences in sequencing quality, reducing diagnostic accuracy.

Figure 1. Comparison of manual vs semi-automated pipetting in cell-based assays (A) up to 22% time saving per plate could be achieved per workflow. (B) Well-to-well variations in cell viability measured 48 hours after seeding. Semi-automated platform shows less variability compared to hand-held multi-channel pipette.

aLH, automated liquid handling; CV, coefficient of variation.

Automated liquid handling platforms minimize variability

Automation addresses this challenge by transforming complex workflows into controlled, repeatable processes, ensuring that the genomic data generated meets the regulatory standards required for clinical use.

Implementation of automated liquid handling platforms in NGS workflows eliminates risk of variation in sample preparation stages, removing the onus of repetitive manual pipetting and the associated risks of errors and repetitive strain injuries, which are significantly higher when analysing large volumes of samples. Examples of sources of variation with manual liquid handling include fluctuations between individual user’s pipetting angle, plunger release speed and immersion depth [1]. Integrating automation into workflows also allows skilled personnel to focus on data interpretation and subsequent decision-making (Fig. 1).

How automation accelerates time-to-diagnosis and healthcare efficiency

In clinical settings, a rapid turnaround is crucial, and delays in workflows can lead to prolonged diagnosis timelines, increasing both patient anxiety and economic burdens. Advances in NGS have accelerated sequencing workflows, either facilitating rapid testing via centralized services, or installation of in-house genomics laboratories, reducing turnaround times (Fig. 2).

By streamlining sample processes and eliminating bottlenecks associated with manual handling, automated liquid handling platforms can further reduce time-to-diagnosis by directly impacting the speed at which clinicians can access actionable results.

Advancing cancer diagnostics through automation

Cancer diagnostics represents a significant opportunity for integration of automation into genomics workflows. The increasing use of NGS in oncology has enabled the identification of disease-promoting mutations, guiding targeted therapies and improving patient outcomes.

Another consideration in oncology is that faster diagnosis can significantly improve treatment outcomes. By reducing turnaround time to a few days, clinicians can initiate targeted therapeutics earlier, minimize unnecessary treatments and improve coordination of multidisciplinary care [2]. These improvements contribute to reduced hospital stays and fewer repeat visits by slowing disease progression and preventing complications.

Genomic testing can also help identify at-risk populations, for example, those predisposed to breast cancer [3]. Multigene panels now allow simultaneous analysis of multiple risk-associated genes, providing a more comprehensive understanding of patient risk profiles and therapeutic options. Alongside the well-known BRCA1/2 mutations, which are seen in women with familial breast cancer, multigene panels also identified associations with ATM, PALB2, TP53 BARD1, and CHEK2 mutations as potential susceptibility genes. Automation plays a critical role in ensuring that these multigene assays are both scalable and reliable, supporting both screening programs and routine diagnostics. Automating NGS is helping to shift cancer diagnostics from a reactive to a proactive approach. Faster and more reliable genomic testing allows clinicians to identify at-risk individuals earlier, initiate preventive strategies, and tailor treatments based on individual genetic profiles.

Figure 2. An automated liquid handling platform compatible with NGS workflows

Automation enables population-scale genomics

Population wide genomics or whole-genome sequencing (WGS) offers a promising approach for identifying associations between genomic variants and disease prevalence [4]. Previously, research has focused on genome-wide association studies (GWAS), where the causal gene is often unclear. By leveraging rare protein-coding variation, more recent studies can readily identify new causal pathways and underlying mechanisms of disease. National genomic medicine initiatives have long been established in the UK, France, Australia, and the USA, with other countries now following their lead.

In the UAE the Emirati Genome Program aims to draw a comprehensive map of UAE citizens to accelerate development of preventive and personalized healthcare solutions, while in the Kingdom of Saudi Arabia the Saudi Genome Program (SGP) is capturing the genetic blueprint of Saudi society to drive down healthcare costs and uplift quality of life [5,6]. These localized initiatives are generating extensive genomic datasets to increase understanding of population-specific disease risks.

In parallel, initiatives such as the H3Africa Consortium are expanding genomic research across diverse populations, integrating human health studies with broader biological and environmental contexts [7].

These efforts are dependent on the ability to process large volumes of samples with high consistency over extended periods of time. In experiments where high throughput is the priority, use of automated platforms can facilitate the scale-up of operations without the proportional increases in staffing, enabling delivery of WGS at a fraction of the cost seen in manual laboratories. An additional benefit is ensuring inter-run and inter-site reproducibility, which is essential when combining datasets from large cohorts [8].

Future outlook: toward fully automated workflows

As NGS technologies continue to evolve, the next phase of automated clinical diagnostics, and genomics testing more broadly, will likely include end-to-end workflows that integrate sample processing, sequencing and data analysis. There is the potential for combined closed-loop systems of integrated liquid handling and sequencing platforms, as well as significant opportunity for AI-driven workflow optimization.

Decentralized genomic testing will be more prevalent as advanced miniaturized NGS systems become commercially available, with all these factors supporting the delivery of rapid sequencing in clinical environments [9].

Automation will continue to be instrumental in enabling laboratories to meet the demands of modern healthcare. From supporting large-scale genomic initiatives to accelerating cancer diagnostics, automated liquid handling systems are reducing variability, increasing throughput, and shortening time-to-diagnosis, bridging the gap between technological innovation and clinical application.

 References
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The author

Mahesh Kalikiri MSc, Automation Product and Application
Manager Eppendorf EMEA, Dubai, United Arab Emirates

For further information see: https://www.eppendorf.com/gb-en/