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Long-read Whole Genome Sequencing: Enhancing Diagnostic Power Across Clinical Applications

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The webinar delivered data-driven insights into the current state of long-read sequencing, with a focus on clinical practice, presented from the perspectives of both a clinician and a medical genomics expert. It is essential viewing for clinical operations managers and organizations seeking to improve diagnostic yield and ensure that their strategies for 2026 are aligned with newer technologies that are cost-effective, practical, and make a meaningful contribution to patient care.

The Importance of Clinical Genomics, and the Missing Pieces

Genetic variation is the root cause of many diseases. While many variants are well characterized and their clinical implications are understood, the genetic causes of many rare and complex conditions remain unknown or only partially elucidated. Single-nucleotide mutations and other small variants play an important role in genetic disease, but they do not tell the full story. Larger variants, including structural variants and repeat expansions, are known contributors to disease, but their full impact on the genetic disease landscape remains poorly understood. Short-read sequencing is highly effective for detecting small genetic variants, but it struggles to resolve larger variants, leaving many patients without a definitive diagnosis and clinicians with limited information with which to guide treatment.

Long-Read Sequencing Comes of Age

Dr. Nahas opened the discussion with an overview of current long-read sequencing technologies, highlighting how the field has undergone a dramatic transformation in recent years. Historically, long-read sequencing has been low-throughput and expensive, and used only for niche applications and small cohort studies. Today, it offers much higher throughput at a lower cost, making it suitable for clinical and commercial applications.

Dr. Nahas explained how long-read sequencing provides accurate detection of different variant classes to support rare and complex disease diagnosis. It is also valuable in pharmacogenomics, where it enables accurate star-allele resolution, and in population genomics, where it enables high-accuracy phasing. Long-read sequencing can significantly improve clinical interpretation and epidemiological insights, especially for populations underrepresented in existing genomics studies. It also excels in preclinical GLP gene-editing assessments, where it helps evaluate clonal stability, detect unintended edits, and generate high-quality reports for regulatory review. In short, it is a powerhouse across commercial, clinical, and translational pipelines, and is already in use by early adopters.

Dr. Nahas also presented a practical framework for implementing long-read whole-genome sequencing (WGS) within CLIA/CAP-regulated clinical environments, including detailed guidance on the analytical validation of short tandem repeat coverage across diverse loci. This section of the webinar is a must-watch for any organization considering adopting long-read WGS into their clinical workflows.

A Clinician’s Perspective on Long-Read Sequencing

In the second part of the webinar, Dr. Ellsworth provided her perspective on long-read sequencing as a clinician working with patients with genetic disorders. Dr. Ellsworth began by highlighting the power of short-read sequencing in rapid clinical genetic testing. She then outlined the limitations of short-read sequencing, including alignment ambiguity caused by high sequence similarity, reduced sensitivity to larger variants, and difficulties detecting repeat expansions and epigenetic features that are critical for the analysis of many neurological disorders.

Dr. Ellsworth presented several practical examples illustrating the contrasting ability of long-read and short-read sequencing to resolve short tandem repeats in clinical samples. Some short-read sequencing reads spanning repeat regions were lower in quality, leading to less reliable variant calls, whereas long-read sequencing provided improved resolution in these regions. Based on these findings, the team at RCIGM recognized the value of incorporating long-read sequencing to improve diagnostic yield and reduce final report turnaround time in certain cases. Dr. Ellsworth and her team now include long-read sequencing as an integrated part of their WGS pipelines for repeat expansion detection.

Making Large-Scale Long-Read Sequencing a Reality

Dr. Nahas and Dr. Ellsworth agreed that the question is no longer whether long-read sequencing belongs in clinical diagnostics, but how it can be integrated without disrupting existing operations. As costs decrease and throughput increases, the application of long-read sequencing is likely to expand significantly in the clinical setting. Laboratories that invest early and maintain flexible sequencing and downstream analysis infrastructure will be best positioned to benefit.

To conclude the webinar, Dr. Nahas and Dr. Ellsworth engaged in an insightful discussion on what it truly takes to implement long-read sequencing at scale, covering critical considerations such as DNA quality and quantity, extraction methods, and the need for purpose-built facilities. Their conversation reinforced that success depends not only on technology, but on robust, CLIA/CAP-compliant frameworks and expert-led processes that integrate seamlessly into existing clinical genomics programs.

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Sampled is a Certified Service Provider (CSP) for the PacBio Revio and offers end-to-end long-read sequencing services.

Contact our team to see how you can use long-read sequencing to unlock genomic insights and achieve improved outcomes in your clinical or commercial workflows.

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The Sampled breakout session featured our Chief Scientific Officer (CSO) Shareef Nahas, PhD alongside the CEO and Founder of Nucleus Genomics, Kian Sadeghi. Their discussion covered many sub-topics within the multiomics umbrella, including how genome sequencing has evolved over the last 20 years, where the field is going, and how to bring genomic sequencing to the clinic and make it more widely available to the public.

The Evolution of Multiomic Technologies Over the Last 20 Years

Multiomic techniques are not a recent breakthrough. However, they have yet to reach their full potential. Modern research, including clinical studies, demands the ability to perform multiomics at scale, providing multidimensional insights into patient health before, during, and after treatment. This level of information, including data generated by NGS, opens the door for truly personalized medicine. Ensuring this information can be extracted at scale and with quality requires dedicated infrastructure and expertise.

Achieving Quality at Scale to Drive the Personalized Medicine Revolution

The discussion between Shareef and Kian focused on how to bring the promise of genomics-based medicine to the real world. Part of the solution, they believe, lies in providing the scalability and quality needed for actionable insights at scale.

Their chat covered the early years of omics and is a fascinating discussion of where we have come from and where we are going. Genomics offers valuable insights at both the individual and population levels. Large-scale studies are deepening our understanding of disease, while growing access to genome sequencing, along with improved education about it, empowers individuals to take greater control of their health.

Expanding Access to Genetic Insights

Many diseases have genetic roots, yet 90% of people are unaware they may carry genetic risk factors. This untapped information could empower individuals to take a more proactive approach to their health, improving their long-term wellbeing and lessening the burden on the healthcare system. Early tools like microarrays offer only limited genetic insights, but NGS can now analyze entire genomes at rapidly lowering costs. With recent advances in technology, logistics, and data reporting, NGS insights are more accessible and affordable than ever, bringing us closer to a future where a single cheek swab can reveal a person’s complete genomic health profile.

Shareef and Kian emphasized the need to shift our understanding of genetics, from viewing it as a separate or secondary aspect of medicine to recognizing it as a central component of healthcare, providing essential information for guiding personalized, effective care.

The Need for Technology and Expertise at Scale

A key challenge highlighted during the breakout session was managing the massive volume of data and samples needed to make genome sequencing practical at the population level. Each full genome generates an enormous amount of information that must be accurately analyzed and converted into actionable insights. Scaling personalized genomics to serve a broader population requires advanced logistics, expert sample handling, and high-quality analytical infrastructure, resources that only a few facilities can currently provide. Sequencing is a highly sensitive technique, and maintaining data accuracy is crucial for effective patient care, making expert oversight essential at every stage. To support this level of quality and scale, large, centralized facilities are indispensable.

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The GEN Summit highlighted the crucial role of multiomics in the future of healthcare. Here’s a snapshot of the talks you don’t want to miss out on:

Jacob Thaysen, PhD, CEO of Illumina

• How Illumina is driving down the cost of sequencing
• The importance of AI in large cohort studies and multiomics approaches

Cecilia Lindskog, PhD, Research Group Leader at Uppsala University & Fabian Coscia, PhD, Research Group Leader at Max Delbrück Center for Molecular Medicine

• Exciting developments in spatial proteomics for precision medicine
• Mapping the “Human Protein Atlas” to understand health and disease

Robert Meltzer, PhD, Associate Principal Scientist at Illumina

• Enabling single cell RNA sequencing in any lab setup

Clive Brown, Former CTO of Oxford Nanopore Technologies

• Insights from a veteran of nanopore technology

You can watch these sessions, and all of the others, for free online!

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In this article, we look at how the GIAB can integrate these omics technologies, so that researchers can gain a comprehensive understanding of complex biological systems, unlocking new insights into health, disease, and drug development.

The Value of Multiomics

• Genomics: Studies the entire set of DNA within an organism. It offers foundational insights into genetic variations and predispositions to diseases.
• Transcriptomics: Focuses on RNA transcripts produced by the genome. It sheds light on gene expression patterns and regulatory mechanisms under various conditions.
• Proteomics: Examines the entire set of proteins, including their modifications and interactions. It provides a direct measure of the functional molecules driving cellular processes.
• Metabolomics: Analyzes the complete set of metabolites, which are the end products of cellular processes. It reflects the physiological state of cells in real-time.

Key Benefits of a Multiomics Approach

The integration of these diverse datasets through a multiomics approach yields comprehensive insights that cannot be achieved by any single omics analysis. This holistic perspective enables researchers to:

• Unravel complex disease mechanisms by connecting genetic predispositions with phenotypic outcomes.
• Identify novel biomarkers and therapeutic targets by revealing the underlying molecular pathways.
• Accelerate drug discovery and development by providing a more precise understanding of drug mechanisms and patient responses.

Integrating these perspectives, multiomics provides a holistic view of biological systems. This approach enables researchers to uncover hidden connections, identify biomarkers, elucidate disease mechanisms, and discover novel therapeutic targets. It accelerates research in the discovery and pre-clinical phases, helping biopharmaceutical companies save time and resources by focusing on the most promising drug candidates.

How the GIAB supports Multiomics

At Sampled, we understand the transformative potential of multiomics at the research and discovery/pre-clinical stage. That’s why we offer a wide range of services tailored to support multiomic workflows. From sample collection and processing to sequencing and bioinformatics, we provide end-to-end solutions designed to meet the diverse needs of our clients.­­

Analytical Sample Processing

We offer a suite of analytical sample processing services, including sample aliquoting, DNA/RNA extraction, fractionation, normalization, and sample processing quality control (QC). In our aliquoting workflow, we handle samples received from various sources, ensuring proper storage throughout the handling process.

These critical first steps ensure the integrity and uniformity of biological samples, laying a solid foundation for downstream multiomics analyses. By employing stringent QC protocols, Sampled ensures the reliability and reproducibility of data generated from its repository, which is particularly important for research involved in clinical trials.

Sequencing

Our sequencing services give our clients invaluable insights into their samples, expediting academic, industrial, and clinical research. By partnering with key technology platform manufacturers such as 10X Genomics, Illumina and PacBio, Sampled facilitates a wide range of omics analyses, including whole genome sequencing (WGS), whole exome sequencing (WES), targeted sequencing, Sanger sequencing, RNA sequencing, methylation sequencing, and advanced proteomics.

This complete and comprehensive suite of sequencing services enables researchers to delve deep into the genetic, transcriptomic, and epigenetic landscapes of biological samples, uncovering novel insights into disease mechanisms, biomarker discovery, and personalized medicine.

Proteomics and Protein Biomarker Discovery

Through partnership with Olink, we offer advanced proteomics and analyses through the Explore HT and 3072 platforms, allowing researchers to dissect the functional aspects of biology and uncover novel biomarkers for disease diagnosis and treatment. The Explore HT platform allows levels of over 5400 proteins to be determined from minimal sample volume giving researchers unprecedented access to discover new biomarkers from a wide range of medical fields including but not limited to oncology, cardiology, neurology, inflammation, and diabetes.

Microarrays

Sampled’s GIAB also offers microarray services, including genotyping, transcriptome profiling, and methylation profiling arrays. These high-throughput platforms enable researchers to interrogate genetic, transcriptomic, and epigenomic variations on a genome-wide scale, facilitating the identification of disease-associated biomarkers, therapeutic targets, and molecular signatures. By harnessing the power of microarrays, Sampled empowers researchers to unravel the intricacies of complex diseases and accelerate drug discovery efforts.

Bioinformatics

In addition to its analytical capabilities, Sampled offers comprehensive bioinformatics services, including data analysis and custom reporting tailored to individual client needs. Sampled obtains data from its in-house analytics pipeline or directly from clients. The data is securely stored on the laboratory information management system (LIMS) and can be accessed through SampledSphere. We offer tailor data analysis to meet client-specific requirements, which vary based on sequencing or array types.

Outsourcing multiomics services to Sampled offers numerous benefits, including access to state-of-the-art technologies, expertise, and scalability. Our platforms are designed to streamline sample processing and analytical workflows, reducing turnaround times and maintaining sample integrity throughout the analysis pipeline. This efficiency ensures that you receive your results promptly, allowing you to move forward with your research without unnecessary delays.

In conclusion, the Global Integrated Analytical Biorepository represents a critical advancement in the era of multiomics, offering researchers unprecedented opportunities for discovery and innovation. By providing end-to-end support for multiomics workflows, Sampled empowers researchers to gain a comprehensive understanding of complex biological systems. This holistic approach paves the way for breakthroughs in disease diagnosis, treatment, and prevention, highlighting the benefits of outsourcing multiomics services to accelerate research. For those ready to explore the frontiers of multiomics, Sampled stands ready to guide you through this exciting journey, unlocking the mysteries of life one molecule at a time.

For more information on accelerating your research through outsourcing multiomics workflows, contact Sampled today and speak with one of our experts.