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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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Ready to try long-read sequencing for yourself?

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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This research involves collecting biospecimens from 7,000 birthing parents and their children to investigate how prenatal and postnatal experiences influence children’s neural, cognitive, behavioral, social, emotional, and health outcomes.

The Impact of Early Experiences and Exposures on Infant Health Outcomes

The development of the human nervous system is a complex process, beginning a few weeks after conception and continuing throughout gestation and long after birth. This development is driven by a complex interplay of genetic and environmental factors, with the late prenatal stage and early infancy marking a period of exceptionally rapid and significant change. Although it is well understood that these factors impact childhood development across biological and social domains, the precise causal relationships between early exposures and subsequent behavior remain unclear. Therefore, gathering diverse data from birthing parents and their children during both prenatal and postnatal stages is essential for uncovering the biological mechanisms that link early-life exposures to developmental outcomes.

In this manuscript, the research team presents the rationale behind the study, detailing the selection of specific biospecimen collections (e.g., blood, saliva, nails) and other tests conducted at various developmental stages (i.e., prenatal, 0–1 month, 3–9 months, 9–15 months). The study design aims to balance the depth of phenotypic information collected with considerations of participant burden and other relevant factors.

EL Sullivan, R Bogdan, L Bakhireva, et al., Biospecimens in the HEALthy Brain and Child Development (HBCD) Study: Rationale and protocol, Developmental Cognitive Neuroscience, Volume 70, 2024, 101451, ISSN 1878-9293. https://doi.org/10.1016/j.dcn.2024.101451.

Cohort Selection

The HBCD study was designed to consider population diversity and specific substance exposures. Accurate representation of the broader population is essential to minimize bias in large cohort studies. At the same time, a key goal of the study is to examine infant exposure to substances such as opioids, marijuana, alcohol, tobacco, and others. To achieve both aims, the researchers organized the cohort into three categories.

1. 50% – Racially, ethnically, and socioeconomically diverse cohort representative of the U.S. population
2. 25% – Pregnant persons with use of targeted substances
3. 25% – Individuals demographically and behaviorally similar to group two but without substance use during pregnancy

All participating birthing parents are between 18 and 50 years of age and will have given birth 12 months before the start of the study.

Parameter Selection

Data is collected from biospecimen analysis (i.e., genomics/epigenomics), questionnaires, interviews, biosensors, behavioral, electroencephalogram (EEG), and magnetic resonance imaging (MRI). This enables researchers to link prenatal and postnatal experiences, including:

• Physical health
• Behavior
• Neurocognition/language capabilities
• Neurodevelopment
• Activity and sleep

Biospecimen collection is a central component of the HBCD study, providing researchers with objective insights into various biological mechanisms and exposure to specific target substances. The types of biospecimens to be collected and the rationale for their collection include:

• Blood: To assess biomarkers and environmental exposures in the birthing parent
• Urine: To assess proteins and environmental exposures
• Nails: To index substance exposure
• Saliva: For genetic material and to track epigenetic changes over time
• Stool: To facilitate microbiome studies in child participants

Sampled, a CAP-accredited and CLIA-licensed analytical laboratory and biorepository, performs the ongoing specimen collection logistics, sample storage, and analytical processing.

Implications for Research

The HBCD study aims to generate a comprehensive collection of high-quality biospecimens and associated data for future use by diverse research teams. In addition to providing these resources, the researchers offer guidance on effectively applying the data to various fields, including genomics, nutrition, toxicology, inflammation, microbiome, and metabolomics. The depth and robustness of this data will support a wide range of research areas and help address longstanding questions about how early experiences and exposures influence neurocognitive and behavioral development.

“The design of the HBCD study, pairing the longitudinal collection of extensive phenotypic data with varied biospecimens, will enable researchers to interrogate the complex relationships in child development between genetics, environment and maternal drug exposure using state-of-the-art multiomics approaches including bulk and single cell next generation sequencing, epigenomics, metagenomics, and metabolomics.“

Michael Sheldon, PhD

Dr. Sheldon has a career spanning more than 30 years in genetic research and biobanking. In 2021, he founded the Scientific Affairs department at Sampled with the mission to provide expert technical resources to clients, discovery and adoption of new technologies, and the coordination of outreach initiatives. Prior to that he served as Senior Director of Sample Processing Services at RUCDR Infinite Biologics (now Sampled), with oversight of all sample processing services relating to blood fractionation, cell and stem cell culture, and nucleic acid extraction.

Dr. Sheldon received his B.A. from Cornell University in 1983 and a Ph.D. from SUNY at Stony Brook in 1993. He is an Adjunct Professor of Genetics at Rutgers University and is a published researcher in Genetics, Neurodevelopment, and Stem Cell biology.

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.

Watch the Full Summit Online

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!

Already thinking about your next big multiomics project?

Get in touch with one of our experts today to discover how we can scale your research to generate even greater insights.

Speak to a Multiomics Expert

November 15, 2022 – Piscataway, NJ – The Chief Scientific Officer at Sampled¹ issued a call to action for greater diversity in clinical trial recruitment and the collection of biosamples in a letter in the current issue of Biopreservation and Biobanking.

The letter by Sheldon et al, “Biobanks and International Initiatives Are Playing a Critical Role in Redressing Historic Inadequacies in Biosample and Data Access from Underrepresented Minority Populations,” states that the development of effective precision medicine tests must have broad representation from Underrepresented Minority (URM) populations in sample collection, processing and analysis.

“Genomic testing is revolutionizing the development of medicines, and Sampled is at the forefront of helping companies and academic institutions to unlock the genetic information that will lead to new treatments and cures,” said, Shareef Nahas, Ph.D., Chief Scientific Officer at Sampled. “However, the basis for these advancements lies in the ability of researchers to identify patterns and characteristics from many kinds of genetic profiles. Greater diversity in the collection of biomaterials and biosamples will speed our ability to develop and implement cutting-edge analytical approaches.”

“Biobanks such as Sampled play a critical role in helping to address the historic lack of representation of minority communities in medical research,” said Robin Grimwood, Founder and CEO of Sampled. “For instance, our Minnesota laboratory collaborated with state public health officials to offer free COVID testing to local minority communities. Our focus on public outreach and communication about the importance of testing, along with our ability to combine storage, management, and analytical approaches in one facility made this joint effort with the state health officials a great success.”

Traditionally, as many as 86% of participants in clinical trials have been characterized as being of European descent². Contributors to these racial and ethnic disparities include inadequate clinical trial recruitment programs and mistrust of the medical community by those in minority communities. Dr. Nahaas calls on the biopharma industry to increase outreach to URM communities, and to implement studies and testing in strict compliance with regulations over protected health information, adherence to validated standard operating procedures for processing genomic data and a storage infrastructure designed to safeguard specimen integrity.

You can access the paper here temporarily, after the 8th of decembet please get in touch to receive a copy: Biobanking Diversity Article

About Sampled

Sampled is a next-generation laboratory that unlocks the valuable data in any biological sample. Through our integrated Sampled Lab services, we can Store, Manage, Analyze, Research and Transport biological materials, offering partners a seamless solution for all research samples. Our vision is a world where we make it faster and easier for health innovators to improve human health, with a mission for Sampled Labs to be behind every transformative health innovation. Sampled is headquartered in Piscataway, N.J. with labs across the US and Europe and partner labs in the Netherlands, China and Australia.

Infinity BiologiX LLC, Roylance Stability Storage Limited and Roylance Scientific Limited are doing business as Sampled. For more information, please visit www.sampled.com

Sarah brings a wealth of experience in precision medicine and biopharmaceutical research and development gained from leadership positions throughout the pharmaceutical industry.  Sarah joins current Board members Robin Grimwood, Co-Founder and CEO and Brian Rose, Managing Director, Viking Global.

“Appointing Sarah to our board adds a wealth of experience to our business as we continue with our growth strategy,” said Robin Grimwood, Sampled’s CEO.  “We are particularly excited to have Sarah bring her insights in precision medicine, to help guide our expanding service offerings.  We welcome Sarah and are very excited to have her on our Board of Directors.”

“I am thrilled to be joining Sampled’s Board of Directors at such a significant time for the company,” said Sarah Hersey.  “Sampled’s vision of making it faster and easier for health innovators to improve human health guides the company in its future growth, and I look forward to applying my experience in precision medicine and translational science in helping Sampled realize this vision.”

Sarah is an accomplished leader and is responsible for leading a world-class research and development team of over one hundred scientists including MDs and PhDs supporting translational sciences and diagnostics.  Sarah is currently at Bristol Myers Squibb serving as Vice President, Head of Translational Sciences and Diagnostics, where she leads a team that supported more than twenty drug approvals, top-line results and other key regulatory milestones in a single year during the Pandemic. Prior to Bristol Myers she was Head of Precision Medicine, Vice President at Celgene (which was acquired by Bristol Myers Squibb in 2019) where she built and led a world-class precision medicine team. Prior to Celgene, Sarah was the Global Head of Future Precision Medicine at Novartis where she developed innovative solutions to support accurate and precise use of advanced diagnostic platforms, such as NGS.  Prior to Novartis, Sarah held multiple positions at Johnson & Johnson, Ortho Clinical Diagnostics, and Charles River Laboratories. Sarah received an MS, Biology, Biochemistry from Northern Illinois University and an MBA from California State University, Dominguez Hills. She received a BS in Chemistry from Northern Illinois University.

About Sampled:

Sampled is a next-generation laboratory that unlocks the valuable data in any biological sample. Through our integrated Sampled Lab services, we can Store, Manage, Analyze, Research and Transport biological materials, offering partners a seamless solution for all research samples. Our vision is a world where we make it faster and easier for health innovators to improve human health, with a mission to be behind every transformative health innovation. Sampled is headquartered in Piscataway, N.J. with labs across the US and Europe and partner labs in the Netherlands, China and Australia.

Infinity BiologiX LLC, Roylance Stability Storage Limited and Roylance Scientific Limited are doing business as Sampled.

For more information, please visit www.sampled.com 

Media Contact: Mike Thurogood Mike.Thurogood@sampled.com

We are proud to announce that four upcoming talks and a poster will be presented at ISBER 2022, which will be returning to the in-person conference setting in Atlanta, Georgia. Filled with innovative technology news and research findings that cover a wide range of disciplines from biorepository news, to assay development and stem cell banking, you won’t want to miss these presentations. Kicking off the series of talks, CEO of Sampled, Robin Grimwood will present his plenary talk “Innovative strategies for protecting sample integrity with an eye towards the future”. Robin will discuss why ensuring samples are available as an active resource for analytical studies, whilst continuously innovating strategies to create renewable resources for future use and discovery is crucial for biorepositories to succeed.

Following this, Head of Scientific affairs, Dr Michael Sheldon will be partnering with Fluidigm (now Standard Biotools) to give a workshop that address sample identity and sample quality challenges. Here, Dr Sheldon will be covering what best practices should be followed involving genetic testing and Quality Control in a biobanking environment. A discussion on the need for, and challenges involving high-throughput solutions for polygenetic risk testing will be given by Christian Bixby and Jess McDevitt. Christian and Jess will explain how Sampled achieved an impressive 10-fold increase in NGS COVID sequencing weekly capacity over a 30-day period and what it took to complete this incredible feat.

The final talk, “Strategies for generating the highest quality isogenic iPSC lines” will be given by Dr Azadeh Jadali. Similarly,  a poster titled: “Induced Pluripotent Stem Cells- The next step in the modelling of genetic diseases” will be also presented throughout the duration of the conference.

We’re honored to see the expertise within the Sampled team recognised by ISBER and excited to share and gain insights from our contemporaries look forward to sharing our insights on biobanking in practice, but if you can’t wait to learn more, why not check out our brand new website to learn about our Sampled Labs.

Register for the conference directly with ISBER here.