How our custom NGS panels are being used for clinical utility
By Victoria Simms on November 29, 2023 | Reviewed by Celina Whalley
Targeted Next Generation Sequencing (NGS) panels have revolutionized clinical diagnosis and treatment of genetic disorders and cancers by being able to precisely identify disease-associated variants.
By focusing only on a subset of the genome, targeted NGS is not only a cost-effective solution, but it can rapidly deliver insights into a patient's genetic profile.
This has been utilized within the clinical oncology setting, where targeted NGS has helped clinicians to make informed decisions on personalized treatment strategies like targeted therapies.
High on-target rates and uniform coverage are crucial for successful sequencing
High on-target rates indicate that a significant portion of the sequencing reads align with the intended genomic regions, minimizing the chances of capturing irrelevant data. Uniform coverage, on the other hand, ensures that all targeted regions are sequenced to a comparable depth, preventing any bias and guaranteeing a comprehensive analysis of the entire genomic region of interest.
This precision in panel design is essential for the success of targeted sequencing approaches. It directly impacts the reliability and trustworthiness of the genomic variant calls, ultimately contributing to the effectiveness of diagnostic and treatment strategies in clinical applications.
Achieving this level of precision is no easy feat, especially when using custom panels. Many factors can contribute to off-target sequencing and uneven coverage, leading to inaccurate and unreliable results. However, Nonacus has overcome these challenges by developing innovative panel design algorithms and utilizing cutting-edge sequencing technologies.
With Nonacus, you can be confident that your custom panels will deliver the high-quality data you need to make informed clinical decisions. Our team of experts will work closely with you to design a panel that meets your specific needs and ensure that it performs flawlessly in your lab.
The Nonacus Panel Design Tool empowers researchers and clinicians to design custom-tailored targeted sequencing panels for a wide range of clinical applications. This cloud-based tool streamlines the panel design process, ensuring high on-target rates and uniform coverage for optimal sequencing efficiency.
Nonacus customized NGS solutions are already being successfully implemented in clinics across the UK, demonstrating their versatility and effectiveness in various clinical settings.
Whether you need a small or large NGS panel for your clinical requirements, its built-in algorithms maximize on-target regions, and uniformity of coverage ensures high sequencing efficiency every time, helping you improve sample throughput while reducing sequencing costs.
Our customized NGS solutions are being used in clinics across the UK.
Read on to discover how our panels have been successfully implemented to:
- Consolidate clinical testing strategies
- Monitor patients for early minimal residual disease detection
- Profile childhood cancer using liquid biopsies
1. The first NGS solution created to consolidate testing strategies for myeloid and lymphoid neoplasia – FLT3-ITD debunked
This pioneering pan-haematological NGS solution was created in collaboration with Joanne Mason, Head of Haemato-oncology at the West Midlands Regional Genomics Laboratory in Birmingham, UK.
The new targeted NGS panel can detect SNVs, indels and CNVs in genes associated with both myeloid and lymphoid neoplasia. The resulting test has huge advantages for her laboratory in the reduction of turnaround times and cost burdens associated with multi-testing approaches.
Hematological malignancies are currently the fifth most prevalent cancer type in the UK and are classed as cancers affecting the bone marrow, blood, and lymph nodes.1 The effectiveness of treatments and the overall prognosis of these malignancies is significantly influenced by the promptness and efficiency of diagnosis.
However, due to the intricate nature of hematological malignancies, a comprehensive and iterative testing approach, using multiple platforms in clinics is often necessary.
Given the increasing complexity and number of targets relevant to both myeloid and lymphoid malignancies, there was a recognized imperative to consolidate the clinical workflows into a unified, single test to enhance diagnostic efficiency. To address this, Joanne Mason, in collaboration with Nonacus, designed and created a targeted NGS panel to include all of the clinically relevant test directory targets for both myeloid and lymphoid neoplasia.
For prognostic reasons, it was vital that SNV, INDELs and CNVs could be called with high precision. In particular, partial tandem duplications in genes such as KMT2A and FLT3 needed to be detected. The tiling strategy used in the panel design process ensured that FLT3-ITD duplications in excess of 200 bp could be achieved and this was validated by orthogonal techniques.
"We have worked with Nonacus to develop a program for our Hamilton robot, such that this panel can automate hybridization capture steps for enrichment; the resulting impact for our clinical service is time and cost-effective testing of hematological malignancies."
Joanne Mason, Head of Haemato-oncology at the West Midlands Regional Genomics Laboratory in Birmingham, UK.
Within the design process, automation of the technical processes was required to help increase efficiency in the clinical service. Nonacus developed an automation program in the clinical lab for the Cell3™ Target hybridization and capture steps on the Hamiliton robot, which enables batch processing of 96-samples, resulting in significant time and cost-saving benefits.
The implementation of this NGS solution for pan-hematological malignancies has had huge advantages for this clinical service, with a reduction in turnaround times and costs, which were associated with multi-testing approaches.
2. Ultrasensitive personalized NGS panels for longitudinal monitoring of minimal residual disease (MRD)
Our small, ultrasensitive Cell3 Target MRD patient-specific panels have been utilized for longitudinal patient studies, determining evidence for early detection of metastatic variants and tumor evolution in ctDNA, in patients with esophageal adenocarcinoma.
Mark Openshaw, from the University of Leicester, recently presented his research using our MRD panels at the ESMO GI congress.
Liquid biopsy emerges as a more sensitive and less invasive approach for MRD detection. By assessing the levels of cell-free circulating tumor DNA (ctDNA) released primarily into the bloodstream by cancer cells, liquid biopsy offers a glimpse into tumor cell evolution.
Through the systematic analysis of repeated liquid biopsy samples over time, it becomes possible to longitudinally monitor cancer patients and precisely gauge the presence of MRD.2 This innovative method provides a timely and comprehensive understanding of the patient's response to treatment and aids in the early detection of cancer recurrence.
In the case of esophageal adenocarcinoma (OA), currently no specific routine blood-borne biomarker exists,3 so ctDNA analysis from blood plasma is often used in clinics to track disease and relapse.4 However, little was known about how well ctDNA from OA patients reflects the genetic tumor evolution over time.5 To address this, Mark Openshaw from The University of Leicester, used two Nonacus custom NGS panels to carry out longitudinal monitoring using ctDNA from OA patients.
The study revealed for the first time that there is utility of ctDNA monitoring in patients with OA. The results showed that the NGS solution detected both primary tumor and emergent variants. This ability to confidently and accurately track metastatic specific alterations during disease progression promises new insights into OA evolution.
3. The first pan-cancer panel for liquid biopsy profiling of childhood cancer
This first-of-a-kind NGS solution for pediatric cancer was created in collaboration with researchers at the Institute of Cancer Research, UK.
The targeted NGS panel can be used to profile tumor-derived DNA present in the blood of pediatric cancer patients. This clinical solution can help clinicians make more informed treatment selections and monitor the response of their patients more closely.
In the Western world, among children, cancer remains the leading cause of death from disease. From birth to 14 years old, the most common cancer types diagnosed are leukemia, lymphoma, central nervous system and brain tumors.6 Whilst solid tumor profiling for pediatric cancers is still commonly used, the procedure can very rarely be repeated, due to its invasive nature.
Liquid biopsy profiling on the other hand, enables serial sampling of a patient, and profiling of hard-to-reach tumors. Although now widely used in the oncology field, liquid biopsies are less commonly used to investigate pediatric cancers.
To address this, Reda Stankunaite and fellow researchers Professor Louis Chesler and Dr Mike Hubank at the Institute of Cancer Research, UK, in collaboration with Nonacus designed and created a pan-cancer sequencing panel to profile tumor-derived DNA present in the blood of pediatric cancer patients.
"We used the Nonacus Cell3 Target technology as this not only provides a highly efficient library preparation and capture but uses UMIs, which combined with background noise suppression allowed us to push the limit of detection to 0.125% for known variants and 0.3% for cfDNA-unique variants."
Reda Stankunaite, Institute of Cancer Research, UK
The pan-cancer NGS solution was designed to target 67 clinically relevant genes in solid pediatric tumors, focusing on hotspot regions of oncogenes and full coverage of tumor suppressors, with the inclusion of predictive, prognostic and diagnostic SNVs and CNVs. A particular requirement was to be able to call ultra-rare genomic variants, as low as <0.3% VAF.
By utilizing the highly efficient Cell3 Target library preparation and capture, which incorporates UMIs combined with background noise suppression, the new NGS solution pushed the limit of detect to 0.125% for known variants and 0.3% for cfDNA-unique variants. It was also possible to use the same sequencing library preparation to detect large scale CNVs by low-pass whole genome sequencing as well as SNV and indels from the panel sequencing.7
This had a huge impact on the clinical interpretation of the results, as it was possible to estimate the fraction of ctDNA within the cfDNA sample. To learn more about how this pan-cancer panel was created, read our interview with Reda Stankunaite, alternatively you find more information in this publication.
“We used the expertise of scientists at Nonacus to optimize our design ensuring we had sufficient and even coverage of our targets. This allowed us to minimize the amount of sequencing needed per sample, keeping our sequencing costs low.”
Reda Stankunaite, Institute of Cancer Research, UK
This panel met all clinical diagnostic standards meaning it can now be used to bring liquid biopsy into the clinical setting for pediatric cancer testing. This opens up possibilities to routinely sample cancer patients, allows clinicians to make more informed treatment decisions and helps ensure the best possible outcome for patients.
The Nonacus Panel Design Tool empowers researchers and clinicians to design custom-tailored targeted sequencing panels for a wide range of clinical applications. This cloud-based tool streamlines the panel design process, ensuring high on-target rates and uniform coverage for optimal sequencing efficiency. Nonacus customized NGS solutions are already being successfully implemented in clinics across the UK, demonstrating their versatility and effectiveness in various clinical settings.
With Nonacus, you can be confident that your custom panels will deliver the high-quality data you need to make informed clinical decisions. Our team of experts will work closely with you to design a panel that meets your specific needs and ensure that it performs flawlessly in your lab.
So, if you're looking for a partner who can help you achieve the precision and reliability you need for your targeted sequencing projects, look no further than Nonacus.
If you would like to create a custom NGS panel to meet your clinical requirements, please visit our Panel Design Tool to start designing the NGS solution that’s right for you. Alternatively, if you would like to set up automation procedures in your lab, to enhance your clinical service, please reach out via our contact form and a member of our team will be in touch.
References
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- Blood cancer - what is it, symptoms and treatment | Blood Cancer UK Accessed Nov 29, 2023
- Honoré N, Galot R, Van Marcke C, Limaye N, Machiels JP. Liquid Biopsy to Detect Minimal Residual Disease: Methodology and Impact. Cancers 2021, 13, 5364.
- Thrift AP. The epidemic of oesophageal carcinoma: Where are we now? Cancer Epidemiol. 2016;41:88-95.
- Openshaw MR, Suwaidan AA, Ottolini B, Fernandez-Garcia D, Richards CJ, Page K, et al. Longitudinal monitoring of circulating tumour DNA improves prognostication and relapse detection in gastroesophageal adenocarcinoma. British journal of cancer. 2020;123(8):1271-9.
- Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, et al. Circulating mutant DNA to assess tumor dynamics. Nat Med. 2008;14(9):985-90
- Childhood cancerss. https://www.cancer.gov/types/childhood-cancers. Accessed Nov 29, 2023
- Stankunaite R, George SL, Gallagher L, Jamal S, Shaikh R, Yuan L, et al. Circulating tumour DNA sequencing to determine therapeutic response and identify tumour heterogeneity in patients with paediatric solid tumours. European Journal of Cancer. 2022;162:209-20.