Report of the fourth conference on next-generation sequencing (NGS) for adventitious virus detection in biologics for humans and animals: Validation and implementation of NGS

Report of the third conference on next-generation sequencing for adventitious virus detection in biologics for humans and animals

Next-generation sequencing (NGS) technologies are enabling breakthroughs in how the biomedical community is developing and evaluating medical products. One example is the potential application of this method to the detection and identification of microbial contaminants in biologic products. In order for the U.S. Food and Drug Administration (FDA) to be able to evaluate the utility of this technology, we need to have the information technology infrastructure and bioinformatics tools to be able to store and analyze large amounts of data. To address this need, we have developed the High-performance Integrated Virtual Environment, or HIVE. HIVE uses a combination of distributed cloud storage and distributed cloud computations to provide a platform that is both rapid and responsive to support the growing and increasingly diverse scientific and regulatory needs of FDA scientists in their evaluation of NGS in research and ultimately for evaluation of NGS data in regulatory submissions.

The US Food and Drug Administration (FDA) is a remarkable hybrid. Part regulatory agency, part public health agency, it sits at the intersection of science, law, and public policy. The FDA’s mission can be considered in the context of 2 broad dimensions: the products it regulates and its core functions. Both fall under the rubric of protecting and promoting the public health. The FDA’s remit is both broad and diverse: altogether, the agency has regulatory responsibility for >20% of the US economy. The products it is charged with overseeing through its various centers1 encompass food and cosmetics (regulated by the Center for Food Safety and Applied Nutrition); food and drugs for animals, including companion animals and animals used for food (regulated by the Center for Veterinary Medicine); and medical devices, drugs, and biologics (regulated by the Centers for Devices and Radiological Health, Drug Evaluation and Research, and Biologics Evaluation and Research, respectively). Tobacco products were added to the FDA’s portfolio by the Tobacco Control Act of 2009, and are overseen by the Center for Tobacco Products. Regardless of the specific product regulated, the FDA’s core mission remains the same: to protect the US population by helping to ensure the fundamental safety of the food Americans consume and the medical products prescribed by their clinicians. At the same time, this primary mission is complemented by a mandate to promote the public health by reviewing research and taking appropriate action on the marketing of regulated products in a timely manner. Not only do people need access to advances in nutrition and medical therapies, but also the American spirit is itself characterized by a strong current of scientific and technological innovation. At first glance, differences in these 2 priorities, protecting the public safety and promoting the public health through encouraging innovation, might …

On July 1st, 2013, the Ministry of Health, Labor and Welfare (MHLW) issued an official notification regarding the co-development of companion diagnostics (CDx) with a drug which requires any exclusive diagnostic test or medical device to predict efficacy or adverse reactions to the drug. The main frame and contents in the MHLW's notification are quite similar to the summaries in the final guidance issued by the US Food and Drug Administration (FDA) on August 6th, 2014 Guidance for Industry and Food and Drug Administration Staff (In Vitro Companion Diagnostic Devices, [2014] ), and these recommend industries to develop, study and submit CDx and the corresponding drug contemporaneously as much as possible. Following the MHLW's notification, the Pharmaceutical and Medical Device Agency (PMDA) notified on December 26th, 2013, "the technical guidance for co-development of CDx and the drug" that mentioned the regulatory requirements for clinical trial of the drug and CDx as well as analytical validity of CDx required for the trials. These official notifications from the Ministry and the Agency may be useful for pharmaceutical and diagnostics makers to understand how they should co-develop and validate CDx for clinical trials and regulatory submission. However, since the most anticipated technologies such as the next generation sequencer (NGS) are more complex and its medical risks could be high level, the existing regulatory system focusing on only diagnostics reagents and devices that are developed and manufactured by in vitro diagnostics (IVD) makers may be no longer suitable for the characteristics of CDx for the future.As an increase of clinical needs for multiple biomarkers assay by DNA sequencer, on November 19th, 2013, the FDA cleared 510K for NGS and its universal kit. On October 3rd, 2014, moreover, the agency notified two drafts of guidance (Anticipated Details of the Draft Guidance for Industry, Food and Drug Administration Staff, and Clinical Laboratory in Framework for Regulatory Oversight of Laboratory Developed Tests (LDTs), [2014]; Anticipated Details of the Draft Guidance for Industry, Food and Drug Administration Staff, and Clinical Laboratory in FDA Notification and Medical Device Reporting for Laboratory Developed Tests (LDT), [2014]) for oversight of laboratory developed tests (LDTs) with medium or high medical risks. These FDA's strategic decisions and new regulatory frameworks may allow the clinical laboratories to develop and perform more easily NGS-based CDx under the certification of Clinical Laboratory Improvement Amendments (CLIA). However, neither law nor regulated quality management system similar to the CLIA exists in Japan. To effectively validate LDTs and NGS for medical practice, Japan should learn more the current regulatory changes and initiatives in the US, as well as to reform the regulatory frameworks and create any regulated quality management system for clinical laboratory testing to be reimbursed.

On February 20, 2015, as part of the Precision Medicine Initiative, announced by President Obama, the Food and Drug Administration (FDA) held a meeting at the National Institutes of Health (NIH) all day. The meeting was titled “Optimizing FDA's Regulatory Oversight of Next Generation Sequencing Diagnostic Tests” (Food and Drug Administration, 2015). The meeting convened thought leaders in laboratory science and clinicians in industry, academia, and advocacy. The President earmarked $10 million in his fiscal year 2016 budget for the FDA to acquire additional tools and expertise to help generate knowledge about which genetic changes are important to patient care and foster innovation in genetic sequencing technology, while ensuring that the tests are accurate and reliable. Next generation sequencing (NGS) can be used for many things, and that makes it difficult to regulate under the existing framework. If used in a clinical context, NGS might be considered an in vitro diagnostic test. The FDA would typically regulate those tests (although this regulation is also very controversial [Pathak and Terry, 2014]). However, NGS identifies more than one or two specific biological markers and may find much variation in one test application. Because some of these, perhaps the majority in the coming years, will be of unknown significance, clinicians and patients may not know what to do with the information. With the goal of appropriate oversight of NGS, the FDA posed several questions to five panels throughout the workshop. These included the topics of analytical and clinical performance. Many of the analytical questions were focused on the better use of standards and on a standard-based approach to regulating whole exome and genome sequencing. The clinical performance discussion ranged from what to communicate to whom and when, to the sharing of data in large databases, such as ClinGen. There appeared to be a great deal of consensus that sharing variants should be the norm. In addition, most clinicians and laboratorians clearly do not want the FDA to regulate the practice of medicine. I spoke at this meeting from the point of view of a patient/participant in genomic medicine. I do have some “science cred”: I am the curator of the part of the Leiden Open Variation Database at the National Center for Biotechnology Information for ABCC6; this gene causes the condition that affects my children, pseudoxanthoma elasticum. Most of my comments arose from Genetic Alliance's work with all of the stakeholders of NGS. In recent years, we have conducted both focus groups and structured interviews with individuals who have conducted NGS. My personal perspective is that we don't really base much of medicine on strict evidence—it's a combination of art and science, and its actual implementation varies widely because of the choices individuals make in response to recommendations and prescriptions. It seems to me that we are attempting to apply more rigid standards to an NGS just because it is digital and we think we can measure it better than other kinds of testing. The solution to understanding what all of these data mean, and doing it sooner than later, is to deliver results to people. With it, we must convert patients to participants, a place many people want to go anyway. Data sharing with phenotypic information is going to be critical to get us to where we understand the results of NGS. Transformation of the oversight system is required. The President is asking for this. There is no one-size-fits-all answer for what NGS results should be returned. It seems we wish there were a simple answer to the question “What should we be giving back to people, back to patients?” In most areas of our lives, we have some ability to articulate our preferences for knowing or not knowing something. We need to apply this to NGS, and we have the technologies to do it. There is a robust science around uncertainty and risk in other disciplines from which we can borrow, including studies on what it means to return results to individuals, even when those results might indicate risk for high morbidity (Chung et al., 2009). The FDA is conducting some innovative work in patient preference: the patient-focused drug development work from the Center for Drug Evaluation and Research and some of the patient preference work with algorithms on obesity by the Center for Devices and Radiological Health. The same patient/participant preference work should be considered in the oversight of NGS. The preferences of participants are critical in a learning healthcare system.

Introduction: Liquid biopsy as a novel and non-invasive test for the surveillance of cancer is rapidly growing, by next-generation sequencing (NGS) technologies with multi-gene panels. Objective: The aim of this study was to describe the validation and implementation of a cell free tumor DNA (cfDNA) from the patients with non-small cell lung cancer (NSCLC), to sequence for 19 genes and copy number variation analyses for 5 genes via a novel NGS platform; GeneReader NGS System. Materials and Methods: We performed the complete NGS workflow with modifications, and sequenced the cfDNA extracted from 100 NSCLC patients. The multi-gene panel includes 19 lung cancer related genes (AKT1, ALK, BRAF, DDR, ERBB2, ESR1, KIT, KRAS, MAP2K1, NRAS, NTRK, PDGFRA, PIK3CA, PTEN and ROS) to sequence and additional copy number variations of 5 genes (RICTOR, EGFR, MET, FGFR1 and ERBB2) that all were selected to represent the most actionable genes for the clinical oncology and molecular diagnostics. The sequencing was performed using a novel NGS platform (GeneReader NGS System, Qiagen). Results: The validation process and the implementation of genetic testing from the cfDNA by this novel NGS system have been utilized for the clinical use. After quality assessment, the data from this NGS system was bioinformatically processed and a tertiary analysis was performed using QCI-Analyze and QCI-Interpret bioinformatics tools. The data was then reviewed on alterations and those reported in different mutation databases. The clinically relevant alterations were identified and reported due to the testing indications. Overall, actionable variants in EGFR, ALK, KRAS, PIK3CA, MET, FGFR1 and ERBB2 genes were detected and reported in 62 % of all NSCLC patients while the majority were in EGFR. Conclusions: For each of the 100 samples tested thus far, at least one variant was detected showing the high sensitivity and specificity of both the multi-gene panel and this novel NGS platform. Our evaluation yielded good results for the actionable multi-gene panel selected and provides a comprehensive NGS analysis and workflow for this new platform. Citation Format: Atil Bisgin, Ozge Sonmezler, Ibrahim Boga. Validation and implementation of next-generation sequencing in liquid biopsies by a novel NGS platform: Focus on non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3602.

The future of drug safety: What the IOM report may mean to the emergency department

Successful Investigational New Drug Preparation without Reinventing the Wheel

172 Background: Next generation sequencing (NGS) is the laboratory cornerstone of precision oncology treatment. In advanced colorectal cancer (CRC), current guidelines recommend testing RAS, BRAF and MMR biomarkers as standard of care. The added value of comprehensive genomic profiling is so far unclear. Traditional NGS operations are complicated, requiring specialized equipment and personnel. In many jurisdictions, cancer patients are treated in publicly-funded community hospitals, where NGS is not typically utilized and access to testing via send-out services is associated with lengthy turnaround times. Here, we have validated and implemented one of the world's first "point of care" NGS services. Our early experience on NGS implementation and impact in CRC patients is described. Methods: All NGS studies were performed using the Oncomine Precision Assay (OPA) on the genexus integrated sequencer. NGS was performed at the request of the treating physician. All NGS was performed in a local community pathology lab by histotechnologists, simultaneously responsible for IHC testing (such as MMR) and interpreted by anatomic pathologists in conjunction with routine diagnostic pathology services. Retrospective chart review was performed for all patients undergoing sequencing studies and key data, including turnaround time and NGS findings were extracted from the electronic medical record for analysis. Results: A total of 51 cases with CRC were tested using point of care NGS from November 2020-August 2021, initiated by treating physicians. The median turnaround time for results was 3 days. Oncogenic driver events were identified in 46 (90%) cases, including canonical mutations in KRAS, NRAS and BRAF (Table). Actionable mutations were identified in 13 (25%) samples that would not have been identified with single-gene testing. Conclusions: Here, we show that comprehensive NGS can reveal occult resistance mechanisms to standard therapy and identify actionable biomarkers in a substantial proportion of patients with CRC. NGS added valuable information compared to guideline-recommended testing standards. Our study demonstrates that local testing can have rapid turnaround times. To our knowledge, this is the first report of “point of care” NGS in CRC. Further follow up is needed to explore the utility of these expanded roles for NGS testing. [Table: see text]

When should we order a next generation sequencing test in a patient with cancer?

FDA‐approved Next‐Generation sequencing system could expand clinical genomic testing

Next Generation Sequencing Reveals Potentially Actionable Alterations in the Majority of Patients with Lymphoid Malignancies

External quality assessment (EQA) is a keystone element in the validation and implementation of next generation sequencing (NGS)-based HIV drug resistance testing (DRT). Software validation and evaluation is a critical element in NGS EQA programs. While the development, sharing, and adoption of wet lab protocols is coupled with the increasing access to NGS technology worldwide, rendering it easy to produce NGS data for HIV-DRT, bioinformatic data analysis remains a bottleneck for most of the diagnostic laboratories. Several computational tools have been made available, via free or commercial sources, to automate the conversion of raw NGS data into an actionable clinical report. Although different software platforms yield equivalent results when identical raw NGS datasets are analyzed for variations at higher abundance, discrepancies arise when variations at lower frequencies are considered. This implies that validation and performance assessment of the bioinformatics tools applied in NGS HIV-DRT is critical, and the origins of the observed discrepancies should be determined. Well-characterized reference NGS datasets with ground truth on the genotype composition at all examined loci and the exact frequencies of HIV variations they may harbor, so-called dry panels, would be essential in such cases. The strategic design and construction of such panels are challenging but imperative tasks in support of EQA programs for NGS-based HIV-DRT and the validation of relevant bioinformatics tools. Here, we present criteria that can guide the design of such dry panels, which were discussed in the Second International Winnipeg Symposium themed for EQA strategies for NGS HIVDR assays.

Report of the second international conference on next generation sequencing for adventitious virus detection in biologics for humans and animals

Noncanonical Gene Fusions Detected at the DNA Level Necessitate Orthogonal Diagnosis Methods Before Targeted Therapy.