Divyaa Ravishankar's Blog


Respondents Show Significant Interest in Developing Clinical NGS-based Tests for Infectious Disease Testing Applications

22 May 2017

Published: 5 May 2017

Next-generation sequencing and the use of genomics in diagnosis and treatment have generated many headlines in recent years, both for advancements on the research front, as well as in the development of diagnostics and pharmaceutical products that leverage genomics in oncology and other early-adopting fields. The question is no longer “if” or even “when” genomics will move bench to bedside, it’s happening now. It is imperative that healthcare providers position to integrate genomics and other ‘omics’ information into standard care today, so that their patients don’t miss out tomorrow.

The next-generation technologies have created many capabilities and opened up newer applications within the clinical space. The brisk evolution of sequencing technologies has flooded the market with several sequencing platforms and bioinformatics tools whose diverse applications stand as another obstacle restricting the potential of next-generation sequencing. Today, several factors, such as price, access, and lack of reimbursement stand as barriers to the adoption of this technology in the clinic.

To investigate this further, the editors of Clinical Lab Products magazine and Frost & Sullivan conducted a brief survey with the lab managers of clinical NGS laboratories during August – November 2016. The primary goal of this research was to analyze the current and future adoption plans of NGS for clinical applications. The insight details outsourcing needs, top clinical NGS service providers, interest areas of clinical NGS, purchase patterns for instruments and reagents, predominant methods, platforms for NGS clinical data interpretation, and most popular instruments and brands.

To qualify for survey participation, respondents had to be working in a private or public laboratory, clinical research institution, reference laboratory, academic medical center laboratory, hospital lab, or diagnostic company that employs NGS for clinical use. Respondents had to be constant users of this technology, belong to the scientific community, and be in a position to authorize purchases. The target group was screened to ensure that only qualified respondents participated. In total, 69 decision makers qualified for the survey of the total 185 who had expressed interest in participating. Global in scope, respondents indicated a wide range of job titles such as lab directors, scientists, lab managers, clinicians, pathologists and lab technicians from academic medical center labs, clinical research institutes, hospital laboratories, and reference laboratories.

Survey Participant Demographics

The demographics of survey participants are graphed on this and the following page. A majority (82%) of respondent labs are based in the United States. Almost 50% of the respondents hail from hospital laboratory, indicating that this segment is the highest user of the technology for clinical use, followed by reference laboratory. A majority of the respondents (52.7%) were end users of the technology, and a majority (31%) held the position of a lab manager, director, or supervisor. More than half of the survey respondents (56%) indicated they were pursuing clinical applications through CLIA-regulated, laboratory-developed tests.

Current and Future Interest Areas for Clinical NGS Testing

On probing the future application areas for clinical NGS testing, there was tremendous interest in conducting NGS-based tests for oncology germ line mutation and somatic mutations. Rare genetic disease testing and pharmacogenomic (PGx) testing were the second and the third highest areas of interest. Pharmacogenomic testing underpins personalized medicine, Over 1,000 labs in the United States offer PGx testing. PGx testing helps physicians select the right medication and prescribe safe combinations based on a patient’s genetic composition. This ensures that there are no severe side effects, or, in some cases, no effects on drug efficacy.

Pathology labs and toxicology labs are early adopters of PGx testing, given that the former group focuses on tissue, while the latter focuses on screening people for drug abuse and for prescription drug over use. Companies such as Kailos and Admera are offering PGx tests for 100 commercial drugs.

The current interest areas did not change in terms of perceived interest areas in oncology somatic and germline mutation; however, HLA typing did appear in the top-four current areas of interest. This also correlates with the fact that the PacBio RSII sequencer, which is capable of generating long reads in a single molecule using real-time sequencing, was specifically developed for HLA typing. Using a PacBio RSII analyzer, one can resolve issues with phase ambiguity, which is one of the critical challenges of HLA typing methods.  When we queried the sequencing methodology used for HLA typing and pharmacogenomic testing, we found targeted sequencing received the highest number of responses, followed by exome sequencing and methylation sequencing.

Based on the interests of current and future application, the survey respondents were also asked to pick their most frequently used instrumentation for clinical applications. Of the 9 different instruments surveyed broadly for clinical use, the current users indicated high use of Illumina HiSeq (35.3%). HiSeq has become an undisputed workhorse due to its wide breadth of use across exome, targeted resequencing, whole transcriptome, and denovo. This instrument was closely followed by MiniSeq (26.7%) and MiSeq (23.5%).  Among the future users who intend to use the instrumentation for clinical use, Ion Torrent PGM (31.3%) from Life Technologies (ThermoFisher Scientific) remained a popular model. On correlating specific applications to the instrument use, users performing oncology somatic mutations and germline mutations were users of Illumina HiSeq. In the case of MiniSeq, users were largely performing HLA  typing and cardiomyopathy testing.

Interest in Infectious Disease Testing

While several fields have taken the lead in using genomics, there is still much to be learned in early-adopting applications, as well as other clinical areas in which genomics may play a role, such as in infectious diseases and disorders caused by the microbiome.

About 51.6% (majority) of the respondents showed a keen interest in using this technology to develop assays for certain infectious diseases. Among current applications, c. difficile was the most common, followed by influenza A/B and antibiotic resistant pathogens. Among the future applications, the highest cited disease area was meningitis (90.9%), followed by respiratory diseases–bacterial. This can also be correlated to the development of point-of-care assays on molecular platforms aimed at CLIA-waived assays. Companies are increasingly using NGS-based technologies to target infectious diseases. (Note that survey respondents could select multiple responses; hence, the total does not add up to  100%.). Of all the types of sequencing methods surveyed, targeted sequencing received the most responses for the diagnosis of infectious disease testing in general. Targeted sequencing is also the recommended practice, given the prior knowledge of the pathogen being tested for.

Infectious diseases diagnosis requires rapid and actionable results, sometimes within hours. Delayed diagnosis can lead to incorrect initial diagnoses and can result in fatalities. As a result, NGS-based infectious disease diagnosis creates opportunity to improve efficiency in detection, much faster than microbial methods. The draft guideline for NGS Dx devices explains how the Center for Devices and Radiological Health (CDRH) unit plans to regulate these devices for class II premarket notification.

Interest Areas in Infectious Diseases, Global, 2016

Factors Limiting Adoption

The survey respondents were asked to rank several factors on a scale of 1 to 5 (1 = low importance; 5 = high importance) that they perceive as obstacles to the adoption of NGS for clinical application. One might anticipate that the cost of the instrument itself might be a significant attribute limiting adoption. The survey results are surprising and point out additional areas that vendors need to be aware of that are challenging to technology adoption.
Although most of the factors received an equal weightage, a few parameters, such as price of the consumables (3.94); complexity of NGS data analysis (3.76); unplanned costs (3.76); and lack of reimbursement, coverage, and coding (3.53), seem to flag as the top market restraints slowing down the transition of the technology to the clinic. On probing the aspect of cost of consumables, cost of the sample is determined by the consumables used for the experiment. Consumables are the largest contributors to operational expenses, especially in both library preparation and sequencing. Several companies sell library preparation kits based on the application and the study size. A lab must pay careful attention to selecting a sequencing technology for which kits are sold.

One might wonder why outsourcing remains a common strategy for interpreting complex bioinformatics data. Currently, costs associated with NGS data management, primary analysis of NGS data, and biological interpretation make up approximately 55.0% of total NGS costs. However, by 2020, NGS informatics costs are likely to make up a larger share—65%—of costs. The costs associated with biological interpretation will most dramatically increase, from 35.0% of costs observed in 2012 to 55% of costs in 2020. While primary and secondary data analysis tools are likely to become commoditized as pipelines grow more standardized, biological interpretation and clinical reporting tools are expected to remain a high-value component of NGS informatics.

Because customers employ NGS for an incredibly broad range of applications, no ideal universal product exists for NGS informatics. For example, customers may work in an academic institution conducting basic biomedical research, in a biopharmaceutical setting conducting clinical trials, in a hospital conducting diagnostics testing, or in an agricultural setting conducting plant research. Moreover, these customers may use NGS for whole genome sequencing, exome sequencing, targeted panel-based sequencing, or RNA-seq. Without a one-size-fits-all approach to NGS informatics, customers struggle to identify the appropriate informatics tools, while vendors struggle to provide the most appropriate solution. Often, vendors are forced to take a bespoke approach, providing consulting and extensive customer support in addition to their shrink-wrapped product. Moreover, NGS customers are often overwhelmed by the large number of informatics tools that they can employ for their NGS data analyses. There is an incredibly broad selection of public domain and commercial tools from which customers can select the pieces of their pipeline.  This high degree of fragmentation often results in purchase delays and an amplified reliance on internal bioinformatics teams to build pipelines from scratch. The concept of cloud-based platforms has certainly become more popular recently; however, Frost & Sullivan research finds that 60% to 70% of customers are still reluctant about using cloud-based solutions. While academic customers are generally comfortable with the cloud, they may not drive the major future market opportunities associated with clinical sequencing.

Conclusion:

Newer capabilities enabled by next-generation sequencing are expanding opportunities for the platform in clinical applications. While the proliferation of sequencing technologies has flooded the market with several solutions, their success will depend on supportive bioinformatics tools that analyze and interpret biological information, competitive pricing, access, and reimbursement.

2016 Global Survey on Clinical Next-generation Sequencing report, part of Frost & Sullivan’s  Life Sciences Growth Partnership Service program, analyzes the market based on an online survey of a carefully selected group. Click here for complimentary access of this report and to register for a Growth Strategy Dialogue, a free interactive briefing with Frost & Sullivan’s thought leaders.

About the Author:

Divyaa Ravishankar has over 12 years of experience in market research and management consulting. In addition to authoring numerous reports in the area of in-vitro diagnostics, she has advised clients on market trends, implications, and strategies on such diverse topics as next-generation technologies, end-user and product/feature/pricing analysis, merger and acquisition target analysis, international market expansion strategies, detailed demand modeling, and competitive analysis. Ms  Ravishankar earned her  Master’s Degree in Biological Sciences from Birla Institute of Technology.

Formal Adoption of Changes to European Regulation of In Vitro Diagnostics Begins in 2014

17 Jan 2014

The current regulatory framework for in vitro diagnostics (IVD) is provided by the Directive 98/79/EC of the European Parliament. The new and stricter regulation framework is expected to start in 2014 and is in accordance with the Global Harmonization Task Force on Medical Devices (now operating as the International Medical Device Regulators Forum) guidelines. Examples of major changes include the risk classification system with special requirements for companion diagnostics. According to the current EU IVD directive, companion diagnostics are classified as low risk, so most manufacturers tend to self-assess and self-certify companion diagnostic products to obtain a CE mark for the European market. The new IVD regulation is specifically targeted toward tests such as genetic tests and companion diagnostics that have a key role in providing information to product treatment response or reactions. As per the new classification, all of these tests will be required to have proper authorization, pre-market clinical evaluation, post-market clinical follow-up, and surveillance.

It is expected that the new European Union (EU) regulatory framework for in vitro diagnostics (IVD) will introduce significant changes to the previous regulatory framework, which could affect costs associated with new product launches and thus the product development pipelines of major IVD companies. Compared to the
FDA regulations for IVD, the EU IVD regulations have been less stringent and, consequently, IVD companies often launch products in Europe before the United States. While a framework for co-development of targeted therapies and associated companion diagnostics has been established by the FDA to guide the commercialization of these
drug-companion diagnostic pairs, the lack of framework in Europe for this relatively new industry has been a challenge for companion diagnostic companies that plan to market a targeted drug or companion diagnostics in Europe. Nearly all diagnostic tests in Europe are classified as low risk and are exempt from pre-market evaluation.
This is an incentive for companies to launch products in Europe as there is a higher rate of approval for new tests and products compared to the US, for instance. The new IVD directive will position companion diagnostic tests in the high-risk category with additional regulatory hurdles that would increase costs and timelines in co-development, requiring IVD companies to update their regulatory strategies for Europe.

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