What Clinical Sequencing Needs

What Clinical Sequencing Needs

Kalorama completed our study of the market for Next Generation Sequencing (NGS) last month - https://www.kaloramainformation.com/Generation-Sequencing-Instrumentation-Consumables-Services-Competitive-Trends-11594541/   The report says the global DNA sequencing market is a large market with an estimated $4.5 billion in product revenues in 2017, which are projected to continue to grow and reach approximately $8.9 billion in revenues in 2022.  The report has also found a number of challenges that clinical efforts need to overcome, and they are detailed in this article.  

For clinical testing, whole genome sequencing provides the most comprehensive coverage, identifying variants such as rare variants and copy number variants, and structural variations that can have a significant influence on the disease phenotype. However, at this time, whole genome sequencing is not effective in terms of cost and turnaround time. Whole exome sequencing is also an option that could be cost-effective as the cost of sequencing decreases, as it provides a high degree of confidence in the variants detected, although the incomplete coverage of the exome can pose a problem for clinical applications. For such applications, targeted, amplicon sequencing appears currently to be the best suited type of sequencing, as it permits a deeper coverage of the genes of interest compared to whole exome sequencing.

Despite the advances in NGS technologies, their successful application and translation to clinical diagnostics must overcome various challenges, including:
• The need for sample preparation solutions that use very low, limited sample inputs, as NGS typically required larger amounts of DNA
• The need for simpler sample and library preparation solutions that require minimal specialized skills
• The need to lower the cost of sequencing and consumables, particularly library preparation kits, to levels acceptable for reimbursement by third-party payers
• The development of lower-complexity data interpretation solutions, integrated in the NGS platform’s capabilities
• The acceleration of turnaround time for NGS-based clinical tests, as typical NGS results take about 10-20 days
• The development of solutions for the analysis, storage and management of genetic data, including ethical considerations of genomic data handling, interpretation and impact

The quality and amount of DNA samples is another important aspect for the development of clinical diagnostics, as a large proportion of samples are FFPE tissues, in which the DNA is typically degraded. The quality of DNA is a significant issue in particular for nanopore sequencing, therefore the development of this technology for clinical diagnostics has been challenging thus far. Moreover, given the miniaturization of samples in clinical diagnostics, the amount of sample inputs required by each technology is important in selecting the appropriate method for the development of clinical diagnostics.

As expected, Illumina’s platforms are the most favored in the development of such applications, partly due to their performance and availability, but also to their regulatory clearance by the FDA and other regulatory agencies worldwide. Additionally, the introduction of smaller sequencers is expected to further accelerate their development and commercialization for clinical sequencing applications.

As the development of NGS-based clinical diagnostics has intensified in recent years, companies activating in the NGS market introduced various solutions to address these challenges, including sample and library preparation reagent kits optimized for low input and degraded DNA samples, or for types of samples commonly used in clinical practice, such as FFPE, blood and saliva. Other approaches include technologies that reduce the overall number of steps involved in library preparation, eliminate the sample preparation step entirely, enable single tube chemistries, or permit the multiplexing of large numbers of samples.

Pace of Test Approvals a Positive Sign

In addition to the above-mentioned trends, the NGS market has been influenced by the recent momentum shift from basic to translational research, which led to the development of several NGS-based clinical diagnostic tests for a variety of therapeutic areas, with a current emphasis on oncology.  Some of these tests also received regulatory clearance in major markets, with three of them being approved by the US FDA in 2017, compared to only three other sequencing-based tests approved between 2013 and 2017.  Rare genetic or inherited diseases, followed by cancer and pharmacogenetics.   . 

 The tests approved in 2017 are Illumina’s Praxis Extended RAS panel for colorectal cancer, ThermoFisher Scientific’s Oncomine Dx for non-small cell lung cancer, and Foundation Medicine’s Foundation ONE CDx for melanoma, breast, colorectal, lung, and ovarian cancer. 

 However, clinical NGS testing is more difficult to regulate, as NGS-based tests generate large amounts of data that do not fit exactly into the previously-established categories of clinical diagnostics tests; while such tests typically detect a single disease or condition, one NGS test is equivalent to numerous tests belonging to the previous categories. To facilitate and accelerate the development of NGS-based tests, the US FDA released in July 2016 a draft guidance for the regulatory oversight of NGS-based in vitro diagnostics tests used for diagnosing germline diseases.  The agency offers recommendations for designing, developing and validating NGS tests, and proposes the use of data from FDA-recognized public genome databases in order to support a test’s clinical validity. The agency also created the precisionFDA cloud-based portal, which is intended to facilitate the sharing of data and tools among researchers in this field worldwide.