NGS-based Clinical Testing (Part I)

The adoption of genetic services is key to our ability to provide personalized medicine in the future. The goal is to better diagnose diseases, predict their outcome, and choose the best possible care option for a patient. We still have a long way to go to achieve this goal. While there is agreement about the ultimate goal, there is still a lot of uncertainty about the timing of the adoption. Essentially, it is a widely debated topic among experts. Here is what we know. There are three phases of the adoption (see also Fig. 1):

  • Early Stage: Strong focus on science and research; understanding underlying genetic mechanisms and pathways.
  • Moderate Adoption: Utilizing available results in the clinic on a selected basis. The science and clinical communities focus on increasing the number of therapeutic areas as well creating infrastructure to improve scale.
  • High Adoption: At this point, genetic services are part of standard care.
NGS Testing Adoption Curve

NGS Testing Adoption Curve

There are a number of success factors that are key to drive adoption in the moderate phase of the curve:

  • Regulatory Environment: This is a wide open field. The FDA is paying increasing attention to how genetic information about individuals is handled. Very publicly, it engaged with 23andMe to review their processes and procedures. While this gives the adoption process a pause in the short-term, it might mean that in the mid- and long-run, we can hope for a consolidated governing body protecting patients while enabling clinicians to make informed decisions.
  • Testing Technology: There is already clinical experience leveraging genetic markers via gene panels. Many experts believe that the usage of Next-Gen sequencing data, including whole exomes and genomes, will ultimately give us the insights needed to diagnose or predict diseases and select treatment options at the highest level possible.
  • Reimbursement: The adoption of these tests in the clinic hinges on the ability for doctors to recover the expense associated with genetic tests. For this to occur, the quality of the results of these tests has to be very high and their clinical utility must be proven. Also, price points have to become reasonable for payers and insurance companies to accept these tests as part of standard care.
  • Physician Education and Acceptance: We are facing the need to educate a wide range of health care specialists involved in designing, conducting, interpreting and utilizing genetic tests: translational researchers, pathologists, geneticists, genetic counselors, bio-statisticians, etc. This also includes the personnel supporting these professions, such as nurses and medical assistants.
  • Bioinformatics Capability: There is a plethora of new tests in the development stage that require a massive computing resource to deal with a sheer amount of data. The storage requirements for a whole genome, depending on the coverage, ranges between 100 and 200 GB for a single person. Added to that are the results of the variant analysis and other datasets generated as part of analysis. For a wider scale usage, these datasets and their interpretation have to be part of the patient record. This requires investment in an infrastructure to provide, gather, store, and research and clinically interpret this data on a large scale that is not currently in place.
  • Patient Demand: Any test requires patient consent. Because of this, a more global adoption of genetic tests is also dependent on patients agreeing to use their DNA for this purpose. So far, the early successes of direct consumer companies such as 23andMe seems indicative of a general positive attitude of patients towards utilizing their DNA information for clinical purposes. Ease of use and affordability will be crucial. Also, as with any new technology being rolled out on a global basis, there are concerns that need to be publicly discussed. Data security or the potential use of this data for purposes outside of the specific clinical use by insurers or other third parties must be considered.

The genetic testing technology and infrastructure is evolving quickly. There are a few areas where adoption is expected first with significant testing volume:

  • Oncology
  • Pediatrics and Newborn Screening
  • Rare diseases

Beyond these areas, there is strong potential in areas such as obesity, diabetes, and cardiac disorders. In addition to this, there is a huge uptick in the adoption expected in the area of pharmacogenomics to determine safety, efficacy, and cost of care. New applications of genetic testing will result in changes to current care teams and processes. It will reshape how pathologists, oncologists, geneticists, genetic counselors, biostatisticians, and bioinformaticians work together.

Hospitals and healthcare organizations around the globe are getting ready to build the infrastructure necessary to handle the increasing testing volume. This blog series will review issues regarding setting up and running a NGS Lab.

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