Aug. 17, 2013

edited by Ginny Allain

The integration of advanced sequencing technologies into diagnostic medicine has had an enormous impact on clinical laboratories. Physicians now have access to highly accurate information in a timely manner, and this can tremendously improve patient care. However, as new procedures are adopted in genomic testing, new challenges also will need to be met.

DNA sequencing—applications in the Microbiology laboratory

DNA sequencing techniques, in particular next generation sequencing (NGS), have made tremendous impacts in Human Molecular laboratories, allowing for rapid sequencing of human genes and genomes. These techniques have influenced—and continue to influence—other clinical laboratories as well. Recently, NGS has been used in Microbiology laboratories to sequence microbe genomes. One application of this genomic sequencing is the identification of the species of an isolate. If an isolate is particularly difficult to identify based on traditional typing techniques, one can obtain evidence of species relationships by entering a sequenced genome into web-based applications that compare submitted genomes with known genomes.

Another application of NGS in the Microbiology lab involves sequencing isolates from apparent outbreaks. This approach has been particularly useful in confirming true outbreaks and in identifying asymptomatic carriers who are unknowingly causing recurrent infections. Upon identification, an individual can be treated, thus ending the recurrent outbreaks. NGS can also be useful in defining the genetic variance leading to unique virulence or resistance to antibiotics, prompting more appropriate patient care choices. DNA sequencing has already impacted Microbiology labs around the world and will undoubtedly have even greater impacts in other hospital laboratories.

-Laurel Estabrooks, PhD, FACMG
Vice President of Genetics Business Development
SCC Soft Computer

Expanding landscape of genetics and genomics

The market landscape of genetics and genomics is rapidly expanding. Molecular testing has accelerated in recent years and continued growth is projected, leading to the emergence of new testing and regulatory expansion. The market is shifting from a reactive, volume-based model to one that is value-based and proactive, and uses a consolidated view to deliver personalized medicine.

The cost of sequencing is declining, as evidenced by next generation sequencing, a fast, inexpensive platform in which the entire human genome can be sequenced. The amount of data and information that is available is outpacing human cognitive ability, and clinicians and providers must be able to manage and interpret this data for patient diagnoses and decisions.

Successful genomic and genetic testing depends on lab workflow, robust bioinformatics, and professional interpretation. Bioinformatics requires large data set storage, interaction with multiple third-party databases, and third-party software for managing the extremely complex data analysis algorithms. Interpretation requires integration with clinical information, and organization and reuse of previously gathered knowledge and professional reports.

The process must start in the laboratory. Efficient lab testing processes support increasing molecular testing while maintaining data and quality control. Utilizing the clinical laboratory for molecular testing helps to manage the workflow while integrating results for consolidated, personalized medicine.

-Megan Schmidt, BS (Biology)
Senior Product Manager
Sunquest Information Systems

Widespread use of genomic testing: the challenges we face

In order to achieve widespread adoption of genomic testing, a number of hurdles need to be overcome: the cost of technology; the requisite regulatory approvals; and fair, equitable, and sustainable reimbursement. While many continue to tout the coming of the $1,000 genome, most fail to factor in the total cost including the capital equipment required, the consumables, the highly trained personnel, and validations required. In addition, the not-always-present bioinformatics capabilities must be available to fully understand, interpret, and report the results.

The changing reimbursement landscape also needs to be considered, as reduced payments can negatively influence adoption. As the Centers for Medicare and Medicaid Services (CMS) reimbursement landscape in molecular diagnostics continues to evolve away from the former “stacked” CPT codes to the new “bundled” codes, battles are still being fought to achieve reimbursements that both payers and providers can live with. Already some of the previously announced reimbursement rates have been driven upward as a result of backlash from the lab industry. As new genomic tests continue to come on line, payers are going to demand convincing evidence of clinical utility, not only showing improved clinical outcomes, but also meeting or exceeding current performance levels at costs that won’t bankrupt the healthcare system.

Moreover, factoring in the lack of training and experience of many private practice physicians in the area of genomics, the field also needs to diligently work to bring this much needed component into the equation. Even when these challenges are met, it is also becoming increasingly clear that new legal challenges are on the horizon. Malpractice insurance premiums are likely to increase as physicians seek to protect themselves from legal actions resulting from failing to act upon either gene sequences screened for or those incidentally found. It’s going to be an interesting ride.

-Richard A. Montagna, PhD
Senior Vice President for Scientific Affairs
Rheonix, Inc.

Sequencing technologies making strides in diagnostic medicine

The recent integration of advanced sequencing technologies into diagnostic medicine has led to incredible achievements in patient management. The progress in DNA sequencing has led to more efficient delivery of medically relevant information in far less time and with much lower investment than just a few years ago. In particular, the emergence of non-invasive prenatal testing (NIPT), in which next generation sequencing technology is used to detect fetal abnormalities at very early stages of a pregnancy through a simple blood test, enables new options for managing a pregnancy. Using this technology offers physicians highly accurate information in a timely manner, while at the same time eliminating the risk of miscarriage associated with current, more invasive methods.

Technologies like NIPT are becoming increasingly prominent in the clinical setting, and have already begun to change the paradigm for the detection of a range of diseases and conditions as they are accepted into professional recommendations and medical society guidelines. In the coming years, the role and scope of these advancements will only expand as medical professionals learn more and can fully harness their potential for the sake of patients around the world.

-Dirk van den Boom, PhD
Executive Vice President R&D