Vol. 24 • Issue 5 • Page 6

Cover Story

Tools for the Technologist: Molecular Diagnostics

Next-generation sequencing helps to personalize disease diagnoses, treatments and prevention.

By Kelly Graham Bocich, Kerri Hatt and Valerie Neff Newitt

(Editor's note: This is part 2 of a special "Tools for the Technologist" series. Part 1, addressing automation, appeared in the April issue.)

While science fiction movies and the mainstream media often equate molecular diagnostics (MDx) with the ability to look at the entire genome and determine a patient's susceptibility to disease, full genetic risk panels on a broad scale are a bit further out on the horizon, according to Alexander Lazar, MD, PhD, FCAP, associate professor of Pathology at The University of Texas MD Anderson Cancer Center, member of the College of American Pathologists Cancer Committee and liaison to the Molecular Oncology Committee.

Current applications are, however, making remarkable headway with diagnosing, treating and even preventing disease. In the realm of inherited cancers, for example, MDx is helping to define the genetic basis of cancer predisposition syndromes.

Stephen C. Peiper, MD, chair of the Department of Pathology, Anatomy and Cell Biology at Thomas Jefferson University Hospital, reports the biggest push in the field of hereditary cancer syndromes is prevention. "Many new tests for diagnosing and preventing hereditary cancer syndromes are being developed based on our understanding from molecular genetics and biology."

These findings allow patients to make very informed and highly personal decisions about how they want to manage their risk, notes Dr. Lazar. Knowledge about the genes that underlie inherited cancer syndromes often provides insight into the pathogenesis of non-inherited cancers as well. "It's a virtuous cycle," he relates.

Elizabeth Mansfield, PhD, the director of the FDA Personalized Medicine program, tells ADVANCE in some cases, drugs may be developed that can target these diseases and may lead to preventative strategies, providing a personalized approach of the best possible treatment specific to the patient's disease.

Similarly, the Pathwork Tissue of Origin Test (Pathwork Genetics) relies on a gene expression profile of more than 2,000 genes to help diagnose the root of metastatic and complex cancer cases, providing valuable information clinicians can use to develop a treatment plan and prognosis.

Preparing for Next-Gen Sequencing

The vast increases in sequencing throughput and an exponentially rapid decrease in cost are combining to allow the production of massively parallel (next generation) sequencing approaches. Dr. Lazar notes the advent of next-generation sequencing is rapidly decreasing the cost and increasingly the feasibility of testing large and complex genes. "We are heading for a time when the analysis of large and complex genes underlying a variety of syndromes can be rapidly assessed by relatively numerous providers of such esoteric testing," he says.

Next-generation DNA sequencing of an individual's genome offers a blueprint to health risks, actionable mutations and drug metabolism specific to that individual. However, a number of analytical issues must be resolved before next-generation sequencing can be implemented into the clinical lab, including ethical concerns, analytical and clinical validation guidelines, laboratory and clinician education, and of course regulatory and reimbursement issues. Susan M. Orton, PhD, D(ABMLI), MT(ASCP), associate professor, Division of Clinical Laboratory Science, School of Medicine, The University of North Carolina, notes that there are several working groups (CDC and CAP) in the process of developing guidance documents on next-generation sequencing in the clinical lab.

"Understanding the underlying genetic etiology of disease, of health, is the crux of personalized medicine," says Jennifer Morrissette, PhD, FACMG, scientific director of Cytogenics Lab and director of the Center for Personalized Diagnostics and Hospital of the University of Pennsylvania (HUP), Philadelphia. "This is a rapidly changing field. A year ago, people were saying this technology will be 5 years away before it is in clinical use. But that's just not true. It will be much sooner."

For all the understandable excitement, it's a "double-edged sword," says Dr. Morrissette. "It's difficult to put all of this information into perspective. We can do a whole exome sequence in a short period of time, but the really time-consuming part comes afterward-sifting through the data, determining what is real, what is actionable, what is prognostic and what is not. That will be the battle cry for clinical laboratorians going forward."

No Substitutes for Humans

There are multiple sequencing technologies on the market, but all include basically three steps using various methodologies: template preparation, sequencing and imaging, and data analysis. The voluminous data generated from next-gen sequencing platforms requires substantial information technology support in terms of data assembly and analysis, quality control and, of course, interpretation. While software developers are racing to perfect programs to help manage experiments, identify variants and their significance, there is as yet no substitute for a human bioinformatician.

"Bioinformaticians have become an important arm of the diagnostic testing," concurs Matthew Ferber, PhD, FACMG, Mayo Clinic, Rochester, MN. "They no longer just help compile years of testing data; now they are required within a lab as part of a test, to help shepherd the data off the sequencer into the analytics pipeline and help develop tools for things that are truly actionable."

"My advice for a technologist who wants to be a master of his domain is: Start now," says Dr. Morrissette. "In 5 years you are going to be the expert."

Dr. Orton agrees. "Medical laboratory professionals need to start learning as much about next-gen sequencing as possible so that when the time comes, and it will, laboratorians can be an important resource for clinicians who are likely to be approached by their own patients with questions about their own genetic data."

While there seems to be a dearth of available training for new-age bioinformaticians, "There are resources on the web where you can start looking at published sequence data and see what you can find," says Dr. Morrissette. And Dr. Ferber points to the Broader Institute at MIT, which offers online resources, as well as lectures and slides as close as your computer.

Training on the Fly

But the best hands-on training may be where you work. Seek out a lab that is doing new-generation sequencing, and don't be afraid to learn on the fly, say the experts.

"That's always the way it goes for the early adopters," says Dr. Ferber. "They learn on the job-the bleeding edge is always very painful; the leading edge gets a little bit easier. Once you are past that crest of the wave, official training programs begin to develop."

The nature of lab work is likely to change. "There will be constant learning and reapplication of learning from the past," says Dr. Morrissette. "Reports will become more complicated as we understand more about what is actually occurring in the human body, in tumors, etc."

"It's very fertile ground," assures Dr. Ferber. "The types of things laboratorians will be doing will be different, but there will be plenty to do."

Kelly Graham Bocich is senior associate editor; and Kerri Hatt and Valerie Neff Newitt are managing editors of ADVANCE.