Genomics, proteomics, cytomics, and genetics

April 1, 2012

Whole exome sequencing

The arrival of whole exome sequencing on the menu of clinical diagnostics has been long anticipated. In January 2012, Ambry Genetics released the first three clinical reports from its new exome test. The results came from three separate families, each of whom had been unsuccessful in their pursuit of a diagnosis for their children—odysseys that had lasted anywhere from months to many years.

In each case, traditional genetic testing approaches, which often include microarray and next–generation sequencing panels, eluded diagnosis. But exome sequencing, followed by variant annotation and filtering using proprietary software, led to a short list of candidate mutations. This was further narrowed to a single gene in each case following medical interpretation and correlation with clinical history and confirmation by co–segregation analyses.

The challenges to whole exome sequencing are widely recognized. However, these early successes highlight how far this field has come and the power of investing in a strong bioinformatics pipeline and medical team. Although the day has not yet arrived, we believe clinical exome sequencing may someday replace conventional single and panel–based gene tests as costs decrease and interpretability improves. The first three cases demonstrate the power of the technique to help families with elusive diagnoses today.

—Elizabeth Chao, MD
Director of Translational Medicine
Ambry Genetics
Provider of the Clinical Diagnostic Exome test

New approach in hematoflow

European laboratories are working with in vitro diagnostic companies to expand the routine use of flow cytometry in their hematology processes for validating abnormal samples. These labs are pioneers in this new approach for hematology to deliver white blood cell (WBC) differential results with greater consistency than manual microscopic assessment. The University Hospital, Rennes, France and Erasme University Hospital, Brussels, Belgium, alongside smaller private labs, are already implementing this approach, using Beckman Coulter's combined hematology and flow cytometry solutions to characterize abnormal WBC populations. The reagent, a five–color antibody cocktail, has autogating software for subpopulation differentiation and uses six monoclonal antibodies to establish the extended flow WBC differential, detecting and quantifying nine cell subsets. The labs have already reported a significant impact. Benefits include improvements in workflow and turnaround time, access to additional diagnostic information and the precision of flow cytometry. These new products are not yet available in the United States for in vitro diagnostic use.

For additional information see Faucher JL, Lacronique–Gazaille C, Frébet E, et al. '6 Markers/5 Colors' Extended white blood cell differential by flow cytometry. Cytometry. 2007;71:934–944.

—Dr. Josee Naegelen
Senior Global Product Manager for Hematology and Hemostasis
Provider of HematoFlow Solution and CytoDiff reagent
(not yet available in U.S.)
Beckman Coulter, Inc.

Comprehensive clinical testing

Clinical testing historically was ordered and interpreted in a rather piecemeal fashion, usually resulting in physicians ordering a slew of separate tests and then receiving their results with no correlation. With increasing knowledge of how genes impact protein generation and expression and how this parlays into cellular manifestations and phenotypic variations of given diseases, the process of interpreting test results reflecting each of these aspects has become more holistic. Understanding disease as a multifaceted entity and correlation of test results have become more common, thus providing more accurate disease identification, prognostication, and treatment. This has led to the concept of personalized medicine, where understanding a given patient's unique disease presentation on all levels allows a physician to select treatment most effective for that patient.

In order to facilitate test result correlation, clinical laboratory testing will need to be viewed differently. What was once considered esoteric testing needs to be redefined as an integral part of laboratory testing. Traditional genetic testing such as molecular and cytogenetic testing needs to be incorporated with cytological testing such as flow cytometry, and cellular pathology in turn needs to be integrated with traditional laboratory testing such as enzymatic, biochemical and proteomic testing. The test results then will require further correlation with patient phenotypic observations as well as patient and family histories. This paradigm shift requires physicians and diagnosticians to possess the ability to interpret these various test results in a cumulative manner, producing a single comprehensive report. Integrated databases will also be necessary not only to support this cumulative interpretation and comprehensive reporting, but also to provide the opportunity to gather data for analysis on a population level so as to understand the genomics of a disease.

—Laurel Estabrooks, PhD, FACMG
Vice President of Genetics Business Development
SCC Soft Computer
Provider of the SCC Genetics Information Systems Suite™

Standardized immune monitoring assays

During clinical trials of novel therapies, immune monitoring assays are essential to understanding the therapeutic immune response and speeding new drugs to the market. Use of standardized immune monitoring assays minimizes intra– and inter–assay variability, allowing higher assay sensitivity and reducing interference from irrelevant factors. This may permit recognition of small changes affecting the disease state which are otherwise hidden under assay variability. However, the development of standardized immunoassays has been slow.

Disease specific ICS staining panels, enabling the analysis of both surface markers and cytokine production, allow monitoring of immune responses following vaccination and during disease progression. We have developed a panel for tracking vaccine induced T–cells producing IFN–γ, TNF–α, IL–2 and IL–4 in vaccination studies on a 14–color BD LSR Fortessa flow cytometer for trials such as those for HIV and cancer. New panels are in development for IL–17, a key pro–inflammatory cytokine in diseases such as rheumatoid arthritis and inflammatory bowel disease. Standardized disease specific ICS panels increase the quality of data generated during clinical trials, decreasing time to market for compounds in development.

—Faith Bahunde, PhD
Senior Scientist in the Immunology Department
SeraCare Life Sciences
Provider of AccuMune Cellular Immunology products

LDTs and genomics

Laboratory Developed Tests (LDTs) represent a class of in vitro diagnostic tests that has, thus far, operated outside of the standard regulatory oversight of the U.S. Food and Drug Administration. While regulated devices must undergo rigorous clinical studies to support 510(k) submissions to the Agency, LDTs, developed under CLIA regulations, have been subject to “discretionary enforcement” by FDA. Since initially the number of tests was relatively low and there existed a close relationship between the requesting physician and the laboratory performing the test, the traditional LDTs represented an effective means to meet the needs of patients. During the past 5 to 10 years, however, the reach of LDTs has grown worldwide. Not only have the interactions between physicians and laboratories been reduced, but in some cases FDA has noted poor or no clinical validation of the methods. For these reasons, greater FDA oversight of LDTs will take place. In addition, as genomic data have increased our knowledge of the influence of genetics on disease states, as well as responsiveness to therapeutic approaches, the issues surrounding LDTs becomes even more critical since many labs have developed elegant LDT–based tests for genomic testing. Although providers of LDTs may resist the coming changes, we find ourselves at a crossroads where it is imperative for cooperation among CLIA labs providing LDTs, potential manufacturers, and the FDA to work together to achieve a level playing field and to assure compliance with Agency regulations.

—Richard A. Montagna, PhD
Sr. VP for Corporate Business Development & Scientific Affairs
Rheonix, Inc.
Provider of the CARD® system for genomic testing

The “omics” revolution

With the advent of multiplex testing methods that illuminate the molecular components of cell biology, the “omics” revolution in laboratory testing technology began to move rapidly from the research laboratory to the clinical laboratory. One key to its successful integration into clinical care is the extension of electronic health record (EHR) technology to store and utilize complex test results. Cerner has been at the forefront of these efforts through the development of the first fully market–ready LIS module capable of supporting molecular diagnostic, genetic and cytogenetic test findings. Each of the “omics” disciplines has a unique workflow and requires considerable flexibility in the LIS system. Incorporating these results into the EHR in a manner that enables decision support is a critical factor in this rapidly changing field. Many clinicians will need to evaluate how “omics” results should influence their clinical decisions, whether for cancer management or antidepressant prescribing. As new technologies such as whole genome sequencing multiply the amount and complexity of information available for each patient, the computational strategies applied to solving these problems will need to provide flexibility to the laboratory and clinician.

—Mark Hoffman, PhD, VP of LifeSciences Solutions (left)
—John David Nolen, MD, PhD, MSPH,
Dir. of Laboratory Strategy (right)
Provider of Milennium Helix LIS module

Smarter medicine

In the past, physicians largely practiced what I call “trial–and–error medicine.” Physicians diagnosed, treated, and managed disease without insight into the unique genetic and molecular profile of the individual patient. The same treatment was provided to all patients for a given diagnosis. Sometimes therapy worked, but in many cases it did not.

Today's genomics revolution is quickly replacing this outdated mode of medicine with personalized treatments. Only about a decade has passed since the human genome was mapped. Yet, scientific understanding of the molecular and genetic basis of disease has already facilitated the development of lab tests that more effectively diagnose, select specific treatments for and manage several diseases, including HIV and breast cancer. And we are only on the cusp of this revolution!

Personalized medicine is smarter, more effective medicine. It is better for our patients, and reduces waste in our overburdened healthcare systems. But to fulfill the potential of personalized medicine, we need sensible regulations and reimbursement policies that foster innovation. Laboratory professionals will also need to take on greater responsibility for counseling physicians in the uses and limitations of diagnostics for personalizing pharmaceutical treatments.

—Kenneth L. Sisco, MD, PhD, FCAP
Medical Director
Quest Diagnostics