Propelled by Next-Gen Sequencing, MDx Gains on Antimicrobial Resistance

Fast-Evolving Pathogens Elude Standard Tests. But They May Be Run Down by New NGS Assays.

Author: Emil Salazar

With NGS diagnostics, the onus on the lab is shifted considerably from hypothesis-driven diagnosis to the interpretation of more data-rich results. [© ktsdesign/]

Next-Gen SeqencingIf molecular diagnostic tests are to keep pace with fast-evolving microbes, they will have to find an “extra gear.” Existing gears—single pathogen tests and multiplexed panels—have their advantages, mostly with respect to specificity. But specificity is of little help when one is chasing a moving target, as one is obliged to do when typing pathogens or profiling resistant strains. To keep up with such elusive quarry, molecular diagnostics may need to shift to next-generation sequencing (NGS).

Already, NGS is moving into the clinical laboratory, improving the responsiveness of disease control in healthcare settings, and promising to advance the personalization of patient therapy. And now NGS is poised to go yet farther, nimbly bypassing obstacles that have slowed molecular testing’s progress.

· Specificity Goes a Long Way, but…
Molecular assays that consist of carefully selected primers and probes are powerful tools, but they lack adaptability once they enter use in the majority of clinical labs. The fluid genetics of particularly virulent and antimicrobial-resistant strains and clones are at times capable of escaping the specificity of selected molecular probes and primers.

To overcome this problem, which is a matter of narrow analytical scope, established molecular assays such as real-time PCR (or quantitative PCR) can incorporate multiplexed reagents. The benefit of multiplexed panels, particularly in the case of critical infections, is the positive identification of the infectious agent with shorter turnaround than repeat single-pathogen tests.
Despite issuing calls for larger panels, labs are well aware that such panels come with drawbacks. These include higher test product prices and undesirable selections of panel targets. Multiplexed molecular assays must often balance panel breadth with accuracy and clarity of results. False positives can result from the inclusion of too many targets, and sensitivity may be compromised.

Despite the success of multiplexed molecular assays, the inherent specificity of PCR and microarrays—still a competitive strength of molecular diagnostics over immunodiagnostics and traditional microbiology—can also prove to be a weakness, particularly in more complex applications. Assay kits that serve detection purposes are often incapable of further pathogen characterization such as genotyping or resistance profiling.

NGS, however, has demonstrated it can overcome the limitations of other assays. NGS has flexibility. It can detect any number of genetic variants. Also, NGS assays can do without the level of target definition required by other molecular assays, and still deliver accurate multiplexing. And so, NGS can offer clinicians profound capabilities—namely, rich results for clinical and epidemiological use.

· Where Conventional Assays Fall Short, NGS Rises to the Occasion
Specificity is molecular diagnostics’ major strength, but is also a weakness when assay development isn’t caught up with microbial adaptation. NGS can overcome this limitation with the flexibility to detect any number of genetic variants.
Next-generation sequencing will not replace and has yet to compete with common molecular diagnostics such as PCR. The latter remains effective through syndromic panels that screen patients for common and likely pathogens based upon presented symptoms. The same multiplexed test or follow-up can additionally detect common resistance genes and established marker sequences for virulence and high-risk strains.

The specificity of PCR assays, however, makes them less suitable for clinical epidemiology and personalized medicine. These are two significant areas of health spending that are growing because of the unfortunate challenge of healthcare-acquired infections (HAIs).

· Early NGS Assays
Multiplexed HAI assay kits remain largely unavailable for the clinical market, but some are emerging using NGS. Among the leaders in the NGS space for clinical infectious disease testing and antimicrobial resistance surveillance is BioInnovation Solutions (formerly Pathogenica). The company’s CE-IVD-marked HAI BioDetection Kit is multiplexed for the 12 most common nosocomial infections and 15 drug-resistance genes.

The assay kit uses hundreds of probes to amplify loci of interest. Amplicons are compiled in a library and subsequently sequenced and analyzed by means of a bioinformatics package. Sequencing results are referenced against databases for species, strains, substrains, and resistance genes.

Approved for clinical diagnostic use in Europe, the HAI BioDetection Kit is an excellent representation of the duality and unique value of clinical sequencing. The kit not only informs individual patient treatment, it also serves as a tool for disease control and surveillance in a healthcare setting. The detailed results provided by the sequencing kit enable outbreak tracking through the identification of bacterial clones or distinct strains and substrains.

Standardized sequencing assays for infectious disease testing are also available from a couple of additional diagnostics companies. Abbott Molecular offers its CE-IVD HBV sequencing assay for the determination of hepatitis B virus genotype and drug resistance prior to antiviral therapy. Singapore’s Vela Diagnostics has developed Sentosa NGS, a genotyping assay for hepatitis C. It is a research-use-only platform that integrates with a number of Vela components. It is intended for viral genotyping from plasma or serum.

Vela also offers Sentosa assays for oncology that already have CE-IVD marking. However, the majority of NGS assays are available only as laboratory-developed tests or testing services that do not require premarket approval or other clearance processes for clinical use otherwise required of test kits.

· Outstanding Regulatory Issues
The above companies demonstrate the feasibility of introducing a standardized NGS assay kit to the market, but the relative scarcity of such products hints at ongoing regulatory uncertainty regarding the assessment of NGS. This uncertainty arises from a paradigm shift inherent to NGS. That is, with NGS, the interpretation of results goes beyond positive/negative determinations to translation of highly specific and variable sequence data into actionable diagnostic knowledge.

One company working to accomplish this paradigm shift is PathoQuest. The company is one of several offering bioinformatics solutions for NGS users in the clinical field. Bioinformatics software assists the interpretation of results by referencing against updated databases and reduces the need for skills and expertise on the part of the user. A more automated analytical approach will be increasingly standard in the clinical space and key to winning regulatory support.

The market introduction and acceptance of NGS-based clinical diagnostics has at the same time been propelled by the technology’s unique capabilities and also held back from greater market development because of the challenges presented in assessing risk and suitable performance. With NGS diagnostics, the onus on the lab is shifted considerably from hypothesis-driven diagnosis to the interpretation of more data-rich results. In the case of infectious disease testing, the risk is considerable as it surpasses individual outcomes and could impact public health, and it calls for careful deliberation on the part of the regulators and healthcare adopters.

FDA-Ok’d Drugs W/ Biomarkers Growing

Targeted drugs, personalized medicine, stratified therapy–whatever you call it, using biomarkers to identify particular patients for particular drugs has been hailed as a boon for patients and a savvy strategy for pharma.

Advocates can talk up approval numbers, labeling changes and Phase III therapies. But it’s according to the 80/20 rule: A small number of pharma companies account for the lion’s share of targeted meds. And the star of personalized medicine is just the company you’d expect: Roche ($RHHBY), with its drug-plus-diagnostic approach to cancer R&D, its stable of blockbuster HER2-positive therapies, and a total of almost $20 billion in sales from its targeted drugs.

Just ask Diaceutics, the U.K. research firm, which keeps close tabs ondiagnostics-aided medicine. Yes, the number of FDA-approved drugs linked with a particular biomarker has leapt over the past three years, to more than 80 from just over 20. And while only 7 new drugs with companion diagnostics have made their market debuts, 53 others have new FDA labeling that flags safety-related biomarkers–bringing the percentage of targeted therapies on the market to 19% from 6% in 2010.

This blog post was originally written by Tracy Staton with the title Who are the stars of personalized meds? Roche, Novartis and J&J

Mutations That May Enable Earlier Diagnosis of Colorectal Cancer Recurrence Identified

A multidisciplinary team of doctors and scientists from Singapore has characterised the genetic changes associated with the spread of colorectal cancer to the liver. This finding is significant in helping to develop personalized diagnostic tests for patients with colorectal cancer based on the genetic changes present in each individual’s colon tumour. The research team comprises representatives from National Cancer Centre Singapore (NCCS), Singapore General Hospital (SGH), Duke-NUS Graduate Medical School (Duke-NUS), A*STAR’s Genome Institute of Singapore (GIS) and Cancer Science Institute Singapore (CSI Singapore) of the National University of Singapore (NUS). The findings were published online in Genome Biology.

Colorectal cancer is Singapore’s most common cancer and incidence rates continue to rise. Most patients are initially diagnosed with an early stage disease. However, a proportion of these patients will develop a recurrence of the cancer (metastasis), typically in the liver, one to three years after their colon surgery. If identified early, the liver metastasis may be amenable to surgical removal, and cure may still be possible.

The Singapore team used leading edge DNA sequencing tools, some of which were developed in-house, including specialised laboratory techniques and computational methods developed at Duke-NUS and GIS to characterise genetic alterations associated with the spread of colorectal cancer to the liver.

Out of 750 genes measured, they found that every individual’s cancer had a unique set of about 15 key genetic mutations. Whilst there was little overlap in the specific mutations present between 2 different patients, the large majority of the mutations found in each patient’s colon tumour were identical to the mutations present in the same patient’s liver metastasis. The team seeks to exploit this biological finding to develop new diagnostic tests in the search and identification of early spread of the cancer based on the genetic information found in the removed cancer from the colon surgery in the first instance.

Cancer survivors dread having their cancer recur. Even if this happens, we still have a chance to cure our colorectal cancer patients provided we diagnose it early. The research findings can have a significant impact on our patients’ quality of life, and improve the precision of the treatment they receive,” said co-author of the study, Assoc Prof Tang Choong Leong, Head, Department of Colorectal Surgery at SGH.

“Based on this study, we intend to customise a diagnostic test for each colorectal cancer individual. We will use the unique set of mutations present in that individual’s cancer, as a barcode or thumbprint that we can exploit as innovative diagnostics to monitor for cancer recurrence and diagnose it early,” explained Dr Iain Tan, co-lead author of the study who is a Consultant Medical Oncologist at NCCS and also a clinician scientist at GIS. The team has been awarded a grant from the National Medical Research Council (NMRC) to further develop this diagnostic test. Dr Tan cautioned that this R&D effort will take several years although he is optimistic that with this finding, further progress could be realized.

This study was performed in partnership with the POLARIS program, a strategic national program funded by A*STAR to translate local research findings towards “fit-for purpose” applications that improve the diagnosis and treatment of diseases in Singapore.

“POLARIS continues to seek opportunities to work with leading local researchers to enable the transition of their research findings from bench to bedside,” explained Prof Patrick Tan from Duke-NUS who is a co-lead author of the study and the Program Director of POLARIS.

Story Source: The above story is based on materials provided by SingHealth. Note: Materials may be edited for content and length.

New Drugs at FDA: CDER’s New Molecular Entities and New Therapeutic Biological Products

Innovation drives progress. When it comes to innovation in the development of new drugs and therapeutic biological products, FDA’s Center for Drug Evaluation and Research (CDER) supports the pharmaceutical industry at every step of the process. With its understanding of the science used to create new products, testing and manufacturing procedures, and the diseases and conditions that new products are designed to treat, FDA provides scientific and regulatory advice needed to bring new therapies to market.

Novel New Drugs
The availability of new drugs and biological products often means new treatment options for patients and advances in health care for the American public. For this reason, CDER supports innovation and plays a key role in helping to advance new drug development.
Each year, CDER approves a wide range of new drugs and biological products. Some of these products are innovative new products that never before have been used in clinical practice. Others are the same as, or related to, previously approved products, and they will compete with those products in the marketplace.
Certain drugs are classified as new molecular entities (“NMEs”) for purposes of FDA review. Many of these products contain active moieties that have not been approved by FDA previously, either as a single ingredient drug or as part of a combination product; these products frequently provide important new therapies for patients. Some drugs are characterized as NMEs for administrative purposes, but nonetheless contain active moieties that are closely related to active moieties in products that have previously been approved by FDA. For example, CDER classifies biological products submitted in an application under section 351(a) of the Public Health Service Act as NMEs for purposes of FDA review, regardless of whether the Agency previously has approved a related active moiety in a different product. FDA’s classification of a drug as an “NME” for review purposes is distinct from FDA’s determination of whether a drug product is a “new chemical entity” or “NCE” within the meaning of the Federal Food, Drug, and Cosmetic Act.

Monitoring EGFR mutational status in lung cancer patients

SAN DIEGO—Trovagene Inc. announced recently that it has entered into a clinical collaboration with California-based City of Hope to conduct studies to determine the clinical utility of detecting and monitoring EGFR mutations in lung cancer patients using Trovagene’s Precision Cancer Monitoring platform.

Trovagene“Tracking various alterations in the EGFR oncogene, particularly emergence of the T790M mutation, has potential to improve therapeutic strategies for treating patients with non-small cell lung cancer,” said Dr. Mihaela Cristea, lead investigator and associate professor for the City of Hope Lung Cancer and Thoracic Oncology Program. “We look forward to evaluating Trovagene’s molecular diagnostics for the monitoring of circulating tumor DNA found in both urine and blood, with the goal of delivering highly personalized cancer treatment to improve patient outcomes.”

The clinical study is expected to enroll 75 patients with lung cancer. Primary objectives of the study include evaluating concordance between urinary circulating tumor DNA (ctDNA), blood ctDNA and tumor tissue for determining EGFR mutational status. Additionally, the study investigators will evaluate the quantitative and qualitative performance of longitudinal EGFR mutation monitoring using both urine and blood specimens, as they relate to response to therapy over time. Exploratory objectives include evaluating the feasibility of identifying the TKI-resistant mutation, T790M, in urinary and blood ctDNA at the time of progression.

“Enabling physicians to detect the emergence of problematic mutations in real-time is a key benefit of our Precision Cancer Monitoring platform, and one such mutation is EGFR T790M, which drives treatment resistance in non-small cell lung cancer patients,” said Dr. Mark Erlander, chief scientific officer of Trovagene. “This is an important part of our strategy to realize the full potential of our platform, as we partner with major cancer treatment centers in the U.S. to obtain clinical utility data and to integrate our technology into clinical practice.”

FDA Regulations

The U.S. life sciences industry is a business sector which faces the significant task of developing, FDAtesting and manufacturing pharmaceuticals. Due to the complex environment in which pharmaceuticals are developed, there is a strong need for IS and other quality systems to monitor, manage and control the production processes. The quality systems can drive each of the steps with the product life cycle and is a critical factor for guaranteeing that the optimum quality standards are met.

The FDA plays an important role in this systematic testing process by applying rigorous oversight to the pharmaceutical industry, to ensure high quality standards, efficacy, and the safety that the general public demands. Throughout the research, development, and the manufacturing life cycle of drugs, vaccines, and other biopharmaceutical products, the FDA’s role is that of a principal supervisory agency. Their job is to assure that optimum quality is being achieved, and the best practices are being followed.

So how can you prepare your bio-pharmaceutical company for one of these surprise inspections? Well, one thing you can do is to hire a life sciences consulting firm that specializes in the development of quality systems, in which they can design, or redesign your entire system, to meet FDA regulations. The FDA uses it’s oversight to guarantee that such issues and problems with contaminants and failed processes are quickly sniffed out and identified. Without the help of an experienced consulting firm, your company may fail to take the preventive actions necessary to successfully pass an FDA audit. Because of the severity of the consequences in developing possible faulty pharmaceutical products, the FDA has very little tolerance for variability or deviation from its quality inspection regulations. This means if your products do not pass this FDA quality inspection, you will be shut down, and shut down fast.

The pharmaceutical industry, like any traditional manufacturing industry, uses traditional, older production processes and many companies have outdated information systems. In the past, the work flow in the pharmaceutical industry was optimized for straightforward production including cost reductions, rather than focusing on transparency and quality production. Furthermore, even though many pharmaceutical companies are starting to catch up to the rest of the manufacturing industry, and have begun to develop more sophisticated systems, many companies wouldn’t be able to pass a simple FDA regulatory inspection if they had to. If you want your company to be properly prepared, talk to a pharmaceutical consulting firm that specializes in quality control, and they will be able to prepare your company properly in case of a surprise FDA inspection in your company’s future.

Article Source: Nigel Smart, Author

The CDO Fast Track Advantage

The CDO Fast Track Advantage

A CDO is a Contract Diagnostic Organization that specializes on the development of diagnostics, companion diagnostics (CDx) and in vitro diagnostics (IVD) for the pharmaceutical, biotechnology, research, and diagnostic industries. Unlike other providers with internal biases toward their own products and platforms, a CDO is solely focused on the customer’s goals and objectives.

A CDO can offer a comprehensive array of services including:
• Assay development
• Platform evaluation and validation
• Validation of clinical samples in CLIA-licensed CAP-accredited clinical laboratory
• Project management of all levels of regulatory compliance, processes, applications and approvals
• FDA submissions for 510(k) or Premarket Approval (PMA) clearances
• GMP manufacturing

A CDO provides a complete outsourcing partner to seamlessly initiate and manage the parallel development of companion diagnostic tests in synergy with drug development through FDA approval. A CDO provides integrated services, including diagnostics research, an accredited clinical laboratory, project management, regulatory expertise, manufacturing, and consulting. By combining all of these services under a single organization, a CDO can ensure the fastest and most cost effective path to market.

For more information on what a CDO can do for your company, contact ResearchDx at (Louis Sintasath) or call 858-344-8398.