The Ion Personal Genome Machine (PGM) utilizes game-changing semiconductor technology.

Genetic testing methods for cancer testing have evolved to the use of sequencing, encompassing such techniques as RNA-Seq, also called “Whole Transcriptome Shotgun Sequencing” (“WTSS”) and ChIP-sequencing (ChIP-seq).

Life Technologies Inc, Carlsbad, Calif, produces the Ion AmpliSeq™ Cancer Panel for research use only; it offers such features as:

  • Low–DNA input protocol (10 ng) compatible with research formalin-fixed, paraffin-embedded (FFPE) samples;
  • Transformative technology that generates 190 amplicons using a simple, single-tube, multiplex PCR assay;
  • Rapid, affordable sequencing in just 90 minutes;
  • Go from extracted DNA to variant report in 9.5 hours;
  • Molecular bar codes enable cost-effective sample multiplexing; and
  • Scalable technology for deep sequencing of low-frequency mutations in heterogeneous samples or for germline mutation detection.

According to Paul Billings, MD, PhD, chief medical officer, Life Technologies, the AmpliSeq panel includes 46 genes and about 190 or so amplicons (separate, amplified regions of genes); 700 key mutation spots in genes are reported.

Billings says that there is no “gold standard” used to determine which genes are selected. The panel was constructed with input from the American Society of Clinical Oncology (ASCO), the National Comprehensive Cancer Network (NCCN), international standards, and investigators at prestigious cancer centers. There’s a heavy reliance on expert opinion, he notes, adding that others use different-sized lists—it varies. He says it’s vital to know what mutations are inside tumors for several reasons: Tumors with different genetic profiles behave differently and metastasize differently, for example. And knowledge of mutations driving tumors can lead to the increased development of drugs, which are targeted at these mutations to slow or reverse their impact and provide a target for treatment. Many mutations are the targets of drugs in clinical trials, so patients need to have these tests in order to enter these trials.

“Sequencing has historically been esoteric and has required specialized training, PhDs, etc,” Billings says. “With the Ion Torrent AmpliSeq panel, the information is provided right on the desktop, is fully integrated, sample-to-answer, very straightforward, and requires almost no human intervention or expertise. It can be used in unsophisticated labs; the sophistication will be more about how to use the information and how to get patients into clinical trials, not because the information is difficult or esoteric to generate.”

An operator scans sample bar codes for the cobas HPV Test, which runs on the automated cobas 4800 platform and individually identifies HPV 16 and 18 while simultaneously detecting 12 other high-risk HPV genotypes. Image courtesy of Roche Diagnostics

Oregon’s OHSU Knight Cancer Institute and the Fox Chase Cancer Center will soon be implementing the tests in their CLIA labs. The Ion Torrent (sequencing instrument) will be presented to the FDA for approval this year, Billings says, and Life Technologies will assess if AmpliSeq or a different panel will be best for presentation to the FDA.

When will this type of sequencing move into greater numbers of clinical labs? “As validation and research progress continues, the pace will determine the speed of acceptance,” Billings says. “If a lab wants to use our home-brew process and issue that with a CLIA license, we make it clear it’s for research only, but it could end up in clinical assays. However, the market, experts, patients, and the law will determine the outcome (the FDA, CLIA, and some states have laws regarding what kind of information should be given to patients from research trials). We think all patients should be enrolled in clinical trials so outcomes can get better and faster.”

And whether more panels will be added to what are already being used will depend on what experts and the markets need, Billings says. There might be a move to smaller, more specific panels for such disorders as breast cancer, cardiovascular, autoimmune, and other areas; and more-focused panels will develop in a variety of other sectors as well. Billings foresees elective surgery panels, which might screen for rare but predictive bad reactions due to genetics, allergies, or other factors that exist but aren’t easily accessible via other testing.


ZELBORAF (vemurafenib), the first drug to go through the FDA approval process with a companion diagnostic, the cobas 4800 BRAF V600 Mutation Test, is designed to selectively target and inhibit a mutated form of the BRAF protein found in about half of all cases of melanoma, the most aggressive and deadly form of skin cancer. Image courtesy of Roche Diagnostics

For Roche Diagnostics Corp, Indianapolis, the cobas® HPV Test and the cobas 4800 System are its current state-of-the-art oncological genetic testing offerings.

“One of the biggest recent developments from Roche in oncology diagnostics is in the area of cervical cancer screening and HPV genotyping—in particular our new cobas HPV Test, which was approved by the FDA in 2011,” says Andy Plank, group marketing manager, Women’s Health, Roche Diagnostics Corp. Plank says that as part of the clinical trial for the new test, Roche has undertaken the largest cervical cancer registrational screening study in the United States—the ATHENA trial—with more than 47,000 women, and it has provided clinical validation of the critical role of HPV 16 and 18 genotyping in identifying women at highest risk for cervical cancer.

The ATHENA trial, the largest cervical cancer registrational screening study in the United States, involving more than 47,000 women, provided clinical validation of the critical role of HPV 16 and 18 genotyping in identifying women at highest risk for cervical cancer. Image courtesy of Roche Diagnostics

The cobas HPV Test offers clinicians and patients a unique benefit in that it is the only FDA-approved test that individually identifies HPV 16 and 18, the two genotypes responsible for 70% of cervical cancers, while simultaneously detecting 12 other high-risk HPV genotypes, Plank says, so they receive three results in one test. “Individually identifying HPV 16 and 18 at the outset of screening [instead of requiring a reflex test] provides physicians with certainty about their patient’s high-risk status, empowering them to act decisively to prevent the disease,” Plank says.

He notes that the cost for patients will be similar to what they pay now for HPV testing (which is comparable to the cost of a Pap test), but the value of the cobas HPV Test will be much greater because physicians will get more information, and get it faster. And because the test could mean fewer return visits, less retesting, and earlier identification of women at risk, it could have a significant impact on reducing health care costs overall.

The cobas HPV Test runs on the new cobas 4800 System (introduced in the United States in 2011), which is an automated platform that also runs the cobas CT/NG (chlamydia and gonorrhea) test—which just received FDA clearance in February 2012—as well as other tests that are in development. The cobas 4800 system automates nucleic acid purification, PCR setup, and real-time PCR amplification and detection, which translates into less hands-on time, true walk-away performance, and, as a result, maximum efficiency for the lab. For example, it takes less than 30 minutes of hands-on time to begin a run of 96 samples. Roche also has plans to introduce additional assays and expand the menu for the cobas 4800 system in the near future, which will allow small- and medium-volume labs to maximize their investment in the platform.

New Guidelines for Cervical Cancer Screening

The American Cancer Society (ACS), the American Society for Colposcopy and Cervical Pathology (ASCCP), and the American Society for Clinical Pathology (ASCP) recently joined forces, issuing new guidelines for cervical cancer screening, including the role of HPV testing and genotyping. The guidelines, an update from those issued in 2002 for the early detection of cervical cancer, encompass recommendations on testing for and vaccination against human papillomavirus (HPV) in addition to the traditional Pap test. The guidelines are published in the April 2012 issue of the American Journal of Clinical Pathology.

“The new joint guidelines for cervical cancer screening represent a landmark development in women’s health, and they highlight the key role molecular diagnostics can play in personalized health care,” says Andy Plank, group marketing manager, Women’s Health, Roche Diagnostics Corp. “This is the first time this group of medical experts has recommended HPV 16 and HPV 18 genotyping for certain groups of patients to more fully assess their personal risk for cervical cancer. If it’s treated effectively in the precancerous stage, cervical cancer can be successfully prevented. Molecular tests can help eliminate cervical cancer by providing physicians with state-of-the-art diagnostic tools designed to identify more women at risk earlier.”


John McCune, Roche’s group marketing manager, Genomics and Oncology, Microbiology, says that in just the past year, the area of oncology and genetic-based testing has provided some of the most dramatic examples of personalized medicine and the clinical value that companion diagnostics can offer. “And what’s exciting is that we’re just beginning to tap the potential of what DNA-based testing and pharmacogenomics can offer in terms of fitting treatments to the groups of patients who will benefit the most,” he says. “By identifying on a genetic level which patients will benefit from a specific therapy—and which ones will not—molecular diagnostics can help streamline therapy decisions, improve outcomes, and make the delivery of health care more cost-effective.

“In 2011, we witnessed the first time a drug and companion diagnostic test have ever gone through the FDA regulatory approval process together, with ZELBORAF® (vemurafenib) tablets and the cobas 4800 BRAF V600 Mutation Test,” McCune says. “It happened to be a Roche drug and companion molecular test, but it seems clear that this is a growing trend across the industry and will continue in the future.”

McCune says that a clinically validated companion diagnostic, the cobas 4800 BRAF V600 Mutation Test, identifies patients whose tumors carry the BRAF V600E mutation and are likely to benefit from ZELBORAF, an orally administered therapy for the treatment of metastatic melanoma.

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Visit the digital edition to learn more about this topic:

  • Delve into the new cervical cancer screening guidelines in AJCP.
  • Insight Genetics offers insight into meeting the need for advanced anaplastic lymphoma kinase (ALK) diagnostics.
  • Check out our Tech Guide spotlighting molecular diagnostics.

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The test is a real-time PCR assay that detects BRAF V600 mutations in human melanoma tumor specimens. ZELBORAF is designed to selectively target and inhibit a mutated form of the BRAF protein found in about half of all cases of melanoma, the most aggressive and deadly form of skin cancer.

The test, which runs on the cobas 4800 system, is performed on DNA extracted from FFPE tissue specimens of malignant melanoma (resected tumors or biopsies). It has a rapid turnaround (up to 96 patient samples available in less than 8 hours), enabling the lab to get vital information to physicians faster so they can make treatment decisions. The availability of the results depends on when the laboratory receives the specimen and when they plan to run the test.

“The cobas 4800 BRAF V600 Mutation Test is designed to combine accuracy, speed, and reliability, and to provide consistent, objective, and reproducible results, allowing health care professionals to make therapy decisions with speed and confidence,” McCune says.

Gary Tufel is a contributing writer for CLP. For more information, contact Editor Judy O’Rourke, .

Frederick National Lab Implements New Integrated Research Management System to Manage and Analyze Cancer Research Data

By Hank Wu, director of Translational Informatics, Remedy Informatics

Remedy Informatics Inc, Sandy, Utah, is collaborating with SAIC-Frederick Inc, Frederick, Md, to implement the Investigate™ Integrated Research Management System at the National Cancer Institute (NCI) Frederick National Lab for Cancer Research (FNL) in Frederick, Md. NCI researchers will use the software to manage and analyze large amounts of research data to accelerate progress against cancer.

The agreement is part of FNL’s Advanced Technology Partnerships Initiative, which aims to further NCI’s mission by speeding the translation of research discoveries into new treatments for cancer and related diseases. SAIC-Frederick is facilitating these partnerships for NCI as the prime contractor for NCI’s federal national laboratory in Frederick.

During this implementation, Remedy Informatics and SAIC-Frederick will collaborate to improve laboratory workflows, biospecimen management approaches, instrument integration, data visualization, and a research project review and approval system, all aimed at improving operations in the nine laboratories of the FNL’s Advanced Technology Program (ATP) and Patient Characterization Center. The nine ATP laboratories include expertise in genetics and genomics, proteins and proteomics, and imaging and nanotechnology, whose services span next-generation sequencing, molecular diagnostics, expression analysis, mass spectrometry, protein isolation, protein expression and purification, and electron microscopy, to name a few. The Patient Characterization Center will be the hub where clinical, laboratory, and biospecimen data combine to enable personalized medicine.

Investigate is the first and only Integrated Research Management System built to be the missing link between the clinic, lab, and biobank. Currently, the life science research software industry is highly fragmented, with a proliferation of specialized or homegrown software applications that serve one or two domains, be it lab information management systems (LIMS), electronic lab notebook (ELN), sample management, or patient registry. None were designed to serve the emerging generation of translational researchers who need a holistic systems view of their data, nor were those specialized software applications intended to interoperate with data types beyond their domain. This fragmentation of data silos causes researchers to spend inordinate time and effort duct taping together systems that remain fragile and turn out to be unaffordable to maintain. Worse, researchers are still unable to efficiently interpret their data and separate signal from noise, due to ontologically incompatible data sets and the lack of intuitive research tools.

Investigate was built from the ground up to aggregate, map, and harmonize disparate data types, governed by a robust ontology engine to ensure data compatibility and quality. Investigate combines the best features of traditional LIMS, ELN, biorepository management, study management, and clinical registries into the only Integrated Research Management System able to traverse clinical, laboratory, and biobanking data types, workflows, queries, and reports. Furthermore, the underlying Mosaic™ platform enables data visualization and dashboards for pattern recognition, intuitive Venn-diagram query building without SQL, a fully Web-enabled user interface, persistent data storage, and maximum configurability by the customer to minimize total cost of ownership and ensure adaptability to changing research needs.

The vision of the partnership with the Frederick National Lab for Cancer Research is to bring powerful new approaches and important insights from genomics, proteomics, imaging, nanotechnology, and translational informatics to bear on identifying and treating cancer.