Industry Playbook

Quest, Memorial Sloan Kettering Collaborate to Advance Personalized Cancer Treatment
Memorial Sloan Kettering Cancer Center (MSK) and Quest Diagnostics have entered a partnership to improve the treatment of breast, prostate, colon, lung, and a variety of other solid tumor cancers. The partners aim to accomplish this by using molecular laboratory testing to give physicians a better understanding of the genomic underpinnings of their patients’ illnesses.

To date, MSK has amassed extensive databases of gene mutations linked to various types of cancer. MSK also has developed pharmaceutical cancer treatments based on scientific literature, treatment of patients by the institution’s multidisciplinary teams, and clinical trials conducted by MSK researchers.

In the first phase of the collaboration with Quest, MSK will use its data resources and clinical and research insights to provide contextual information about mutations identified by Quest’s OncoVantage test. OncoVantage uses next-generation sequencing technology to analyze tumor biopsies for the most commonly mutated exons in 34 genes. This sequencing data, in de-identified form, will be shared with MSK, which will draw on its databases to correlate specific gene mutations to potential therapies and disease progressions. Physicians who order OncoVantage will then receive a report of MSK’s evaluation designed to help assess a patient’s prognosis, select treatments, and monitor disease progression.

MSK also will use the sequencing data from OncoVantage to extend the range of information it uses to assess the clinical significance of gene alterations and potential correlations with therapeutic response. The two organizations believe this real-time data exchange will speed the translation of discoveries into clinically actionable information for managing cancer patients.

The second phase of the collaboration between Quest and MSK will involve work on a more far-reaching test by Quest that will analyze potentially hundreds of genes. The expanded test is expected to launch by the spring of 2015.

Mayo Clinic, Whole Biome Partner on Test to Predict Risk of Premature Birth
Mounting evidence indicates that certain strains of campylobacter bacteria—a foodborne pathogen—may trigger preterm birth, the most common cause of infant death and long-term disability in children. In light of these findings, the Mayo Clinic Center for Individualized Medicine has joined forces with Whole Biome to develop microbiome-based diagnostic tests focused on women’s health and preterm labor. Mayo Clinic experts believe that many preterm births may be delayed or prevented by testing expectant mothers for a range of bacteria such as campylobacter.

To develop such a test, the collaboration will leverage Whole Biome’s Complete Biome Test. This microbiome diagnostic discovery platform can generate a profile with strain-level resolution of a patient’s microbiome—all of the microbes that reside on the inside and outside of an individual. These profiles will help Mayo Clinic researchers identify relevant changes to patient microbiomes and accelerate clinical trials aimed at producing microbiome-based diagnostics for the early indication of preterm labor risk.

Roche Acquires DNA Sequencing Company Genia
With the aim of strengthening its next-generation sequencing pipeline, Roche has made an initial payment of $125 million to buy Genia Technologies, a privately held gene sequencing company based in Mountain View, Calif. Using nanopore technology, Genia is developing a DNA sequencing platform that will allow for single molecule, electrical real-time analysis without the need for optics, labels, amplification, or fluidics. This technology is expected to reduce the price of sequencing while increasing speed and sensitivity.

The heart of Genia’s new platform is a semiconductor integrated circuit with an automated assembly of nanopores in a lipid bilayer that makes the measurement of single molecules possible. Genia’s sensor technology and proprietary NanoTag chemistry also enables accurate base calls, overcoming many of the limitations faced by other nanopore-based sequencing efforts. Once the acquisition is complete, Genia will be integrated into Roche Sequencing Unit and will continue to focus on developing this system.

Qiagen, Biobase to Combine Resources to Aid Labs With NGS-Data Interpretation
Qiagen is expanding its portfolio of bioinformatics solutions with additional content from Biobase, a provider of biological databases, software, and services for the interpretation of next-generation sequencing (NGS) data. Biobase’s expert-curated solutions enable scientists and clinical labs to identify connections between gene variants and disease phenotypes.

Under the terms of this agreement, Qiagen has begun to integrate Biobase products into its growing Ingenuity Knowledge Base, as well as the bioinformatics solutions that draw upon it and that serve as a resource for clinical research and diagnosis. The Biobase products involved include the HGMD Human Gene Mutation Database, which provides comprehensive data on inherited disease mutations, and the PGMD PharmacoGenomic Mutation Database, which identifies all published gene variants that have been shown to affect drug response in patients. The merging of Qiagen and Biobase’s resources will also help create a springboard for Ingenuity Clinical, Qiagen’s forthcoming clinical NGS decision-support solution.

Protea Partners With University of Southampton on Alzheimer’s Biomarker Search
Protea Biosciences Group has teamed up with the University of Southampton in the United Kingdom to study the molecular mechanisms of the aged brain and identify markers that may indicate a risk of developing Alzheimer’s disease. To conduct this biomarker search, a team of Southampton Alzheimer’s researchers will use Protea’s proprietary direct molecular imaging technology, known as laser ablation electrospray ionization. This technology can be used with mass spectrometry to detect the presence of more than 1,000 distinct molecules from a single analysis of samples that can include tissues, cells, fluids, and other sample types. Using the software ProteaPlot, the location of each distinct molecule in a sample can then be displayed, enabling direct molecular imaging.

Protea CEO Steve Turner, PhD, commented, “We believe that the capabilities of our technology to directly identify and image hundreds of molecules produced by cells from a single analysis has the potential to identify new biomarkers and therapeutic points of intervention for use in the development of new Alzheimer’s treatments and patient management tools.”

Enigma, China’s ICDC to Develop Point-of-Care Infectious Diseases Tests
Enigma Diagnostics, a company specializing in molecular point-of-care infectious diseases testing, has inked an agreement with China’s National Institute for Communicable Disease Control and Prevention (ICDC). Under the terms of the collaboration, the two organizations will develop rapid and convenient molecular technology for the diagnosis of infectious diseases using Enigma’s proprietary chemistries, as well as the Enigma Mini Laboratory system (Enigma ML). The Enigma ML is designed for use in developed and emerging healthcare programs, and serves as a hybrid laboratory and stand-alone diagnostic testing platform. Its multiplex assay reporting capabilities enable testing for a wide range of DNA and RNA disease targets, as well as drug resistance, with a fast turnaround time.

“In order to improve the prevention and control of infectious diseases, China has established a national network of laboratories for pathogen testing at state, provincial, city, and county levels,” said Jinxing Lu, MD, deputy director of the ICDC. “The ML system will certainly play an important role in the rapid diagnosis, monitoring, and pre-warning of our infectious diseases programs.”

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