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Open Medicine Institute to Use Affymetrix Arrays to Develop Tests for Chronic Fatigue Syndrome

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NEW YORK (GenomeWeb) — The Open Medicine Institute said last week that it will use Affymetrix expression microarrays to develop tests to diagnose and aid in the treatment of myalgic encephalomyelitis and chronic fatigue syndrome.

In addition, Mountain View, Calif.-based OMI, which aims to improve healthcare by using new approaches and technologies, said that it has become an Affymetrix certified service provider and will use the platform to develop diagnostics for other diseases.

CFS is a disorder characterized by various symptoms including fatigue that is not improved by bed rest, exercise intolerance, muscle pain, and impaired memory. According to OMI, less than a fifth of individuals with suspected ME/CFS will obtain a diagnosis and correct medical attention for the disease, and there are no proven tests or treatments for ME/CFS, forcing patients to rely on anecdotal efficacy claims of multiple therapies in their efforts to get well.

Andreas Kogelnik, the founder and director of OMI, told BioArray News that the institute has been interested in CFS since OMI's establishment in 2009. He said that OMI's new relationship with Affymetrix is "significant because we are establishing a core expertise with this technology and bringing a very mainstream, well-respected biotechnology to bear in a disease that has not had enough recognition as an entity and has not had enough genomic and other molecular techniques applied to it."

Kogelnik currently envisions the creation of two tests relevant to CFS: a diagnostic based on RNA expression profiles obtained from affected individuals and normal volunteers, and a theranostic tool to evaluate treatment efficacy. The institute will use Affymetrix's Human Transcriptome Array in its work, a 6-million-probe GeneChip that covers coding and non-coding transcripts, and has helped to revive sales of the Santa Clara, Calif.-based microarray vendor's expression chips in recent quarters.

"The Affymetrix platform is terrific for this type of study as it gives us a momentary snapshot of the profile of the gene activity in blood or other tissues at that moment," said Kogelnik. "Since ME/CFS patients' … symptoms vary over the course of a day, the Affy HTA array becomes a great tool for doing state-dependent profiling," he said. "This will enable us to build a better picture of where patients are when they first present as well as how they change over time and with different treatments."

While building a test for a condition that so far lacks existing, proven diagnostics may seem like a daunting task, Kogelnik said that OMI has already seen some early fruits of its investment in the Affymetrix technology. After some additional studies, the institute hopes to report some news on its efforts within the next six to 12 months, he said.

"There's a lot of data to sift through but there's nothing more rewarding than seeing molecular data beginning to explain some of the things that we struggle to understand clinically," said Kogelnik. "These patients are really sick and need all the help that they can get, so we are moving as quickly as we can to add to the toolkit of patients and their treating physicians."

A big data approach

OMI's partnership with Affymetrix is not limited to its interest in ME/CFS. According to Kogelnik, the institute will use Affymetrix GeneChips to study a host of neuroimmune diseases, cancer, rheumatology, immunology, and other general medical problems. Diseases slated for additional investigation in the coming year include ME/CFS, autism, Lyme disease, rheumatoid arthritis, ankylosing spondylitis, lymphoma, lung cancer, pancreatic cancer, diabetes, and others, he said.

At the same time, ME/CFS is central to what OMI describes as its "multidisciplinary, big data approach" to tackling complex diseases. "We see CFS as a model system for complex chronic disease," said Kogelnik. "With more than half of Americans having a chronic disease, this is a huge and growing need that is very underserved," he said. "There's a tremendous amount yet to be done with genomic, proteomic, metabolomic, and other technologies in applying them to ME/CFS as well as many other diseases."

All of these efforts are parts of OMI's larger goal to advance the understanding of difficult diseases and improve patient outcomes. The institute maintains a clinical research facility in Mountain View, located next to El Camino Hospital. This facility includes clinical space, a core genomics and biotechnology laboratory, an informatics core, and a physiology laboratory. In addition, OMI maintains relationships with a large network of like-minded international collaborators, including solo physicians, academic centers, laboratories, industry, large health systems and others, all of whom are connected through its OpenMedNet information-sharing platform.

The institute's work with ME/CFS could expand its reach more directly into the molecular diagnostics market, though, and vindicate its big data approach to clinical problem solving.

"Complex chronic diseases are not the usual one-hit-diagnostic-and-treatment type of conditions that we have gotten pretty good at dealing with in medicine," said Kogelnik. "CFS is a condition that is likely part genetic, part exposure, part state-dependent, and very dynamic," he said. "To understand and affect that, we need to look at lots of people over time across many parameters to tease out the differences and changes between individuals," Kogelnik added. "It's a big problem and that mandates big data."

OMI's new role as an Affymetrix certified service provider might also help the institute with its research efforts. Kogelnik said that OMI has already provided services to its first pharmaceutical, diagnostic, and research foundation customers, and is using its resources to support its own research. Being a short drive away from Affymetrix's headquarters also has its benefits, he noted.

"OMI is the closest service provider to Affymetrix so we see this as the beginning of a tight relationship to apply the latest biotechnologies to a growing list of clinical research with a keen eye towards translational discoveries as well as supporting industry and academic research needs," Kogelnik said.

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