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Making genomic research whole
April 2012
by Amy Swinderman  |  Email the author


MOUNTAIN VIEW, Calif.—Recognizing the value that outsourced whole-human genome sequencing may have for its medical researchers, the Mayo Clinic's Center for Individualized Medicine announced in mid-February that it has selected Complete Genomics Inc. to provide sequencing services.  
The clinic's new Center for Individualized Medicine operates a comprehensive sequencing laboratory in its own Medical Genome Facility, but it determined that collaboration with Complete Genomics could supplement the services available to its community of medical researchers.
Complete Genomics Chairman, President and CEO Dr. Clifford Reid explains that the company recently completed a series of small pilot projects with the clinic in which the company sequenced whole-human genomes for research purposes.  
"This gave them an opportunity to try out the approach of outsourcing whole-human genomes and evaluate the quality of data we sent them," Reid says. "At the same time, the Mayo Clinic announced the founding of its new Center for Individualized Medicine. They realized for the first time that they had the opportunity to include whole-human genomes in their research programs and evaluated the pros and cons of outsourcing this function. If you are doing this in-house, you are spending millions of dollars on hardware, sequencing equipment and computational software, not to mention training large numbers of people to be sequencing experts. They realized they could get the data from us and achieve higher quality and lower costs."
Under the terms of the agreement, the Mayo Clinic will send genetic material to Complete Genomics for sequencing and analysis. It will continue to operate and invest in its Medical Genome Facility. Financial details of the agreement were not disclosed.  
"We will take their samples, sequence them and deliver them back to the Mayo Clinic ready for clinical use," says Reid. "We expect this relationship to grow in the years to come, and hope to be a permanent outsourced partner for whole-human genomes."
Complete Genomics was founded in 2005 with the vision of providing academic and biopharmaceutical researchers with whole-human genomic data and analysis at an unprecedented quality, cost and scale without requiring researchers to invest in in-house sequencing instruments, high- performance computing resources and specialized personnel. The company's genome sequencing center, which began commercial operations in May 2010, combines a high-throughput sample preparation facility, a collection of high-throughput sequencing instruments and a large-scale data center. Complete Genomics' customers ship samples via common carrier services such as Federal Express and United Parcel Service. The company then sequences and analyzes these samples, providing customers with assembled and annotated genomic data.  
"Whole- human genomes are the ultimate in genetic diagnostics," notes Reid. "Right now, the industry operates by doing partial-genome measurements or looking at specific markers or genes. For some applications, that is perfectly fine; for many applications, as the price of whole-human genome sequencing comes down, it makes more sense to sequence the genome all at once and look up the data as it is needed in the years to come."  
In particular, "hospital networks realize that whole-human genome sequencing is one of the cornerstones of personalized medicine," Reid adds. "We're seeing a real trend of healthcare systems getting engaged in whole-human genome sequencing. So we're right at the beginning of this. I think whole-human genomes will be seminal in changing healthcare by enabling the whole healthcare industry to understand for the first time that genetic data is the basis for all diseases. I think we are going to especially see a real renaissance in the understanding of cancer and all genetic diseases. This is an exciting time, and the Mayo Clinic has a leadership position in the industry, and we are very proud to be a part of that."  
The Mayo Clinic declined to be interviewed for this story. In a statement announcing the outsourcing deal, Dr. Gianrico Farrugia, director of the Mayo Clinic's Center for Individualized Medicine, said, "Access to quality whole-genome sequencing services can only expedite our efforts to improve care for all of our patients with new individualized medicine tools and techniques."  
Added Dr. Leroy Hood, president of the Institute for Systems Biology and a member of Complete Genomics' Scientific Advisory Board, "This is a big step toward the realization of personalized medicine. It is exciting to see a world-renowned healthcare organization like Mayo Clinic take the next step towards bringing high-quality whole-genome sequencing data into the clinic."  

Mayo Clinic, A&G Pharma to develop test for dementia  
ROCHESTER, Minn.—The Mayo Clinic also announced last month that Mayo Medical Laboratories has signed an agreement with A&G Pharmaceutical Inc. and will receive a non-exclusive license to certain patent rights and proprietary antibody reagents for the detection and measurement of progranulin in blood. The agreement will let Mayo Clinic offer the first commercial blood test to predict progranulin mutation status in patients suspected to have frontotemporal dementia (FTD).
The blood test will be available in late 2012 for all Mayo Clinic patients and will be offered through Mayo Medical Laboratories to hospitals and clinics worldwide.  
FTD accounts for at least 5 to 10 percent of dementia cases and is common among patients with early-onset dementia. FTD affects the brain's frontal lobe, which regulates behavior, movement, mood and language. Most FTD patients are diagnosed when they show changes in personality, memory and ability to use language.
In 2006, researchers at Mayo Clinic published research inNature that found the mutation of the progranulin gene (PGRN) causes a reduction of the protein progranulin in the brain. Along with other changes, this leads to neuronal death and atrophy of the frontal lobes of the brain, ultimately leading to dementia. Genetic testing is available to find the mutation, but it is costly.  
In 2009, Mayo Clinic researcher Dr. Rosa Rademakers and colleagues discovered that FTD patients with PGRN mutations showed a reduction in blood progranulin levels compared to controls and FTD patients without PGRN mutations. Based on these findings and using A&G's proprietary antibody reagents, Mayo researchers developed an easy-to-use, cost-effective blood test for measuring the level of progranulin.
"A&G has pioneered and patented research investigating expression of progranulin in breast cancer and lung cancer," says Dr. Ginette Serrero, CEO of A&G. "Research has shown that breast cancer patients have an elevated level of progranulin when compared to healthy individuals. We are delighted that our clinical studies with breast cancer patients and development of progranulin antibodies and assays also will help FTD patients. "
Code: E041225



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