Making genomic research whole

Mayo Clinic taps Complete Genomics to provide outsources whole-genome sequencing

Amy Swinderman
MOUNTAIN VIEW, Calif.—Recognizing the value that outsourcedwhole-human genome sequencing may have for its medical researchers, the MayoClinic's Center for Individualized Medicine announced in mid-February that ithas selected Complete Genomics Inc. to provide sequencing services.
 
 
The clinic's new Center for Individualized Medicine operatesa comprehensive sequencing laboratory in its own Medical Genome Facility, butit determined that collaboration with Complete Genomics could supplement theservices available to its community of medical researchers.
 
Complete Genomics Chairman, President and CEO Dr. CliffordReid explains that the company recently completed a series of small pilotprojects with the clinic in which the company sequenced whole-human genomes forresearch purposes.
 
 
"This gave them an opportunity to try out the approach ofoutsourcing 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 newCenter for Individualized Medicine. They realized for the first time that theyhad the opportunity to include whole-human genomes in their research programsand evaluated the pros and cons of outsourcing this function. If you are doingthis in-house, you are spending millions of dollars on hardware, sequencingequipment and computational software, not to mention training large numbers ofpeople to be sequencing experts. They realized they could get the data from usand achieve higher quality and lower costs."
 
Under the terms of the agreement, the Mayo Clinic will sendgenetic material to Complete Genomics for sequencing and analysis. It willcontinue to operate and invest in its Medical Genome Facility. Financialdetails of the agreement were not disclosed.
 
"We will take their samples, sequence them and deliver themback to the Mayo Clinic ready for clinical use," says Reid. "We expect thisrelationship to grow in the years to come, and hope to be a permanentoutsourced partner for whole-human genomes."
 
Complete Genomics was founded in 2005 with the vision ofproviding academic and biopharmaceutical researchers with whole-human genomicdata and analysis at an unprecedented quality, cost and scale without requiringresearchers to invest in in-house sequencing instruments, high-performancecomputing resources and specialized personnel. The company's genome sequencingcenter, which began commercial operations in May 2010, combines ahigh-throughput sample preparation facility, a collection of high-throughputsequencing instruments and a large-scale data center. Complete Genomics'customers ship samples via common carrier services such as Federal Express andUnited 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 geneticdiagnostics," notes Reid. "Right now, the industry operates by doingpartial-genome measurements or looking at specific markers or genes. For someapplications, that is perfectly fine; for many applications, as the price ofwhole-human genome sequencing comes down, it makes more sense to sequence thegenome all at once and look up the data as it is needed in the years to come."
 
 
In particular, "hospital networks realize that whole-humangenome sequencing is one of the cornerstones of personalized medicine," Reidadds. "We're seeing a real trend of healthcare systems getting engaged inwhole-human genome sequencing. So we're right at the beginning of this. I thinkwhole-human genomes will be seminal in changing healthcare by enabling thewhole healthcare industry to understand for the first time that genetic data isthe basis for all diseases. I think we are going to especially see a realrenaissance in the understanding of cancer and all genetic diseases. This is anexciting 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, directorof the Mayo Clinic's Center for Individualized Medicine, said, "Access toquality whole-genome sequencing services can only expedite our efforts toimprove care for all of our patients with new individualized medicine tools andtechniques."
 
 
Added Dr. Leroy Hood, president of the Institute for SystemsBiology and a member of Complete Genomics' Scientific Advisory Board, "This isa big step toward the realization of personalized medicine. It is exciting tosee a world-renowned healthcare organization like Mayo Clinic take the nextstep towards bringing high-quality whole-genome sequencing data into theclinic."
 
 

 
Mayo Clinic, A&G Pharma to develop test for dementia
 
 
ROCHESTER, Minn.—The Mayo Clinic also announced last monththat Mayo Medical Laboratories has signed an agreement with A&G PharmaceuticalInc. and will receive a non-exclusive license to certain patent rights andproprietary antibody reagents for the detection and measurement of progranulinin blood. The agreement will let Mayo Clinic offer the first commercial bloodtest to predict progranulin mutation status in patients suspected to havefrontotemporal dementia (FTD). 
 
The blood test will be available in late 2012 for all MayoClinic patients and will be offered through Mayo Medical Laboratories tohospitals and clinics worldwide.
 
 
FTD accounts for at least 5 to 10 percent of dementia casesand is common among patients with early-onset dementia. FTD affects the brain'sfrontal lobe, which regulates behavior, movement, mood and language. Most FTDpatients are diagnosed when they show changes in personality, memory andability to use language. 
 
In 2006, researchers at Mayo Clinic published research inNature that found the mutation of theprogranulin gene (PGRN) causes a reduction of the protein progranulin in thebrain. Along with other changes, this leads to neuronal death and atrophy ofthe frontal lobes of the brain, ultimately leading to dementia. Genetic testingis available to find the mutation, but it is costly.
 
 
In 2009, Mayo Clinic researcher Dr. Rosa Rademakers and colleaguesdiscovered that FTD patients with PGRN mutations showed a reduction in bloodprogranulin levels compared to controls and FTD patients without PGRNmutations. Based on these findings and using A&G's proprietary antibodyreagents, Mayo researchers developed an easy-to-use, cost-effective blood testfor measuring the level of progranulin.
 
"A&G has pioneered and patented research investigatingexpression of progranulin in breast cancer and lung cancer," says Dr. GinetteSerrero, CEO of A&G. "Research has shown that breast cancer patients havean elevated level of progranulin when compared to healthy individuals. We aredelighted that our clinical studies with breast cancer patients and developmentof progranulin antibodies and assays also will help FTD patients."

Amy Swinderman

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