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Complete Genomics Partners with Scripps to Sequence 1K Genomes of the Healthy Elderly for Free


By Monica Heger

Complete Genomics
said this week that it would sequence 1,000 genomes on its own dime from people over 80 as part of a Scripps Science Translational Medicine Institute project to study healthy aging.

Complete agreed to provide the sequencing for free because it will provide the company with access to a dataset of de-identified healthy genomes that it can then make available to other customers to compare against disease genomes, CEO Cliff Reid told Clinical Sequencing News.

The Wellderly Study, which is headed by Eric Topol, director of the Scripps Translational Science Institute, has two purposes, said Reid: to understand the genetics of healthy aging and to provide a set of reference genomes.

The genomes of the 1,000 healthy individuals presumably do not have the variants that lead to chronic disease, he said. So, the data "provides a terrific baseline, a reference set, and our customers can use these genomes to compare to their disease genomes in a case/control method to do a much more efficient and effective job of understanding the genetic basis of the disease they're inspecting."

Reid said that Complete initially planned to look for outside funding for the sequencing, but under that scenario, whoever paid for the data would own it. The only way Complete could offer the data as a reference set for its customers would be if it paid for the sequencing itself.

Reid added that the company is still deciding whether to charge customers for access to the data or whether it will be included as part of its sequencing costs.

The data cannot be made publicly available as stipulated by consent forms that the participants have signed, said Reid, so Complete's customers would similarly have to agree not to share the data.

"We're working with Scripps to decide how to make these genomes available," Reid added, but "unfettered free access is not permitted."

Scripps kicked off the Wellderly study in 2007 with the initial goal of performing array-based genotyping on healthy individuals over 80 years of age. It has so far enrolled 1,117 volunteers, with the oldest recruited individual at 108 years old, and is aiming to recruit 2,000. If Scripps enlists Complete Genomics to sequence the second thousand genomes, Reid said the company would not provide the service for free.

Topol said that the Scripps team decided to move from genotyping to sequencing because they wanted to detect the "rare, low frequency, and structural variants," which sequencing is better powered to do.

Complete will sequence each of the 1,000 genomes to 40-fold coverage using its standard sequencing technology and will provide variant calling and basic analysis. A more in-depth, clinical annotation of the genomes will be done by Cypher Genomics, a company started by researchers at Scripps, including Topol and Nicholas Schork, Scripps' director of bioinformatics and biostatistics.

Cypher Genomics will do "much more advanced, interpretative work," including predictive models to piece together the function of variants, Reid said.

Reid declined to say whether future collaboration with Cypher Genomics for the clinical annotation of genomes is in store, but said that Complete is "actively interested in partnering with a wide variety of analysis companies" and that clinical interpretation "will be an important part of the industry."

The Wellderly study is not the only sequencing project studying healthy aging. The Centenarian Sequencing Project, led by David Goldstein's group at Duke University, aims to sequence the genomes of people over 100 years old to determine the variants responsible for longevity.

According to Scripps' Topol, the main difference between the two projects is that in the Wellderly study, "the phenotype is healthspan," while in the Centenarian Sequencing Project it is "lifespan."

As of January, the Centenarian Sequencing Project had recruited 12 volunteers, and sequenced nine genomes. The goal of that study is to determine a genetic basis for why those individuals live so long, such as carrying a lower overall burden of deleterious mutations.

By contrast, the Wellderly study aims to uncover variants that confer protection from chronic diseases, such as heart disease. Participants in that study must be free of disease and not on any medication.

Have topics you'd like to see covered by Clinical Sequencing News? Contact the editor at mheger [at] genomeweb [.] com.