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Kaiser/UCSF Genotype-Phenotype Data on 100K Patients Will Be Free for NIH-funded Research


By Turna Ray

When Kaiser Permanente's Research Program on Genes, Environment, and Health releases genetic, medical, and environmental data on 100,000 individuals next year, researchers conducting studies funded by the National Institutes of Health will be able to access the information for free.

Kaiser Permanente launched the RPGEH in 2005, but the effort ramped up in 2009 with $24.8 million in funding that it received from the National Institute of Mental Health, the National Institute on Aging, and the NIH's Office of the Director through the American Recovery and Reinvestment Act of 2009 (PGx Reporter 10/21/2009). Under that award, RPGEH partnered with the University of California, San Francisco, to use Affymetrix's Axiom platform to genotype 100,000 Kaiser Permanente members who agreed to donate their DNA to research.

Kaiser and UCSF recently completed genotyping the participants and also measured the length of their telomeres — DNA units at the ends of chromosomes linked to the process of aging and age-related conditions. Participants in the project have an average age of 65.

The collected information still needs to be catalogued by RPGEH and UCSF scientists over the next year, after which the database will be made available to researchers for free if they are using it for an-NIH funded study, a Kaiser Permanente spokesperson said.

"In other cases, researchers requesting access to data and/or specimens from the RPGEH for research will be charged fees to defray costs associated with genotyping, programming, data management, and the preparation and release of data and/or specimens," the spokesperson told PGx Reporter via e-mail.

In completing the first phase of the program, Kaiser Permanente touted the speed with which the RPGEH scientists were able to genotype the large cohort. According to Cathy Schaefer, executive director of the RPGEH, several factors contributed to the pace of the project, including access to Affy's Axiom technology, which quadrupled the number of samples that could be genotyped in a given time as compared to previously available genotyping arrays.

"What would have taken years and years could be accomplished in 15 months," Schaefer told PGx Reporter.

With increasing throughput, the price of genotyping dropped by 50 percent, which nicely coincided with the availability of the ARRA funding. This meant it was "feasible and cost-effective to genotype large numbers" of people, Schaefer noted.

Additionally, Kaiser Permanente built a new, high-throughput laboratory in Oakland, Calif., where researchers implemented "highly automated protocols" enabling industrial-scale DNA extraction and genotyping. "The labs and machines were run at capacity," she added.

Although it took RPGEH 15 months to genotype and analyze the telomere lengths of 100,000 individuals, the consent process, which is arguably the most time-consuming part of the effort, began several years prior. As a result, participants were already consented and samples were already collected by the time researchers were ready to conduct genetic testing.

In 2007, approximately 1.9 million Kaiser Permanente enrollees in Northern California were sent a five-page survey in English, Spanish, and Chinese that explained the RPGEH and invited them to be genotyped. Kaiser Permanente received completed surveys from 400,000 members.

These people were then sent consent forms, "which authorized broad use of biospecimens, survey data, and data from participants’ electronic health records for use in studies of genetic and environmental influences on health and disease," Schaefer said. Those who returned consent forms were sent saliva-collection kits.

When it came time to launch the genotyping project, "we had more than 100,000 participants with completed consent forms and saliva samples," Schaefer said. Although those who agreed to participate in the RPGEH are "fairly" representative of the membership of Kaiser Permanente and the general population in Northern California, older people and women had a higher participation rate than other groups, while response rates were lower among minorities.

As such, in an effort to bolster the diversity of the genotyped cohort, researchers first enrolled all those from racial and ethnic minority groups who returned samples. "The remaining samples needed to reach 100,000 were randomly selected from Caucasian participants," Schaefer said.

As of last month, 188,000 individuals had returned biological samples for analysis. UCSF and Kaiser Permanente said they plan to expand the genotype and telomeres database to 500,000 patients by 2014.

New Cohorts, New Data

Databases like the one being built by Kaiser Permanente and UCSF promise to accelerate the pace of genomic research by providing key insights into disease mechanisms and informing drug development.

The RPGEH database will provide researchers with ready access to environmental and medical data on large populations that otherwise would be prohibitively expensive and time-consuming to collect from scratch. It also arises at a time when partnerships between academic centers and entities such as pharmacy-benefit managers, insurers, and managed care organizations are becoming increasingly common.

Meanwhile, direct-to-consumer genomic firms have emerged as an alternative for researchers seeking genomic and phenotypic data on large cohorts. For example, 23andMe is using its database to conduct internal research studies on several diseases and has also inked a deal with Genentech to use genotyped data from 23andMe customers to advance Alzheimer's research (PGx Reporter 06/29/2011).

23andMe, which launched in 2007, announced it had more than 100,000 genotyped customers as of June this year. More than 76 percent of its customers have agreed to allow 23andMe to use their DNA data in research. Initially, all customers were automatically consented to have their data applied to research conducted by the company. However, 23andMe changed its consent process last year to allow customers to opt out of having to partake in research (PGx Reporter 07/14/2010).

Last November, 23andMe upgraded from Illumina's HumanHap550 chip, which tested around 600,000 SNPs, to Illumina's HumanOmniExpress, which gauges around 1 million SNPs. The phenotypic data collected on customers is self-reported.

In contrast, Affy's Axiom technology, which Kaiser Permanente and UCSF used to test participants' samples, analyzes between 675,000 and 900,000 genetic markers. In addition, the RPGEH database will also report telomere lengths and will contain phenotypic and environmental data from participants' medical records.

While RPGEH will allow drug developers and other commercial entities access to the database, "to date we have not received formal applications for use of RPGEH data from drug developers," Schaefer said.

Researchers interested in gaining access to the database can apply to a six-member Access Review Committee, which will decide whether to grant access based on the scientific merit of the proposed research.

Have topics you'd like to see covered in Pharmacogenomics Reporter? Contact the editor at tray [at] genomeweb [.] com.