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NIH Awards $25M to Kaiser Permanente, UCSF for 100,000-Member Genome-Wide Analysis Data Repository


By Turna Ray

The National Institutes of Health has awarded $24.8 million to the Kaiser Permanente Research Program on Genes, Environment, and Health and the University of California, San Francisco to create a data repository for genomic and environmental data that will facilitate genome-wide association studies into various diseases.

The researchers will use the new Axion platform from Affymetrix to genotype 100,000 Kaiser Permanente members who have donated their DNA for research. The average age of those that will be genotyped is 65 years old.

"In creating this deep genome-wide information … we hugely enable the broader scientific community to look at a wide variety of different scientific questions that potentially address a variety of genetic and environmental influences on health, disease, and aging," Cathy Schaefer, executive director of the RPGEH at Kaiser Permanente's Northern California Division of Research, told Pharmacogenomics Reporter this week.

The two-year grant was awarded by the NIH with funds from the American Recovery and Reinvestment Act, and was doled out by three NIH divisions: the Office of the Director, the National Institute on Aging, and the National Institute of Mental Health.

In a statement, NIA Director Richard Hodes said he hopes the effort "will facilitate studies of gene-environment interaction as determinants of health, disease, and longevity."

The UCSF Institute for Human Genetics will perform the genotyping for the project. Neil Risch, co-director of the RPGEH, will share lead investigator responsibilities for the grant with Schaefer.

"There are relatively few clinical applications of genomic medicine at this point in time," Schaefer said. "As a healthcare delivery organization we're very much interested in discovering things that are clinically useful to people and improve medical care. But there is a great deal of basic research to be done to really understand how genetic and environmental factors influence disease causation.

"There have been many conditions for which a GWAS has not been done, because the population resources needed to do it were not available," Schaefer noted.

Schaefer added that once this resource is established, researchers will be able to use this data for studies either through NIH's database for storing and archiving data for genome-wide association studies, called dbGaP; or scientists can collaborate with Kaiser.

According to Kaiser Permanente, the genetic information generated by the project will include information about drug metabolism and drug response, as well as disease progression, development, and recurrence. Environmental information, lifestyle, and behavioral data will also be incorporated into this resource.

Since the average age of those who have donated their DNA is 65 years old, Kaiser Permanente is particularly interested in looking at the genomic and environmental factors influencing the process of aging.

"Studying an older cohort like this enables us to very efficiently focus on specific diseases that are more common in older age but also look at the underlying processes," Schaefer said. "This resource is specifically able to do that because we have so much legacy data. Close to half of the people in this cohort of 100,000 people have been members of Kaiser Permanente for over 20 years."

In addition to genome-wide genotyping, Schaefer's group will also be working with Nobel Prize-winning scientist Elizabeth Blackburn to measure telomeric DNA in the Kaiser Permanente cohort.

Telomeres are protective regions of repetitive DNA at the end of a chromosome and certain telomere lengths have been shown to be risk factors for diseases such as cancer and cardiovascular conditions. Blackburn, Carol Greider, and Jack Szostak were awarded the 2009 Nobel Prize in Physiology or Medicine for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase.

This data repository for GWAS is part of the larger RPGEH, which was launched in 2005 in the Kaiser Permanente Northern California Division of Research. The research program has so far collected biospecimens for DNA analysis from more than 110,000 Northern California members and plans to collect samples and conduct health surveys with 500,000 members by 2013.

This new NIH grant adds to the $8.6 million Kaiser Permanente received last December from the Robert Wood Johnson Foundation, for the collection and storage of the first 200,000 DNA samples into the RPGEH and for building health and environmental databases.

Only Kaiser Permanente members in Northern California may participate in the RPGEH. Participation in the project is voluntary. Kaiser Permanente's Division of Research maintains separate databases from its health plans and members' medical records to protect participants' privacy and to ensure that genomic data is not used to make healthcare reimbursement decisions.

RPGEH has also received funding from the Wayne and Gladys Valley Foundation, the Ellison Medical Foundation, and Kaiser Permanente’s Community Benefit Program.

Separately, the Kaiser Foundation Research Institute's Katrina Goddard has received nearly $2 million under federal stimulus funding to conduct comparative effectiveness research in genomic and personalized medicine for colon cancer.

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