100,000 Volunteers Contribute Genomic Information and Health Histories – UCSF Creates a Databa
Who says Americans are afraid of sharing genomic information, especially when it’s analyzed in bits? 100,000 Kaiser Permanente patients contributed saliva for DNA analysis as to a subpart of the genome. The subpart – telomeres – is fairly newly discovered and seems important in several ways as to how we age and how cells die (or not). Now, thanks to new technology not available three years ago, the genomic work was completed in less than 15 months, and the data is being linked to health records and California environmental data. The resulting database will be online next year. Set out below are excerpts from UCSF’s online description of the project.
"The genotyping project was made possible by a two-year, $24.8 million grant awarded in September 2009 to the Kaiser Permanente RPGEH and UCSF by the National Institutes of Health. Funding for the grant came from three sources: the National Institute on Aging, the National Institute of Mental Health, and the Office of the Director.
”The completion of genotyping on this large and diverse population marks an unprecedented milestone in population-based genetics research,” said Richard J. Hodes, MD, director of the National Institute on Aging at the National Institutes of Health. “The genetic information, combined with the longitudinal clinical and health data that are already part of the Kaiser Permanente database, along with California environmental data, will create a unique and powerful resource to help answer research questions about aging, health and disease.”
To complete the genotyping project in two years, as required by the funding, Kaiser Permanente first had to build a new, high-throughput laboratory in Oakland, Calif., to extract DNA from more than 100,000 saliva samples in 15 months. The extracted DNA was transferred to UCSF’s Institute for Human Genetics, which worked with Affymetrix to create custom Axiom® arrays for genotyping 675,000 to 900,000 genetic markers – comprised of single nucleotide (SNPs) and insertion-deletion polymorphisms – across all 100,000 samples.
“This project reflects the incredible advances that have occurred in the past decade in the field of genomics and the speed and cost-effectiveness of genotyping technology,” said UCSF professor Pui-Yan Kwok, MD, PhD, who led the SNP genotyping work at UCSF. “Three years ago, we could never have undertaken a project of this size, much less completed it in only 15 months.”
Separate samples of DNA from the same 100,000 individuals were also analyzed in the laboratory of UCSF Professor Elizabeth Blackburn, PhD, who received the Nobel Prize in Physiology or Medicine in 2009 for her discovery of telomeres. The Kaiser Permanente/UCSF project will create the largest resource of telomere data available and will be the first such resource linked to health records of this number and diversity through Kaiser Permanente.
Data from the genotyping project will be processed and cataloged by RPGEH and UCSF scientists over the next year so it can be made available to researchers in late 2012."