More than 100,000 Californians have mailed their saliva samples to genetics researchers to build one of America’s most powerful medical research tools, linking genetic variants to numerous conditions.
The project is co-led by Neil Risch, PhD, of the University of California, San Francisco (UCSF), and studies using the data have already started appearing in the journal Genetics.
Dr. Risch says: “This is an incredible treasure trove of data. The information collected during medical care is much more comprehensive than the isolated measurements we would make in a traditional research study.
“By linking these clinical records with genomic data from each person, we now have the power to track down many genetic and environmental contributions to disease.”
The researchers have already used to the genetic information collected through health care providers to pinpoint variants linked to:
- Prostate cancer
- Macular degeneration
- High cholesterol.
The beauty of this dataset, says Dr. Risch, “is that it covers countless diseases and traits, and the medical records are constantly being updated as the cohort grows older.”
DNA specimens were extracted from saliva samples of 110,266 individuals, with the UCSF researchers working with The Kaiser Permanente Research Program on Genes, Environment and Health.
The first reports published in the journal describe the genetic characteristics of the volunteers, how their self-reported ethnicity relates to genetic ancestry, and details of the innovative methods that allowed them to complete DNA analysis within 14 months.
The team describes how it processed over 100,000 samples to characterize 70 billion genetic variants within just 2 years. Co-author Prof. Pui-Yan Kwok, of the Institute for Human Genetics at UCSF, says: “In 2009, this was a huge task, it hadn’t been done this fast before.”
The very large volume of samples called on the team to develop a high-throughput robotic system, which completed the testing in 4 months.
Because the average age of participants in the cohort was 63 years, the research focused on age-related diseases. It has included investigation into the length of telomeres, the protective caps on chromosomes that influence these conditions.
Telomere length decreased more for men than women between the ages of 50 and 75, but increased modestly for the ages 80 to 90 years in both sexes.
The telomere work was led by Elizabeth Blackburn’s UCSF research group. Prof. Blackburn was awarded a Nobel Prize in 2009 for the discovery of telomeres. She says:
“This is the largest telomere length database ever constructed from a single study population. At the start, some were skeptical that we could get reliable data from saliva. But we had a 96% success rate, and the results are in fact highly consistent with conclusions from studies of blood.”
One of the new articles presents a detailed genetic ancestry study, including the relationship between the genetic results and self-reported ethnicity in the cohort.
Participants identified their race or ethnicity among 23 questionnaire categories. All the possible combinations of these categories produced over 50 different race/ethnicity identities.
Dr. Risch says: “More and more people are identifying as multi-ethnic, which can pose some technical challenges for genomic studies. At the same time, it also presents opportunities for analyzing genetic and social contributions to disease differences between groups.”
The genetic resource created by the researchers is, they say “just a taste of what is to come.”