SFGENOME

Samples have been donated by thousands of Kaiser members.

Still in fine fettle at the age of 87, Ruth Young, a retired Oakland school nurse, jumped at the chance, she said, to “spit for the cause.”  Mrs. Young is one of more than 130,000 members of Kaiser Permanente in Northern California who have volunteered to have their DNA scanned by robotic, high-speed gene-reading machines as part of the largest human genome study of its kind ever attempted.

 

The goal of the study they are participating in is to help scientists uncover the genetic roots of chronic disease and, perhaps, to find out why some people live longer than others.

This month, researchers at Kaiser Permanente in Oakland and the University of California, San Francisco began the highly automated, large-scale process of analyzing that DNA, which is being extracted from tens of thousands of saliva samples donated by Kaiser members in Northern California since 2008.

Each sample of ordinary spit is laden with cells containing the volunteer’s entire set of genes, their genomes, which carry in sequences of DNA the coded instructions for building and maintaining life. The hope for this so-called genome-wide association study is that, when the genes of people with diseases like cancer and multiple sclerosis are compared with the genes of those in good health, computer analysis will pinpoint genes responsible for the illnesses.

With a speed that would have seemed preposterous to contemplate a decade ago, the work of collecting, purifying and digitizing billions of discrete bits of chemical information will be finished in less than 18 months, providing a rich resource for scientists to analyze for decades to come.

Winifred K. Rossi, who is managing the project for the National Institute on Aging, said most genome-wide association studies scan between 5,000 and 8,000 participants, although data from multiple, smaller studies can be pooled to form a larger group. What makes the Kaiser study unique is that members of a single, colossal cohort will have their genomes scanned uniformly, then paired with their medical histories. “It is absolutely the largest study of its kind, and it has enormous statistical power.” Ms. Rossi said.

Mrs. Young, a Kaiser member for 63 years, suffers from arthritic knees and Type II diabetes, which took her father’s life at an early age. “I’m conscientious about my diet, but I do love sweets,” she said.

She had originally been one of nearly two million patients asked in 2007 about participating in the Kaiser study. A huge group of volunteers, ranging in age from 18 to 107, filled out questionnaires. Tens of thousands of them, like Mrs. Young, were asked for specimens.

Following instructions found in a kit mailed to her Oakland home, Mrs. Young deposited the requested spit into a special plastic cup. She sealed it with a blue lid fitted with a built-in preservative and sent it back to Kaiser. Along with her saliva, the samples from the other 130,000 people began arriving in Kaiser’s mailbox.

Experiments like this one underscore how quickly gene-scanning technology is moving from the lab to the home. Last week, officials of the University of California, Berkeley, disclosed that 6,000 incoming freshman and transfer students will be asked to swab their cheeks at home for DNA, to participate in a collective lesson in genetics and a preview of the predicted era when medicine will be tailored to each person’s genetic makeup.

Each student who agrees to participate will be able to tap in a security code on a laptop and check whether they carry gene variants that might affect their ability to process lactose, alcohol or folate, a vitamin found in leafy greens. The Kaiser study participants will not have the same option. Their names are scrubbed from their samples, and only researchers — working with codes instead of names — will be able to link the gene scans to medical histories. Their goal is to discern the larger picture, hoping to spot associations between genes and health that would not show up until very large numbers of individuals are compared at once.

Although this vast experiment has been contemplated for years, it was given a boost last year when Kaiser and the university won a $25 million grant from the National Institutes of Health as part of the stimulus package.

However, the study has begun just as some scientists have started to question the value of these experiments, and when private ventures, like 23andMe, are struggling to find a consumer market for gene tests.

David B. Goldstein, a Duke University researcher, said he believed “interesting and valuable information” would come from the Kaiser study, but he questioned whether it was the most efficient way to gather information about the genetic links to disease. “It’s an awfully expensive study,” Dr. Goldstein said in an e-mail message.

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