Sabin Russell Science Writer


Sending Spit to Kaiser

Technicians at Kaiser's Oakland lab use a highly automated process to extract DNA from 2,500 samples of saliva per week. Photo by Peter DaSilva appears in May 30, 2010 New York Times

I had one more New York Times story left in me. Click that link and read it. Here's what it's about:

During the past two years, more than 130,000 Northern Californians have sent their saliva to Kaiser Permanente -- not a statement about HMOs or private health insurance -- but to participate in the largest genome scan of its kind. I was not aware that ordinary saliva contains enough white blood cells and cells from the lining of the saliva duct to provide more than enough DNA for modern high speed gene scans. Well, it does.

A spinoff from anti-recessionary spending, the Kaiser/UCSF project was one of those "beaker ready" projects on the wish list of big institutions that qualified for federal stimulus money -- $25 million from the NIH that has to be spent by October 2011. Kaiser had already been busily collecting spit from volunteers. With the stimulus money, they were able to process those samples and run the DNA of each patient over a chip that looks for 675,000 different gene variants. It took a while to set up the robots, but now 2,500 samples are spit are being analyzed each week.

The idea is that, by comparing the genes of healthy people to those of people who have various chronic ailments, they may be able to spot the genetic roots of those diseases. These scans are called genome wide association studies, and for the last several years they've been the hottest thing in molecular biology. The problem is that these scans may not be discerning enough to find faulty genes. It may well be that the genes that contribute to disease are not common. Instead, it is the rare variant that misfires and leads to illness -- and perhaps the only way to find those variants is to sequence the entire genome of affected individuals, rather than scanning their genes for selected variants.

We'll have to wait a couple of years to see if this giant project produces enough data to answer the questions, or strengthens the case that whole genome sequencing, rather than these genome wide association studies, are needed to yield the information researchers believe they can find. In the meantime, Dr. Elizabeth Blackburn and her lab will also be analyzing the DNA of these same volunteers to measure the length of telomeres (tee-lo-meers), which are wads of repeating sequences of DNA that bind the ends of chromosomes like the tips on shoelaces, so the the DNA chains don't unravel every time a cell divides. Long telomeres are associated with longer lifespan, shorter teleomeres with shorter longevity. Blackburn will be analyzing telomere length simultaneously with the data from the high speed gene scans.

The first results of this giant study won't be ready until 2011. Until then, read what you can about this technology, which represents in many ways the leading edge of modern genetics. As this story demonstrates, it is has already reached into the homes of 130,000 Northern Californians, who have sent their spit to Kaiser. In time, Kaiser expects to have DNA stored from spit or blood of 500,000 members.   It's where soft, wet chemistry (what is wetter than spit or blood? ) meets the hard dry edge of statistics. Whether or not studies like this one  will solve the genetic puzzles surrounding chronic illness and longevity remains to be seen. Regardless, this spit-propelled project will build up an enormous bank of information that will keep the dry scientists -- those sifters of epidemiological data -- and their computers busy for decades to come.

Read the whole story in the New York Times.

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Posted by Sabin Russell

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