Genetics of the Pleb Plebis

“Our biggest fear is a power-failure” Dr. Pui-Yan Kwok of the University of California at San Francisco notes, a fear shared by tropical aquarium enthusiasts everywhere. However, unlike amateur aquarists, Dr. Kwok is working on human genetic research on a massive scale. Using recent advances in genetic technology that allows for rapid analysis of a human genome, researchers at Kaiser Permanente in Oakland and at UCSF are working to analyze over 130,000 samples of DNA in order to uncover the roots of genetic disorders and to work out just how it is that some people live longer than others.

This project dwarfs others of its kind. Most genome wide studies work with samples of under 10,000, and possibly by using some previously published data from smaller studies. Access to over 130,000 samples, simply put, will provide an enormous statistical pool from which to draw information. Several advances in technology and shifts in the political winds have allowed this to be possible. Although the Human Genome project, started in the early nineties, took over a decade to sequence a group of under a dozen genomes, this project is working on analyzing 2,500 samples… in one week. Politics have also come in to play, as advances in technology have aligned with the Obama Administration’s resolve to keep science and research well funded. The team received the $25 million grant that made this large scale operation possible from Obama’s Federal Stimulus package, passed last year.

There are three prongs to this endeavor. The first is the collection of samples. For this, Kaiser’s large pool of patients is being tapped. Almost two million patients were asked about participation in 2007, and a large group assented. This large pool was winnowed down to the 130,000 participants, who received little plastic cups in which to spit by mail. The saliva of the participants contained enough genetic material for a full analysis. Dr Kwok’s lab at UCSF will analyze the genomes in order to compare genomes of people with diseases such as cancer and multiple sclerosis to healthy genomes, hopefully to pinpoint the genetic causes. Another UCSF researcher, Nobel laureate Dr. Elizabeth Blackburn, will analyze the genomes with a different aim. Her lab will be measuring the length of the chromosome’s telomeres. Telomeres are bits of DNA on the tops and bottoms of chromosomes that seem to regulate lifespan.

The DNA samples are stored in specialized cardboard boxes at room temperature while they await analysis. Special robots costing a quarter of a million dollars each take the saliva samples and processes them, storing the data. This is where Dr. Kwok’s fear of a power failure comes from, as each array filled with 96 analyzed DNA samples costs $10,000. Although some scientists, such as Dr. David B. Goldstein of Duke University, think the money would be better spent on more specialized research focusing on total sequencing of a smaller number of genomes rather than a large number being scanned for variations, it is hard to argue that the scale of this operation will not produce useful data. Even if the UCSF researchers are unable to glean anything useful from the research, this large amount of data will be available for future studies. This study is a landmark, as genome analysis has typically relied on smaller numbers of genomes self selected by paying for a service, or by researchers just taking small samples of people. The technology has moved to the point where truly large numbers of people’s information can be processed, and this study of 130,000 is just the beginning. Kaiser is currently planning to sample 400,000 more patients over the coming years. This huge pool of genetic material will hopefully provide science and medicine with powerful insights into the way our bodies are built, and more importantly, ways to fix ailing ones.

Article by Sabin Russel of the new york times.Original article can be viewed at:www.nytimes.com/2010/05/30/science/30sfgenome.html