April 30, 2006
Founder Population Genetic Scans Accelerate

An article in MIT's Technology Review reports on a Canadian company Genizon Biosciences that is using the genetic homogeneity of the French Quebec founder population to investigate genetic causes of disease just as deCODE Genetics does in Iceland. To someone with an interest in the accelerating rate of biotechnological advance (FuturePundit and I hope quite a few readers of FuturePundit) the most interesting part of the article mentions that Genizon has used improvements gene chip technology to speed up their genetic studies by more than an order of magnitude.

The initial Genizon map, completed in 2004, was created from 1,500 members of the Quebec founder population and had about 81,000 markers. Genizon has now improved its gene hunting capabilities even further, by using a gene chip produced by Illumina, a genetic toolkit company in California, which incorporates markers from both the HapMap and original Quebec map, for a total of more than 350,000 markers per individual. Studies that initially took scientists three months now take just a week, says John Hooper, president and chief executive officer Genizon.

3 months is 13.5 weeks versus 1 week for the same test run now. So in just a few years they sped up their testing by over an order of magnitude. I keep running into reports where researchers mention their experiments use new technology that has sped up their experiments by orders of magnitude and that they can now collect more data and more quickly. These boosts in productivity are going to produce discoveries and effective treatments for diseases which have long been incurable.

To uncover genetic variants that increase risk for a disease, scientists start with DNA from patients and use the gene chips to sift through the markers, searching for particular variants that appear more frequently in people with the disease. Once scientists have identified genes of interest, they create a map of the interacting genes.

Among the diseases they are looking at for genetic risk factors: Crohn's disease, asthma, schizophrenia, baldness, longevity, Attention Deficit Hyperactivity Disorder, Type II diabetes, osteoporosis, and macular degeneration.

The Genizon web site also has an interesting table of genetically homogeneous founder populations around the world. I had no idea that north east Finland has a genetically homogeneous population only about 15 to 20 generations old. Also, the people in Newfoundland are pretty genetically homogeneous. Also, Costa Ricans from the central valley of Costa Rica meet criteria for homogeneity of recent enough vintage that make them good genetic study candidates.

The costs of DNA studies will drop by more orders of magnitude in the next couple of decades. Scientists will identify the vast bulk of genetic variations that affect our disease risk, physical performance, intelligence, behavior, and other characteristics.

Share |      Randall Parker, 2006 April 30 12:05 PM  Biotech Advance Rates

danratherfan said at April 30, 2006 2:48 PM:

Lookin' good. Now if only we could increase it by a few more orders of magnitude. I'd like to start a lab in my basement and sequence all of my families genes to find out why we're so weird.

AMac said at May 1, 2006 10:29 AM:

A few weeks ago, Illumina increased the number of SNPs available on its whole genome chipset from 300,000 to 540,000. The "universe" of human SNPs is between 2 million and 10 million, depending on definition; the 2 million figure is probably the more relevant one. So already, it's possible to "fingerprint" an individual's genotype at about one quarter of the SNP sites worth looking at. Pretty amazing.

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