A new gene chip designed specifically for type 2 diabetes could help resolve a troubling finding plaguing studies of complex human diseases. While scientists have identified a number of genetic variations that raise the risk for developing different diseases, including diabetes, heart disease, and Alzheimer’s, these variants account for only a small portion of the overall risk. In type 2 diabetes, for example, variants identified so far account for only about 9 percent of the genetic risk, said Michael Erdos of the National Human Genome Research Institute at the First Annual Consumer Genetics Conference today in Boston. The rest of the risk likely lies in rarer genetic variations undetectable in existing studies, which have analyzed hundreds to thousands of patients.

Erdos’s group and others are now designing a specialized gene chip for diabetes research, dubbed the metabochip. It will include 50,000 genetic markers, all of those identified to date in genetic association studies, both large and small, of type 2 diabetes, as well as some rare variations found in less than 0.5 percent of the population. Scientists plan to study 200,000 people with diabetes, a number that is about an order of magnitude greater than previous studies. The Wellcome Trust Case Control Consortium, which is the largest genome-wide association study I know of, has analyzed approximately 20,000 patients and controls. The research should help resolve the question of whether larger gene-chip studies can identify the remaining genetic risk factors.

Other scientists are developing new tests for clinical use. Scott Weiss, director of respiratory, environmental, and genetic epidemiology at Harvard Medical School, is working on two new genetic tests for asthmatics. His team has already identified a number of genetic markers that can predict whether a patient with asthma is likely to require hospitalization, and the researchers are working on a test to determine which asthmatic kids taking oral steroids are at risk for stunted growth.

Pharmacogenomics–the practice of selecting drugs and doses based on an individual’s genetic profile–is often predicted to be the first success in the field of personalized medicine. For example, genetic variations in drug-metabolizing enzymes can affect both the effectiveness of a drug and its likelihood of causing side effects. At the conference, Michael Phillips, director of the Pharmacogenomics Centre at the Montreal Heart Institute, pointed out that adverse reactions to drugs are the fifth leading cause of death in the United States. He gave the example of a woman who was an ultrarapid metabolizer of codeine: the 2D6 enzyme metabolizes codeine into morphine in the body, which is responsible for the pain-relieving benefits. Not knowing her ultrarapid phenotype, this woman then breastfed her baby, who later died of a morphine overdose.

Phillips gave a number of examples in which pharmacogenomics could be used today but typically is not, including the prescribing of Strattera, a popular medication for attention deficit/hyperactivity disorder. Poor metabolizers of the drug–about 10 percent of Caucasians–will have about a tenfold greater concentration in their bloodstream. This increases risk of adverse side effects but isn’t fatal, so the FDA does not require genetic testing, said Phillips.

Interesting tidbit: Phillips also said that pharma companies have long known that about 10 percent of Caucasians have a genetic variation in the CYP2D6 gene that makes them poor metabolizers of a number of drugs. Rather than developing a test for this variation, they instead abandoned drug candidates metabolized by the enzyme–molecules that might have proved helpful to the remaining 90 percent.

More from the Consumer Genetics Conference tomorrow.