Monday, December 11, 2006

Searching for Disease Genes Gets Easier

A new generation of gene chips is poised to more effectively identify the genetic causes of diseases.

By Emily Singer

Over the next year, scientists expect to uncover genetic secrets of such complex diseases as diabetes, heart disease, and autism. Studies of these diseases using powerful new gene chips, which can quickly identify a genetic sequence linked to risk of a particular disease, are now under way. The results could lead to new diagnostics, drug targets, and understanding of these complex diseases.

One of the makers of these new gene chips, San Diego-based Illumina, is now looking ahead to the next phase of medical genetics. The company has recently acquired new diagnostic and sequencing technologies, which it plans to use to better identify medically relevant genes. Ultimately, the goal is to diagnose risk of specific diseases and identify the best treatment options for certain patients.

The Illumina chip contains 650,000 short sequences of DNA that can identify SNPs (single nucleotide polymorphisms), carefully selected from a map of human genetic variation known as the HapMap (see "A New Map for Health"). Each SNP represents a spot of the genome that frequently varies among individuals and acts as a signpost for that genomic region. Scientists use the chip to search for genetic variants that are more common in a group of people with the disease of interest. David Barker, vice president and chief scientific officer at Illumina, talked with Technology Review about the company's plans.

Technology Review: Tell me about the Illumina chip.

David Barker: The [DNA sequences] on the chip were chosen to represent the common variation in the genome mapped in the HapMap. The microarray does a good job of capturing all that variation and can help discover genes that control risk of major diseases, such as cancer, asthma, diabetes, and heart disease.

TR: What kinds of projects are under way?

DB: We are working with an Icelandic company, DeCode, which will genotype half the population of Iceland and will look for associations in all kinds of diseases (see "Genomics into Drugs").

Lots of other projects are in progress. Children's Hospital of Philadelphia, for example, plans to type every patient who walks in the door, as well as their parents. They aim to have 30,000 samples by the end of the year and will look for associations with different childhood diseases.

Some studies are already bearing results, even though the chip has been out for less than a year. A paper published earlier this month in Science identified a gene with a strong association with inflammatory bowel syndrome, or IBS, which includes Crohn's disease and colitis. People with IBS have an autoimmune reaction that damages their own tissue. The researchers identified a rare variant of a gene for a protein released during inflammation that actually provides protection against the disease. The findings provide new targets for drugs to treat the condition.