DNA sequencing on a budget

Friday, August 15, 2008
by Joe Caspermeyer

Want a blueprint of your own personal DNA, including every gene in your body? The good news is that scientists know how to make one, thanks to the Human Genome Project. That bad news is that you probably can’t afford it, unless you have $10 million sitting around in your piggy bank.

DNA testing is transforming health care, but today’s tests can only look for one or a few genes. But there are more than 20,000 genes in the human body. If doctors could look at your whole genome—all the information in your DNA—they might be able to provide more individualized care. They could specially tailor treatment and prevention programs for common diseases such as cancer, heart disease and diabetes.

The cost of DNA sequencing has already dropped a lot—from about a dollar per DNA base to a penny. But a human being has three billion base pairs. Even a penny a pair is far too expensive.

Researchers at Arizona State University are trying to cut the price tag of genetic sequencing from about $10 million dollars per person to $1,000 or less. They are also trying to make the process about 10,000 times faster, so that it can be done in days rather than over the course of years.

“If you want to develop a technology to sequence an individual genome for $1,000, you have to think about using nanotechnology,” says Peiming Zhang, a chemist at ASU’s Biodesign Institute. “The technology is available now to pioneer a new approach to sequencing.” Nanotechnology involves working with materials on an extremely small scale—so small they can’t be seen with the naked eye.

Zhang’s goal is to allow scientists to sequence billions of base pairs of DNA in a single day. By increasing the speed of sequencing and reducing its cost, genetic research may start to play a bigger role in everyday medical practice.

In Zhang’s project, billions of base pairs of DNA could be sequenced on a single, cookie crumb-sized chip, like a computer chip. Scientists sequence the DNA by applying a sample of it to single-stranded DNA probes attached to a chip. An atomic force microscope then scans the surface of the chip to see where DNA from the sample has attached to the probes.

Jian Gu, co-leader of the project, has developed nanoprinting techniques that will let the researchers increase the number of probes they can fit on a chip. “Right now, we have a mechanical printing technology that could put down billions of probes on a chip surface at very low cost,” says Gu.

Zhang and Gu’s research is paid for by the National Institutes of Health (NIH). Two other ASU research teams, led by Stuart Lindsay and Peter Williams, have also received NIH funding to try to make DNA sequencing faster and cheaper.

Williams is a professor of chemistry. His goal is to sequence genes that are involved in disease. He wants to do this in a matter of hours, for just a few hundred dollars.

Lindsay, an ASU physicist, is threading DNA through a molecular ring. The ring is actually a sugar called cyclodextrin. It can “read” the DNA sequence by measuring differences in friction as the DNA is pulled through it.

All of the scientists are trying to reach the same type of goal by approaching it from different angles. If they are successful, maybe someday your doctor will be able to treat your health based on your unique genetic makeup.