New method simplifies search for genetic changes associated with disease

It is now significantly easier to search long stretches of DNA for genetic changes associated with disease, thanks to scientists at Washington University School of Medicine in St. Louis.

The researchers developed a method called direct genomic selection that accelerates the transition between family or population-based studies of disease inheritance patterns and identification of genetic variations that may contribute to disease. That transition normally slows down dramatically when scientists have to sequence regions of interest in patients’ DNA, determining the letter-by-letter genetic code found in those regions.

With the base sequences from many patients’ DNA, scientists can conduct comparisons that highlight the changes most commonly linked to disease, providing them the leads they need to better understand and treat a wide range of disorders.

Researchers report in the January issue of Nature Methods that they’ve already applied direct genomic selection to a region of DNA linked to psoriasis, a disfiguring and potentially debilitating inherited skin condition. “We quickly found 100 previously unidentified genetic variations with potential links to psoriasis,” says senior author Michael Lovett, Ph.D., professor of genetics and pediatrics. “It really is a much quicker and more affordable way of getting at these types of variations and has potential for applications in other areas including cancer research.”

Lovett is working with colleagues at the Genome Sequencing Center (GSC) at Washington University School of Medicine to make direct genomic selection available to a much wider group of researchers. The approach will further empower the University’s BioMed 21 initiative, which is dedicated to harnessing genetic studies and other basic research for improved patient diagnosis and treatment. “This is a major technological breakthrough,” says Mark Johnston, Ph.D., professor and chair of the Department of Genetics. “It’s clearly an enabling technology that will let us extract the region of interest from each individual’s DNA and sequence it.”

Direct genomic selection answers a growing need for what geneticists call resequencing — sequencing the same genetic region in many individuals.

Scientists measure DNA by its individual units of code, which are known as base pairs. Current automated DNA sequencing technology can process pieces of DNA 700 to 1,000 base pairs long, but inheritance studies can leave researchers searching for changes in segments of DNA hundreds of times longer.

Scientists formerly had only two unattractive options for circumventing this disparity and sequencing such large regions. One, which reproduces patients’ entire genomes, can take up to a year, costs tens of thousands of dollars and discards most of the genetic material produced. The other uses a process that focuses more directly on the region of interest in patients’ DNA but leaves the genetic materials in a state that requires considerable time and effort to prepare them for sequencing.

Direct genomic selection both zeroes in on the region of interest and produces genetic material in a form that can easily be prepared for automated sequencing systems, according to Lovett.

Direct genomic selection crafts what Lovett calls “fishing rods” from genetic material produced and maintained by the Human Genome Project. For that project, researchers divided the human genome into many sections and copied the sections into bacterial artificial chromosomes (BACs), structures they implanted in bacteria for easy reproduction of DNA.

Scientists interested in a particular region of the human genome can now order the BAC of that region from the genome project and use Lovett’s procedure to modify the BAC with biochemical hooks, making it possible to fish out the corresponding region from a patient’s DNA for sequencing.

Lovett also developed modifications to the steps used to prepare patient DNA. The steps ensure that the material snared by the fishing rods can easily be prepared for sequencing. “The challenge now is that we have many disease genes that are not all-or-nothing factors–they can be linked to increased risk of disease, but not to guaranteed development of the disease,” Lovett explains. “In some such instances, there’s concern that another gene or bit of genetic code sitting somewhere nearby, in the same approximate region, might be able to more completely explain what happens in the disease.”

Direct genomic selection should also be helpful to cancer research, according to Lovett. “In many cancer cases we know there are alterations in the DNA of cancer cells–deletions, additions, or substitutions,” Lovett says. “We’ve had great difficulty in narrowing those differences down, but direct genomic selection could help scientists go in, grab the appropriate region of DNA, sequence it and start to learn what’s going on.”