Cataloguing Genetic Variants to Predict Disease

The human genome contains as many as 10 million genetic variants, the majority of which are innocuous, which distinguish us as individuals. But since genetic mutations are often implicated in disease, it’s imperative to identify which genetic variants are potentially harmful.

Researchers at Washington University School of Medicine in St. Louis have developed a rapid, inexpensive technique to create DNA fragments representing all possible variations in a gene. The ability to study each fragment could allow researchers to determine which genetic variations are disease-causing, and which are harmless.

Current methods of synthesizing DNA fragments are extremely costly, and take up to a week to generate the product. The research was published in the journal, Nature Methods.

“As a pediatric neurologist who does a lot of genetic studies of kids with developmental disabilities, I frequently will scan a patient’s whole genome for genetic variants,” said Dr. Christina Gurnett, the study’s senior author and an associate professor of neurology and of pediatrics. “Sometimes I’ll find a known variant that causes a particular disease, but more often than not I find genetic variants that no one’s ever seen before, and those results are very hard to interpret.”

To test the effects of individual genetic variations, scientists have traditionally replaced bases one-by-one. By translating the DNA into its resulting protein, researchers were able to assess whether the product behaved as it should.

In replacement of this time-consuming and laborious process, researchers have begun to use a method of creating hundreds of variations on a sequence, and then testing all products in the set simultaneously. While more efficient, the high cost of this method has limited its use.

Dr. Gabriel Haller, a postdoctoral researcher working in Gurnett’s lab, found that he could create these sets of DNA sequences using common lab equipment and reagents. By copying a DNA sequence using a nonstandard base known as inosine, Haller was able to create sequences containing the unique base at a random site.

Each inosine was then replaced with one of the standard bases – adenine, thymine, cytosine or guanine – which resulted in a single gene mutation in each copy. As this technique is both fast and inexpensive, whole catalogues of genetic variants for any given gene could be easily generated for research purposes.

“Then, when clinicians find a variant that’s never been seen before in one of these genes associated with aortic aneurysm, they can go through this catalog and say, ‘Yes, this mutation does have a negative effect on that protein, so it’s likely harmful,’” said Gurnett. “It would help them decide what to tell the patient. This would be one piece of the big interpretation puzzle for genetic mutations.”