Software used to identify a rare genetic disorder

Using computational tools to uncover mysterious genetic mutations could have broader implications to identifying more common diseases.
Written by Boonsri Dickinson, Contributing Editor

Now that the price of DNA testing keeps dropping, it seems another critical piece of the genome puzzle has emerged thanks to a sophisticated computational tool. Researchers at the University of Utah and informatics company Omicia, Inc., are using a software program to find the root cause of a disease caused by a rare genetic disorder.

After sequencing two families, the scientists used a program called the Variant Annotation, Analysis & Search Tool (VAAST), to identify a previously unknown syndrome in an individual.

“The big challenge in genomic medicine today is how to sift through the millions of variants in a personal genome sequence to identify the disease-relevant variations,” Omicia's Martin Reese said in a statement.

Currently, DNA testing has a data problem. It has too much data. But it doesn't have to be that way. VAAST solves many of the problems because it's a better tool than what's currently available - and it is statistically powerful. It allows researchers to use fewer people in their study and allows them to hunt down mutations much faster.

The researchers spent the better part of a year examining a rare X-linked genetic disorder, which only affects males. The researchers looked at a lethal mutation in two unrelated families. After the researchers compared family members' genome with sequences from two hundred people, it only took them 10 minutes to run the software program to find the root cause, reports Nature News.

Blame the condition on a gene called NAA10. The gene normally encodes a protein, but it fails to do so when it mutates. When a mutation occurs, the protein has an altered structure and the state of the cells suffers.

"We believe that VAAST will likely accelerate the discovery of disease-causing mutations in both common, complex disorders such as ADHD and autism, and in rare Mendelian disorders,"  researcher Gholson J. Lyon of the Children's Hospital of Philadelphia said in a statement.

The more people who get their genome sequenced, the more data there will be. People who have gotten their genome sequenced will likely have their data interpreted by companies like 23andMe. The approach of using a lot of people in genetic studies was touted as a great way to find links to diseases, but genome-wide association studies haven't exactly lived up to all the hype.

"The real story is in the rare alleles. One in ten percent of us are very affected by these, and the sequencing tests reveal them as long as we are looking for them," Harvard geneticist George Church previously told me. "Almost all common diseases have a rare allele component to it. What happened before is that we went through a fad. Scientists were looking where the light was in the common variants and they mostly ignored rare alleles."

So instead of comparing an individual to a bunch of people in the database, you can learn a lot about individual cases by applying DNA sequencing to a select group of individuals. Sometimes less is more. I wouldn't be surprised to see this new software being used to uncover the genetic mysteries of some of the more common diseases.

via Nature News

Source: University of Utah Health Care

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