An algorithm is sped up to predict harmful effects from specific gene mutations

May 6, 2016, Agency for Science, Technology and Research (A*STAR), Singapore

In 2001, researchers developed a formula, or algorithm, that predicts whether a specific change in a gene sequence can result in harmful effects. While useful, the algorithm was slow; the computations underpinning these predictions used multiple central processing units (CPUs) and a significant amount of time. Now A*STAR researchers have adapted the algorithm to work on a graphical processing unit, a specialized electronic circuit that can process huge amounts of data in parallel.

The faster computational time has allowed the team to expand their "database of predictions" from just the human genome to include more than 200 additional organisms.

Similarities exist between the same of different organisms. Even so, individual organisms have differences in parts of their genomes when compared to other organisms of the same species. Some of these differences affect how proteins function and may lead to disease. By comparing genetic sequences, researchers are able to pinpoint disease-causing gene mutations. But this requires sifting through huge amounts of data.

The SIFT (Sorting Intolerant From Tolerant) predicts which changes in a gene — known as variants — could affect the function of the protein that gene encodes. Using SIFT, A*STAR researchers computed potential changes that can occur to gene sequences in humans to compile a database of predictions. Researchers provide SIFT with the gene variants they are investigating as a possible source of disease. SIFT then looks up the variants in its database of predictions. Variants that are predicted deleterious by SIFT are highlighted and may be considered worthy of further investigation.

Compiling SIFT's database for the involved performing computations on multiple CPUs, which took about four minutes to analyse a single gene sequence.

"I had wanted to make SIFT databases for a lot more organisms, but making the human database took significant time," says systems biologist Pauline Ng from the Genome Institute of Singapore.

SIFT was adapted for use with a to make faster predictions. This allowed the team to expand the scope of the algorithm's predictions to cover more than 200 other organisms. SIFT 4G, the updated algorithm, takes only 2.6 seconds to analyse a compared to SIFT's four minutes.

The updated and algorithm will not only facilitate the identification of disease-causing gene mutations but will help researchers understand the genetic variations that make some animal breeds or plants strains more robust or prone to disease.

Explore further: Yeast against the machine: Bakers' yeast could improve diagnosis

More information: Robert Vaser et al. SIFT missense predictions for genomes, Nature Protocols (2015). DOI: 10.1038/nprot.2015.123

Related Stories

Yeast against the machine: Bakers' yeast could improve diagnosis

April 6, 2016
It's easier than ever to sequence our DNA, but doctors still can't exactly tell from our genomes which diseases might befall us. Professor Fritz Roth is setting out to change this by going to basics—to our billion-year-old ...

Genetic risk factors of disparate diseases share similar biological underpinnings

April 28, 2016
The discovery of shared biological properties among independent variants of DNA sequences offers the opportunity to broaden understanding of the biological basis of disease and identify new therapeutic targets, according ...

Recommended for you

Targeting the engine room of the cancer cell

June 18, 2018
Researchers at Columbia University Irving Medical Center (CUIMC) have developed a highly innovative computational framework that can support personalized cancer treatment by matching individual tumors with the drugs or drug ...

Scientists learn more about how gene linked to autism affects brain

June 18, 2018
New preclinical research shows a gene already linked to a subset of people with autism spectrum disorder is critical to healthy neuronal connections in the developing brain, and its loss can harm those connections to help ...

161 genetic factors for myopia identified

June 15, 2018
The international Consortium for Refractive Error and Myopia (CREAM) recently published the largest-ever genetic study of myopia in Nature Genetics. Researchers from the Gutenberg Health Study at the Medical Center of Johannes ...

Genetic disorder identified in children

June 15, 2018
A genetic defect affecting normal development in children has been identified by a study involving University of Queensland researcher and alumnus Professor David Coman.

Scientists discover biomarker for flu susceptibility

June 13, 2018
Researchers at the Stanford University School of Medicine have found a way to predict whether someone exposed to the flu virus is likely to become ill.

Brain secrets that flow in our blood

June 13, 2018
Our blood can be used to uncover genetic secrets inside the brain, according to University of Queensland research.

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.