Social Media Sidebar

Announcement

Please sign up, comment on articles and bring your friends!

Current poll

PlanetTech is asking:

What do you think about our new web site?

Love it, indeed
Really good solution
Same as old one
The old one was better
This is a new option

Quote of the day

People say we're running out of energy. That's only true if we stick with these old 19th century technologies. We are awash in energy from sunlight.

 

Ray Kurzweil

 

'Deep learning' reveals unexpected genetic roots of cancers, autism and other disorders

RATE THIS! +25
Posted in Science on 27th Sep, 2015 08:28 PM by AlexMuller

In the decade since the genome was sequenced in 2003, scientists and doctors have struggled to answer an all-consuming question: Which DNA mutations cause disease? A new computational technique developed at the University of Toronto may now be able to tell us.

 

A Canadian research team led by professor Brendan Frey has developed the first method for 'ranking' genetic mutations based on how living cells 'read' DNA, revealing how likely any given alteration is to cause disease. They used their method to discover unexpected genetic determinants of autism, hereditary cancers and spinal muscular atrophy, a leading genetic cause of infant mortality.
 
Think of the human genome as a mysterious text, made up of three billion letters. "Over the past decade, a huge amount of effort has been invested into searching for mutations in the genome that cause disease, without a rational approach to understanding why they cause disease," says Frey, also a senior fellow at the Canadian Institute for Advanced Research.
 
"This is because scientists didn't have the means to understand the text of the genome and how mutations in it can change the meaning of that text." Biologist Eric Lander of the Massachusetts Institute of Technology captured this puzzle in his famous quote: "Genome. Bought the book. Hard to read."
 
What was Frey's approach? We know that certain sections of the text, called exons, describe the proteins that are the building blocks of all living cells. What wasn't appreciated until recently is that other sections, called introns, contain instructions for how to cut and paste exons together, determining which proteins will be produced. This 'splicing' process is a crucial step in the cell's process of converting DNA into proteins, and its disruption is known to contribute to many diseases.
 
Most research into the genetic roots of disease has focused on mutations within exons, but increasingly scientists are finding that diseases can't be explained by these mutations. Frey's team took a completely different approach, examining changes to text that provides instructions for splicing, most of which is in introns.
 
Frey's team used a new technology called 'deep learning' to teach a computer system to scan a piece of DNA, read the genetic instructions that specify how to splice together sections that code for proteins, and determine which proteins will be produced.
 
Unlike other machine learning methods, deep learning can make sense of incredibly complex relationships, such as those found in living systems in biology and medicine. "The success of our project relied crucially on using the latest deep learning methods to analyze the most advanced experimental biology data," says Frey.
 
Once they had taught their system how to read the text of the genome, Frey's team used it to search for mutations that cause splicing to go wrong. They found that their method correctly predicted 94 percent of the genetic culprits behind well-studied diseases such as spinal muscular atrophy and colorectal cancer, but more importantly, made accurate predictions for mutations that had never been seen before.
 
They then launched a huge effort to tackle a condition with complex genetic underpinnings: autism spectrum disorder. "With autism there are only a few dozen genes definitely known to be involved and these account for a small proportion of individuals with this condition," says Frey.
 
Frey's team compared mutations discovered in the whole genome sequences of children with autism, but not in controls. Following the traditional approach of studying protein-coding regions, they found no differences. However, when they used their deep learning system to rank mutations according to how much they change splicing, surprising patterns appeared.
 
"When we ranked mutations using our method, striking patterns emerged, revealing 39 novel genes having a potential role in autism susceptibility," Frey says. And autism is just the beginning, this mutation indexing method is ready to be applied to any number of diseases, and even non-disease traits that differ between individuals.

Tags: deep learningAImachine learningautismgeneticsresearch

Read original article » Back to category

Comments

Author: Guest
Posted: 2015-09-28
+2
A lot of genetic data for a range of diseases are now available and keep increasing so finding new computational methods to analyse this is critical - this method can have a great impact Reply


 

Recent headlines

  • Posted in Medicine on 2017-09-24 12:24:41
    Effective help is available for migraine sufferers..read more
    Posted in Business on 2017-09-24 12:20:40
    AR startup Mira bags $1 million for Google Cardboard-like.....read more
    Posted in Medicine on 2017-09-24 12:14:44
    Alarm as 'super malaria' spreads in South East Asia..read more
    Posted in Science on 2017-09-23 08:31:24
    Fly me to the Moon: For some, lunar village takes shape..read more
    Posted in Software on 2017-09-23 08:22:48
    One year later, Microsoft AI and Research grows to 8k.....read more
Posted in Business on 2013-10-10 01:33
China is working towards a manned lunar mission in about.....read more
Posted in Business on 2013-10-20 07:17
Spacex says China is their main competitor for commercial.....read more
Posted in Software on 2013-10-20 06:43
Pirate Bay Browser Clocks 1,000,000 Downloads..read more
Posted in Medicine on 2013-10-10 02:10
Google reportedly investing hundreds of millions into new.....read more
Posted in Medicine on 2013-10-14 03:13
Endothelial Cells Can Repair and Regenerate Organs,.....read more
Posted in Science on 01.01.2010
Spacex says China is their main competitor for commercial.....read more
Posted in Science on 01.01.2010
Staring at Your Phone Could Be Making You Short Sighted..read more
Posted in Science on 01.01.2010
Oculus Rift virtual reality headset coming to mobile, but.....read more
Posted in Science on 01.01.2010
China is working towards a manned lunar mission in about.....read more
Posted in Science on 01.01.2010
Delivering drugs via nanoparticles to target mitochondria..read more

Recent Blog Posts

  • Posted by AlexMuller
    Scientists probe Neptune's depths to reveal secrets of icy.....read more
    Posted by AlexMuller
    New terahertz imaging approach could speed up skin cancer.....read more
    Posted by AlexMuller
    Rebutting the claim that antidepressants do not work..read more
    Posted by AlexMuller
    Artificial neural networks decode brain activity during.....read more
    Posted by AlexMuller
    Four Earth-sized planets detected orbiting the nearest.....read more

Login to your Account

Login to your PlanetTech Account here

Username:
Password:
Remember me
or

Create a New Account

You just need username and password

The following errors occured:
Username:
Email:
Password:
Verify password:
Remember me