Autism: MSSNG

Crowd Sourcing DNA Sequencing for Autism

“Lots of things are mysteries. But that doesn’t mean there isn’t an answer to them. It’s just that scientists haven’t found the answer yet.   – Christopher John Francis Boone, “If you put 10,000 people’s genomes in the cloud, could you demystify autism?”

It’s happening!   Cancer and autism is leading the way “Medicine will soon rely on a kind of global Internet-of-DNA which doctors will be able to search on Goggle’s cloud platform. “Our bird’s eye view is that if I were to get lung cancer in the future, doctors are going to sequence my genome and my tumor’s genome, and then query them against a database of 50 million other genomes. The result will be ‘Hey, here’s the drug that will work best for you.’ ”“

Autism, Crowd Sourcing and Google Cloud Platform

Advancements in genome sequencing will permit Autism Speaks, to sequence the whole genomes of 10,000 people in families affected by autism and to share the results with researchers around the world on the Google Cloud Platform.

Data from 2014 show one in 68 children in the US have autism;  the prevalence has alarmingly increased (see the CNN article, Autism rates now 1 in 68 U.S. children: CDC.  Additionally, the number of children with autism varies widely by community, from 1 in 175 children in areas of Alabama, to 1 in 45 children in areas of New Jersey.   Autism is a group of disorders, it is tangled in genetic and environmental factors causing the disorder, and diet can be used to positively impact symptoms for many (see the post, FOOD MANAGING IBD & AUTISM: THE STUDIES  and check out the slides below for more details):

The Autism Speaks effort is called MSSNG;  the dropped vowels are meant to show all the things about autism that no one has yet observed.

The cloud sequencing data effort is sort of like digitizing a DNA library.  It is crowd sourcing for autism answers.  My readers understand this principle well as many sequencing centers are busy collecting samples from around the world to analyze the composition of the gut microbiome of all peoples with the goal of correlating microbiome to health and disease states (see The American Gut project“, “Ubiome“, and23AndMe.)

The microbiome
The microbiome

  As the article, “Google Wants to Store Your Genome,” explains:

“The explosion of data is happening as labs adopt new, even faster equipment for decoding DNA. For instance, the Broad Institute in Cambridge, Massachusetts, said that during the month of October it decoded the equivalent of one human genome every 32 minutes. That translated to about 200 terabytes of raw data.”

“We saw biologists moving from studying one genome at a time to studying millions,” says David Glazer, the software engineer who led the effort and was previously head of platform engineering for Google+, the social network. “The opportunity is how to apply breakthroughs in data technology to help with this transition.”

Some scientists scoff that genome data remains too complex for Google to help with. But others see a big shift coming. When Atul Butte, a bioinformatics expert at Stanford heard Google present its plans this year, he remarked that he now understood “how travel agents felt when they saw Expedia.”

Cancer resides at Google Genomics & Amazon Data Clouds

The article, “Google Wants to Store Your Genome,” explains:

“The National Cancer Institute said last month that it would pay $19 million to move copies of the 2.6 petabyte Cancer Genome Atlas into the cloud. Copies of the data, from several thousand cancer patients, will reside both at Google Genomics and in Amazon’s data centers.  The idea is to create “cancer genome clouds” where scientists can share information and quickly run virtual experiments as easily as a Web search, says Sheila Reynolds, a research scientist at the Institute for Systems Biology in Seattle. “Not everyone has the ability to download a petabyte of data, or has the computing power to work on it,” she says.”

On how all this practically will be  used:  “The bigger point… is that medicine will soon rely on a kind of global Internet-of-DNA which doctors will be able to search. “Our bird’s eye view is that if I were to get lung cancer in the future, doctors are going to sequence my genome and my tumor’s genome, and then query them against a database of 50 million other genomes.  The result will be ‘Hey, here’s the drug that will work best for you.’ ”

An example of successfully using large amounts of crowd sourced DNA sequencing data

An example of successfully using large amounts of crowd sourced DNA sequencing is that used to see the trending of the gut microbiome due to birthing mode (vaginal) followed by breast feeding.  With the help of bioinformatics, the findings were able to be graphically displayed on this rotating 3D representation, “The assembly of an infant gut microbiome framed against healthy human adults,” that showed infant gut microbiome maturity finally occurring at about 27 months of age:

Questions and answers that surfaced from this effort (that showed the microbiome trending patterns) resulted in convincing evidence that C-Section births begin, microbiome wise, very different then that of vaginal deliveries.

In fact, as explained in Microbirth and  this Press Release,  C-section birth microbiome seeding is coming from the surroundings (e.g., the hospital environment, hospital personnel, and patients).  Also, there are associated consequences for the health of the child due to C-section delivery which could have life-long consequences making our children more susceptible to disease later in life as recent population studies have shown babies born by C-section have approximately:

  • 20% increased risk of developing asthma,
  • 20% increased risk of developing type 1 diabetes,
  • 20% increased risk of obesity,
  • slightly smaller increases with gastro-intestinal conditions like Crohn’s disease or coeliac disease, and
  • These conditions are all linked to the immune system.

For more relevant information, see the posts:

  1. NEWBORN GUT MICROBIOME BEGINS DURING BIRTH,
  2. DELIVERY & BREASTFEED STUDIES & MICROBIOME MANIPULATION, and
  3. “MICROBIRTH” EVERY PARENT NEEDS TO VIEW.

    NPR YouTube, The Invisible Universe Of The Human Microbiome
    Slide source biomeonboardawareness.com
Another example of successfully using large amounts of crowd sourced DNA sequencing data

The  post, OPTIMAL MICROBIOME DIET FROM AMERICAN GUT DATA presented Dr. Rob Knight’s latest  “American Gut” microbiome findings and associated health implications.  In general, increasing plant consumption (5 to 30 different varieties each week preferably) had the most positive impact on the microbiome, but read the cited post for other important findings and factors as well.

MapOfDiversityInTheHumanMicrobiome_HighResolnAttachmetGmailedAug18_2014Download_HarvardThe Huttenhower LabMetaPhlAn Metagenomic
Slide source: MetaPhlAn Metagenomic
The Future of the Autism Speaks Crowd Sourcing Cloud Platform Effort:  “Lots of things are mysteries. But that doesn’t mean there isn’t an answer to them.  It’s just that scientists haven’t found the answer yet.

 – Christopher John Francis Boone, “If you put 10,000 people’s genomes in the cloud, could you demystify autism?”

I am excited for the incredible amount of answers and further questions that will be discovered and which result from the Autism Speaks crowd source cloud platform effort.

For background:  Autism Speaks has been collecting volunteered sequences for years and will open its cloud portal to scientists early next year with 1,000 of the sequences already in the cloud bank. Researchers anywhere in the world will have the opportunity to tap in and look for new clues in that data.  You can bet, bioinformatics will play a huge part in understanding this vast amount of data.

Another way of understanding the impact of this effort was offered by David Glazer, the engineering director at Google, who in the article, “If you put 10,000 people’s genomes in the cloud, could you demystify autism? compared it to using Google Translate on a Web page, a process that is powered by patterns detected in human translations of words from one language to another. The quality of the translations, he said in an interview, has improved with the volume of those patterns that Google can comb. The same, he suggested, could be true for autism researchers.

Truly, the future of health is through awareness, and global bioinformatic discoveries of genome trending patterns, will play a huge part of this.

Signature2

Now I'd like to hear your thoughts... comments are always welcome!