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Chinese Genome-Sequencer Leads World Autism Research
Summary:The world’s largest genome-sequencing facility is at the Shenzhen-based BGI. In 2011, it partnered with a U.S. advocacy group with the goal of unlocking the genetic mysteries of Autism. Preliminary results suggest a stronger genetic role than previously estimated. This could mean diagnosing the disorder will become more routine and the potential for targeted medicine and treatments will increase.


April 8, 2013
By Nick Compton

Apr 2 marked the sixth World Autism Awareness Day.  While surging diagnostic rates and extensive media coverage of the disorder have raised public awareness to unprecedented heights, the autism research community has a new, unlikely star: China. 

The Shenzhen-based BGI (formerly Beijing Genomics Institute) is a privately held, non-profit research institute staffed by thousands of young Chinese scientists and powered by 100 of the most sophisticated DNA sequencing machines on the planet.  Since its establishment in 1999, it’s become the world’s largest genomic-focused institute, and in 2011, it announced a $30 million, two-year partnership with the U.S. autism advocacy group Autism Speaks. Its goal: to sequence the whole-genomes of close to 10,000 individuals with autism.

Autism, like cancer, is a multifactorial disease with at least some genetic roots. This project aims to pinpoint, for the first time, biomarkers and genetic defects that may be linked to the disorder. Although other research institutes, most notably California’s UC Davis, are involved in similar projects, none have the depth or breadth of the project underway at BGI.

The first phase of the project, which included sequencing and analysis of 200 samples from Canada and China, has concluded. The project’s manager, Wang Mingbang, says the results will be published within the next few weeks.

“The results are proving interesting,” Wang says.  “It looks like about half of the early samples show variations in the genes.” 

If these early results hold true, it would mean a significant increase over previous scientific research, which has estimated only 20 to 30 percent of autism cases could be linked to genetic abnormalities.

Wang says his team is working on a hypothesis that there are approximately 1,000 genes related to autism out of the more than 20,000 genes humans have. To date, only a handful of these have been revealed and analyzed by the scientific community.  If a stronger genetic basis for autism is established, Wang says diagnosing the disorder will become more routine and the potential for targeted medicine and treatments will increase.

Although there is no cure for autism, researchers have long maintained that effective early intervention, begun as quickly as possible after a diagnoses is reached, is the best way to teach autistic individuals self-help and communication skills that will empower them to live independent, fulfilling lives. “If we find it early, we can do behavior intervention early,” Wang says. 

Dr. Andy Shih, vice president of scientific affairs at Autism Speaks, thinks the research underway at BGI is potentially “transformative” in advancing the cause of all genomics.

“The vision here is that some day in the very near future some kind of sequencing will be standard care for children that go to the doctor and there is suspicion of autism or [developmental] delays,” Shih says.  “We’re hoping that with the information we can pull from an ambitious program like the one we have at BGI, it will put us firmly on the path to understanding different types or subtypes of autism.”

BGI, headquartered out of a converted shoe factory on the eastern fringes of Shenzhen, was founded in Beijing in 1999.  That year, it completed 1 percent of the human genome project - a massive 14-year, $3 billion effort to map all 20,000-plus genes and 3 billion chemical base pairs that make up human DNA.  Since the project was completed in 2004, the price of sequencing the entirety of a person’s genetic information (their genome) has plummeted from well over $1 million to as low as $3,000.

Since moving to Shenzhen in 2007, BGI has become a force in the genome-sequencing industry with its revenue surging from 343 million yuan ($55.2 million) in 2009 to 1.1 billion yuan ($177.1 million) in 2012. The company’s 4,000 researchers, with an average age of 26 and monthly salary of 10,000 yuan ($1,612), make up roughly 20 percent of the world’s sequencing capacity, according to Wang Aizhu of the company's Branding and Communication Division. Lucrative tax breaks on top of China’s massive pool of cheap scientists have allowed BGI to leapfrog all Western firms in the industry.

On Mar 20, BGI solidified its dominant position after finalizing a $117.6 million acquisition of the U.S.-based Complete Genomics, which has some of the most advanced labs and technology in the world.

BGI’s super computers in Shenzhen and a satellite location in Hong Kong can now tear through a person’s genome in about one month’s time. In a process akin to computer programming, an army of 1,000 specialists clad in jeans and t-shirts then convert the raw data into a decipherable digital map that can be analyzed for abnormalities and known bio-markers. 

“There’s a lot of excitement that, after a decade or so after the human genome project, we actually are starting fulfill some of the promises of that visionary effort,” Dr. Shih said.  “Autism really has been leading the way in helping us understand [genomics], especially the issue of complex psychiatric disorders [like autism, bipolar disorder and schizophrenia].”

Shih says BGI was selected to lead the autism genome project because its sequencing speed and capacity for crunching billions of bits of data is unmatched.

“Their ability to handle large quantities of data, as far as I’m aware, is unrivaled globally,” Dr. Shih said. “That kind of high-quality output, data management, and the speed at which they can deliver information made it an easy decision for us to develop the partnership.”

The work is not without criticism though.

While BGI has succeeded in obtaining terabytes worth of genetic data, there is, as of yet, little scientific utility or practical application within the galaxy of figures. As Wang Aizhu puts it, it’s like having a detailed map to the universe without a legend.

“The most difficult thing for us is handling such large amounts of data,” project coordinator Wang Mingbang says, adding that BGI has teamed up with the national supercomputer center in Tianjin to utilize additional computing juice.

While Dr. Shih recognizes that the big data problem is “pervasive” throughout the scientific community, including in this project, he thinks that the concerns are short-sighted.

“Legitimate concerns are being raised, but the fact that the data is there [is important]. There are always enterprising, smart individuals who will find ways to use that information to support certain objectives.”



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