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Base Pairs to Bedside: A Visit to Beijing Genomics Institute

November 10, 2011 Leave a comment

From left: Drs. Yonghui Jiang, Andy Shih, Huanming Yang, Geri Dawson, and Clara Lajonchere

Posted by Autism Speaks Vice President of Scientific Affairs Andy Shih, Ph.D.

Beijing Genomics Institute (BGI), the world’s largest genome sequencing organization got its start a little more than a decade ago at a moment when idealism, patriotic fervor and more than a little chutzpah converged to create what one of its founders, Huanming Yang, Ph.D., recently acknowledged was “a Mission Impossible.”

Yang, then with the Chinese Academy of Sciences, promised to complete 1 percent of the Human Genome Project–at the time the biological equivalent of the moon shot of the 1960s. There was just one problem: He didn’t have a gene-sequencing machine!

What followed was one of the most thrilling rags-to-riches stories in modern science. Yang and his colleagues overcame immense technical, financial and political obstacles to deliver the DNA sequence of their portion of human chromosome 3. In doing so, they changed Chinese science forever and built a scientific-industrial juggernaut that now represents 20 percent of the world’s capacity for genome sequencing.

That same can-do spirit was clearly on display when I and Autism Speaks-funded Duke University researcher Yong-hui Jiang, M.D., Ph.D., visited BGI in Shenzhen after the Autism Research Collaboration Development Meeting, co-hosted by Children’s Hospital of Fudan University in Shanghai and Autism Speaks. Not coincidentally, Yang gave the keynote address to the meeting, which ended last weekend.

Today most of BGI is housed in a former shoe factory on a small campus that includes several high-rise dormitories for nearly 4,000 employees. In recent years, the institute has produced such high-impact scientific accomplishments as complete genome sequences of rice and potato plants and the human gut microbiome (our digestive microbes). Through genetic sequencing, it also identified the culprit behind this summer’s deadly E. coli outbreak in Germany. In the face of this public health crisis, BGI marshaled the staff and technology to sequence the entire genome of the toxic bacterial strain in less than three days.

From left: Yirui Li (BGI), Yonghui Jiang (Duke), Jian Wang (BGI), Andy Shih, Jun Wang (BGI), and Hongle Chen (Jet Li’s One Foundation) in front of a picture of Mount Everest taken by Dr. Wang

In visiting BGI, I was impressed by more than the arrays of cutting-edge automated sequencers, which run 24/7. I was struck by BGI’s eclectic leadership.

BGI cofounder, Jian Wang, Ph.D., recently scaled Mount Everest, after three attempts over a two-month period. For inspiration he credits BGI’s landmark collaboration with U.S. and European scientists in documenting the rapid evolution of the Tibetan human genome to accommodate life at high altitudes.

BGI executive director Jun Wang, Ph.D., joined the institute when he was 23 and went on to amass 36 publications in Science and Nature over 12 years. For your average researcher, having 1 or 2 publications in Science or Nature is sufficient to secure a tenured position at a top U.S. or European university.

At age 25 years, Yirui Li is leading the bioinformatics efforts of BGI’s recently announced collaboration with Autism Speaks to sequence 10,000 autism genomes. With 16 Science and Nature publications to his name, Li dropped out of China’s elite Tsing Hua University at age 19.

Despite their intellectual firepower, drive and personal and professional accomplishments, they were a down-to-earth group. They thought nothing of coming in on a Sunday to meet with us. Sporting what appeared to be their regular uniform of T-shirts, jeans and flip-flops or running shoes, they looked more like grad students than high-profile executives of a leading international research institute.

Yang and his colleagues also have a refreshingly progressive view on science and its end game. Impatient with traditional distinctions among scientific disciplines–such as genetics versus environmental sciences–they advocate a “trans-omics” approach to scientific development. In their view, decoding the genome is part of a continuum of activities that includes epigenetics, proteomics, cell biology, systems biology and computer science.

Most importantly, perhaps, they see all these activities as integrated and dedicated to “advancing the science of medicine” and “improving the effectiveness of healthcare.” Clearly, they remain driven by the sense of urgency that allowed them to identify and decipher a deadly pathogen by sequencing its entire DNA sequence in three days.

I left BGI inspired by what I saw and heard. The BGI team seemed refreshingly unencumbered by the petty divisions and willful near-sightedness we too often encounter in science and society. They are pursuing a grander vision that I, too, have lost at times. More than ever, I am hopeful that with enough idealism, ambition and even a little chutzpah, Autism Speaks collaborations like this one will soon deliver a better future for all of our families.

After a few drinks and a dinner of simple and very spicy local fare in the BGI canteen, Yang leaned over to me and said matter-of-factly, “We’ll get it done.”

Please visit our science pages for more news and perspective.

Autism and Environmental Health in China

November 9, 2011 1 comment

From left: Drs. Jinsong Zhang, Alycia Halladay, Jim Zhang, Alice Kau, Fenxi Ouyang and Xiaoddan Yu


Posted by Autism Speaks Director of Research for Environmental Science, Alycia Halladay, Ph.D.

To date, relatively few scientists are studying autism in China. Clearly the need there is great, for with its population of over a billion, we may be looking at millions of persons affected by autism. With this in mind, Autism Speaks partnered with China’s Fudan University to convene a meeting of leading international experts in autism and children’s health in Shanghai last week.

As part of this visit, I and development psychologist Alice Kau, Ph.D., of the National Institute for Child Health & Human Development, visited Xin Hua Hospital and its recently completed Shanghai Key Lab of Children’s Environmental Health. Both are affiliated Shanghai’s Jiao Tong University School of Medicine.

There we met the lab’s executive director, Jun Jim Zhang, MD, Ph.D., and his colleagues. In recent years, they have been studying how exposure to heavy metals such as mercury and lead affects child development. Environmental lead contamination, a problem largely minimized in the United States, remains a widespread problem in China, owing to unsafe disposal of lead products including waste from lead battery plants.

The Shanghai Key Lab’s affiliation with Xin Hua Hospital allows its scientists to collect blood samples at birth and throughout a child’s development. Their lab is also collecting information on intellectual function and other developmental behaviors. Among their projects is the Shanghai Birth Cohort, which will recruit 100,000 pregnant women from hospitals throughout Shanghai and follow their children throughout adolescence.

To date, the researchers at Shanghai’s Key Lab have been focusing their research on potential environmental causes of childhood asthma, sleep disorders and leukemia. Looking forward, they are keenly interested in expanding their research to include neurodevelopmental issues such as autism.

Thanks to our new collaboration, they will be participating in Autism Speaks Environmental Epidemiology of Autism Research Network. In doing so, they will be sharing their information with autism researchers in North America and elsewhere, even as they receive guidance on screening for autism spectrum disorder (ASD).

Given the unique physical, chemical and psychosocial environment in China, we believe that this collaboration can greatly advance our understanding of the environmental and genetic risk factors that contribute to the development of ASD. We look forward to working with this wonderful research team to help solve the autism puzzle in China, North America, and around the world.

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