Big numbers — of DNA base pairs sequenced, numbers of genomes completed, volumes of data collected and dollars invested — were in the air Nov. 9 when Dr. Huanming (Henry) Yang, president and cofounder of BGI (formerly the Beijing Genomics Institute) gave a talk on campus.
During his visit to campus, Yang visited the new BGI@UC Davis joint facility at the Sacramento campus as well as the Genome Center on the Davis campus. His visit was sponsored by the Office of Research and the Department of Medical Microbiology and Immunology.
Introducing Yang, Professor Tilahun Yilma noted that when BGI was founded in 1999, China was invisible in the field of genomics. Three years later, BGI published the rice genome and made the sequence available to the world.
Yang began by noting that 2013 marks the 10th anniversary of the completion of the human genome as well as the 60th anniversary of Watson and Crick’s discovery of the structure of DNA.
Sequencing the human genome took 13 years, thousands of scientists and cost $3 billion. Now, BGI’s facilities can sequence a hundred times as much DNA in a day. Driven by advances in both sequencing technology and computing, we are in the era of mass genome sequencing, of “-omicsization,” where genomics is the starting point for both life sciences research and the biotechnology industry, he said.
Yang repeatedly emphasized that genomics cannot be done alone — BGI’s major projects are collaborations with other researchers around the world. About one-third of the data deposited in the publically-accessible Genbank database was produced by BGI and its collaborators, he said.
Among current collaborative projects, BGI aims to sequence about a quarter of all vertebrate species, and most birds. Currently, there are reference genomes for more than six hundred species of large animals and plants.
Going beyond reference genomes, a new trend is to measure genetic variation within a species by sequencing multiple individuals. BGI is working with researchers in Denmark, the Netherlands and Great Britain to sequence a sample of the population. In China, they hope to ultimately sequence over a million Chinese; 60,000 humans have been sequenced in the past decade. Such sequencing shows that “no one is ‘normal,'” Yang said.
Applications of sequencing technology
DNA sequencing also has immediate applications in agriculture, the environment and health. Yang cited as examples sequencing millet to study its potential for biofuel production, sequencing single cancer cells to look for susceptibility to drugs, or looking at the relationship between Type II diabetes and gut microbes by studying their DNA profile.
Researchers have shown that DNA from the fetus circulates in the mother’s blood, making it possible to carry out prenatal testing for genetic disorders more easily. BGI researchers and collaborators are also looking at differences in DNA between infants and centenarians.
Synthetic biology and cloning
BGI is also turning its attention to synthetic biology and animal cloning. In 2010, J. Craig Venter and colleagues announced that they had created a living bacterial cell with a completely artificial genome. BGI is part of an effort to build a eukaryotic cell, more like yeast or a plant or animal cell, with an artificial genome. Teams of collaborators around the world will each take on the task of producing a single chromosome to be combined in a single cell.
“Now we are reading genomes, the next step is to write genomes,” Yang said.
BGI has also simplified animal cloning — taking DNA from an adult animal, transferring it to an egg cell and growing it into an embryo that is a near-exact copy of the original — to a method that can be learned in a couple of weeks. The institute’s scientists have cloned about 500 pigs so far. They are interested in preserving local strains, cloning smaller breeds for research, and creating models of human disease such as breast cancer or Alzheimer’s Disease.
The BGI Model
Yang expressed some amusement at Americans reporting on BGI’s “model” that is “taking the world by storm.”
“We have no model,” he said, “and the world belongs to everybody.”
Rather, he said, BGI is rooted in Chinese culture: high aims, humility, responsibility, confidence, collaboration and appreciation of others.
“Nothing done by BGI could have been done without our partners,” he said. And the advanced sequencing machines used by BGI on such a scale are designed and built in the U.S.
“The most important way to evaluate a collaboration is to see if we become friends,” Yang said. “I’m very proud of our new center at UC Davis — let’s collaborate.”