Celebrating a Decade of Genome Sequencing,” a one-day symposium held last month in Price Center Ballroom, featured presentations on various topics by world-renowned scientists that together illustrated how far the field of genomics has come since the first free-living organism’s genome, a small bacterium called Haemophilus Influenzae, was sequenced a decade ago.
But what, you may ask, is genomics, or even a genome? A genome is an organism’s complete set of DNA. The human genome contains approximately 3 billion base pairs, which are bundled into the chromosomes located in each cell in our bodies, with every cell containing the same genetic information. Genomics is the science of studying and applying information gleaned from genomes.
Some 750 students, faculty and scientists were present at the symposium to listen as leaders in the field of genomics from around the world, including J. Craig Venter, Ph.D., and two Nobel laureates gave talks varying from how genomics might elucidate the key to a longer, more healthy life, to environmental genomics, to how big pharmaceutical companies like GlaxoSmithKline use pharmacogenomics in testing their drugs for safety and efficacy.
These scientists represented important research institutions such as the J. Craig Venter Institute, the Max Planck Institute in Germany, the Howard Hughes Medical Institute, the Salk Institute, Stanford University, UC Berkeley, UCSF, Cal (IT)2 and UCSD.
Dr. Hamilton Smith, Ph.D., of the J. Craig Venter Institute, one of two Nobel laureates present at the symposium, began the day by recounting how Venter approached him in 1992 and asked if he would join The Institute for Genomic Research and collaborate with him in sequencing H. Influenzae. He did, they were successful, and that is where the story began. The method they used, called the “whole genome shotgun sequencing and assembly method,” is what made possible the speed with which genome sequencing can be done today. In fact, every year more genomes are sequenced than were on record for all previous years combined.
Next to speak was Venter, founder of TIGR and Celera Genomics, and the president of the J. Craig Venter Institute. Venter earned his bachelor’s degree in biochemistry as well as his Ph.D. in physiology and pharmacology from UCSD — and both in three years. As the person responsible for discovering much of the technology that enables genome sequencing in its present form, all eyes were on him as he spoke at the podium, waiting to hear what his next big project would be.
Venter filled in a little more of genomics history, reminding those in attendance all that has transpired since that initial genome was sequenced. While it took nearly 10 years to sequence the yeast genome (which has only 13,000 base pairs) using more antiquated methods, the human genome was sequenced in only nine months, and was published in the journal Nature in February 2001. Of course, since then, dozens of others have followed, including: the fruit fly, C. Elegans, the mouse (three favorite model organisms for biologists), E. Coli, the malaria mosquito, numerous plants, the puffer fish, and most recently the chimpanzee.
Venter’s new project is sailing the world’s oceans collecting microbial genome sequences for sequencing and assembly. This expedition has the potential to discover thousands of new organisms and millions of new genes, as Venter and his team are sequencing up to 200 million letters of genetic code every day.
Another presenter, Christopher Somerville, Ph.D., director of the Carnegie Institution at Stanford University, spoke about plant genomics — a topic some might have found boring but for his enlightening style of presentation and passion for his field. According to Somerville, the reason the field of genomics is advancing so rapidly is because small labs can make major discoveries. “Problems that have been around for literally hundreds of years are falling every day,” Somerville said. “It’s hard to convey the impact genome sequencing has had on plant biology.”
However, biologists cannot solve these problems on their own. “We have a problem,” Somerville said. “It’s not a technical problem, but a political one.”
The funds needed for study, especially from the United States Department of Agriculture, which failed to significantly increase funding after genomics came to light, are just not there. In order for genomics to contribute to alleviating national and world needs for food, fiber and nutrition on the level at which it is capable, the government needs to recognize that this is the area it should be focusing its investments.
Many other scientists that presented at the symposium echoed the sentiment that the future of genomics is going to need some special attention. “We are coming to a point where we need to continue sequencing genomes but also move into functional genomics,” said Mathias Uhlen, Ph.D., of the Royal Institute of Technology in Sweden. “We need to start looking at the bigger picture.” The information gained from all of this sequencing needs to be put to use, and many are starting by applying information to cancer treatments and disease prevention, and establishing protein databases.
Salk Institute professor Sydney Brenner, Ph.D., M.D. is considered by many to be a pioneer in the field of genetics. Brenner has witnessed the field of genomics change from the beginning, and has been leading the pack the whole way. Hearing him talk about uncovering the mysteries of DNA, genes and genomes was the highlight of the day. In his talk entitled “What is a Gene?” he reminded those present that it isn’t the number of genes you have that’s important, but how you use them. It is not the number of genes that an organism has, but the expression patterns of those genes, that is the way the genes are expressed, that is most important.
“To be told you’re only four or five times more complicated than E. Coli is a little insulting,” said Brenner, referring to the eye-opening discovery that while E. Coli have 4,400 genes, humans have only approximately 20,000 — far fewer than what was originally thought. “But for all of you people who feel insulted I’ve got good news: You’re really complicated!”
