Santa Cruz Good Times

Thursday
Jan 29th
Text size
  • Increase font size
  • Default font size
  • Decrease font size

Growing The Genome Project

dnaUCSC releases a more readable version of the human genome

“It’s funny, biology is such a mass discipline,” says Jim Kent. “What we focus on is often as much of a reflection on ourselves as it is on anything.” As director of the UC Santa Cruz Genome Browser Project and head of the ENCODE Data Coordination Center, Kent sets quite an example for channeling cultural fascination with science into real-world application.

“Back in the 1960s, when the focus was on energy and physics, people figured out the energy centers of the cell,” says Kent. But in 2012—a time of immense, international collaboration between biologists and computer engineers—the “culture of the age” culminated in September with a much more accessible and informative translation of the entire human genome than was previously available.

The Encyclopedia of DNA Elements (ENCODE) kicked off in 2003, after UCSC sequenced and published a complete human genome sequence draft days before the competing Celera Genomics Corporation attempted to patent theirs.

Funded chiefly by the National Human Genome Research Institute, this publicly available information was vast but largely hieroglyphic (at the time, researchers could only attribute genetic functionality to roughly 2.5 percent of the genome). ENCODE has since then been an effort to put meaning to the madness by determining the actual functions within this DNA “Rosetta stone.”

A probing technique in the project’s pilot phase found that roughly 80 percent of human DNA, once considered wholly inactive, transcribes into RNA. While more recent data points to the conservative estimate that 25 percent has direct genetic functionality, that’s still a tenfold increase in viable DNA.

But a particularly astounding component of this freshly significant amount of the genome is “regulatory DNA.” Regulatory regions determine which genes are expressed and where, giving humans two arms, two legs, and differentiating us from chimpanzees.

“The regulatory region is the control switch,” explains Kent, who wrote the original sequencing project’s computer program as a graduate student at UCSC. “It’s the closest thing that the cell has to the computer system.”

For Kate Rosenbloom, who serves as the technical project manager of the ENCODE Data Coordination Center at UCSC, the interpretation is a step toward completing the genome puzzle. “We’ve had all the parts all along and now we’re pulling them into a story to see how they all connect,” she says.

Detailing these hugely significant regulatory regions were as much a responsibility as a privilege. The amount of data storage and software power required increased exponentially—but Kent and internationally acclaimed colleague David Haussler were still up for the task. The data repository in its behemoth entirety relocated from the NHGRI to the web-based UCSC Genome Browser, which has maintained a culture of public availability since the original genome sequencing.

With the first “revision” of the Encyclopedia’s data and format wrapped up this September, “Our target is so a first-year graduate student in a biomedical discipline can understand,” says Kent. “That’s probably where we’re going to stay for a while.”

In coordination with the City of Santa Cruz, UCSC has been pushing to create a stronger culture of entrepreneurship at the university. To curb the county’s trend of thousands of residents commuting over the hill to Silicon Valley each weekday, the university has leveraged hundreds of thousands of federal, local and private dollars to encourage recent grads to stay and plant their business seeds in Santa Cruz.

Enter Five3 Genomics, a startup company by UCSC Bioinformatics graduates Steve Benz, Ph.D, Charles Vaske, Ph.D, and Zack Sanborn. In addition to keeping Slug brainpower in town, the company is utilizing UCSC’s genome browser to genetically tailor medicine.

“We’re a genomics software company focused on cancer,” Benz, the CEO, explains. “We’re trying to identify key aspects of cancer genome information to target treatment. It’s called precision medicine.”

The trio, currently operating out of NextSpace in Downtown Santa Cruz, says they will officially premiere in approximately one month’s time. They say the culmination of ENCODE’s second phase is more than a windfall.

“Most scientists can’t comprehend how large this is,” says Vaske, the company’s CSO. “Our job would be impossible without [the UCSC Genome Browser].”

Vaske quickly navigates to a page on the Genome Browser’s website, where he points to the sequencing charts and graphs of a breast cancer cell’s DNA, which the company has been studying to discern which gene mutations of the cancer are common, and which are more abnormal and virulent.

“Steve [Benz] and I work on modeling,” Vaske explains. “We try to create … a rough simulation of what is going on, so we can say ‘if you have this [gene], you’re more likely to have this response to this treatment.’”

Benz adds that the goal is to get to causality—the invaluable knowledge that allows doctors to both evolve their preventative medicine as well as prescribe more effective treatment.

Benz explains that while access to the Encyclopedia is like looking at a road map and trying to determine how to get from point A to point B, the information allows their local startup to make a global impact.

Going forward, Five3 will be one of many groups utilizing the genome data. UCSC will convene a panel of medical and legal experts titled “Genomics Gets Personal: Property, Persons, Privacy” on Thursday, Sept. 27 at the UC San Francisco Mission Bay campus to discuss the ethical implications of genome data access as science, and culture, continue to evolve.

 

news2 EncodeNatureGraphic

Comments (0)Add Comment

Write comment
smaller | bigger

busy
 

Share this on your social networks

Bookmark and Share

Share this

Bookmark and Share

 

Throwing It All Away

Everybody’s for recycling, right? So why are we all doing it wrong? Our reporter gets down and dirty to uncover 10 secrets that will finally make the recycling process make sense

 

Aquarius Calling, Humanity Rising

Aquarius (11th sign after Aries) is the sign of service—serving one another, building community. Aquarius is fixed air, stabilizing new ideas in the world. When new ideas reach the masses the ideas become ideals within the hearts and minds of humanity. Air signs (Gemini, Libra and Aquarius) are mental. They think, ponder, study, research, gather and distribute information. For air signs, education and learning, communicating, writing, being social, tending to money, participating in groups and creating sustainable communities are most important. One of the present messages Aquarius is putting forth to the New Group of World Servers is the creation of the New Education (thus thinking) for humanity—one based not on commodities (banking/corporate values) but on virtues. Humanity and Aquarius Aquarius is the sign of humanity itself. We are now at the beginnings of the Age of Aquarius, the Age of Humanity (rising). The “rising” is the Aquarian vision of equality, unity, the distribution and sharing of all resources and of individual (Leo) creative gifts for the purpose of humanity’s (Aquarius) uplifting. This is the message in the Solar Festival of Aquarius (at the full moon) on Tuesday, Feb. 3. We join in these visions by reciting the World Prayer of Direction, the Great Invocation.Tuesday’s solar festival follows Monday’s Groundhog Day, or Imbolc (ancient Celtic fire festival) the halfway mark between winter solstice and spring Equinox). The New Group of World Servers (NGWS) during these two days are preparing for the upcoming Three Spring Solar Festivals: 1. Aries Resurrection/Easter Festival (April); 2. Taurus Buddha/Wesak Festival (May); and 3. Gemini’s Festival of Humanity (June). Aquarius and the new and full moons together are the primary astrological influences behind all of humanity’s endeavors. The NGWS are to teach these things, calling and uplifting humanity. Join us everyone. (301)

 

The New Tech Nexus

Community leaders in science and technology unite to form web-based networking program

 

Job Insecurity

Woman fights for her job in thoughtful, life-sized ‘Two Days One Night’
Sign up for Good Times weekly newsletter
Get the latest news, events

RSS Feed Burner

 Subscribe in a reader

Latest Comments

 

Jeffrey’s Restaurant

Why quick and friendly service matters at a local diner.

 

If you didn't live in Santa Cruz, where would you be living?

I would live in Kauai because the water is warmer, and I just love it there. Maureen Niehaus, Santa Cruz, Dental Assistant

 

Clos LaChance Wines

Pinot Noir 2012

 

Striking Gold

A taste of Soquel Vineyards’ five gold medal-winning Pinots