WU genomics class expands to other schools

| Staff Reporter
A Washington University initiative is providing universities and colleges nationwide with a research-based student curriculum in genomics.

A collaborative effort led by Sarah Elgin, professor of biology and education who also teaches genetics at the School of Medicine, the Genomics Education Partnership (GEP) has found that its research-based genomics class is as effective at teaching science skills as is a full summer spent doing research.

The GEP, established in 2006 with a grant from the Howard Hughes Medical Institute, provides resources to educators for teaching a laboratory-based course in genomics—the study of entire genomes, or an organism’s collection of DNA. Students in a GEP course engage in problem-based learning by doing actual genomic research, and the students’ results are published and made available on the Internet for future research.

Elgin said that implementing the GEP course can help educators provide valuable research experience when opportunities in laboratories are limited.

“If a faculty member can offer this class that incorporates a research activity, she can reach many more students at one time than can usually be done,” Elgin said. “This is a real plus at schools where the number of students seeking a research experience far exceeds the available places in faculty labs.”

In addition, biology curricula everywhere need updating, according to Elgin.

“[Genomics is] a void in everyone’s curriculum,” she said. “Biology is like that. We constantly go through revolutions. I think within five years you’ll probably be able to get a pretty comprehensive look at your genome for $1,000.”

The GEP is growing and currently counts more than 40 members in its faculty.

Finding ways to make classroom research work

One of the participating universities in the GEP is the Rochester Institute of Technology (RIT), which joined the group at its inception in 2006. Gary Skuse, professor of biological sciences and director of the bioinformatics program at RIT, said that the course has supplemented the school’s standard biology curriculum.

“Our students learn the concepts in the course, but they don’t get a chance to apply it,” Skuse said. “It makes it more worthwhile and allows us to take it further than we could without Dr. Elgin.”

Many of the schools in the GEP, however, lack enough faculty to provide research experiences to every interested student. Other schools are seeking cost-effective means to incorporate more problem-based learning methods into their science curricula. Elgin noted that schools often work to employ teaching methods based upon problem-solving and critical thinking—teaching methods that help student instruction beyond group lectures.

“We resort to the lecture because we think it’s time- and cost-effective,” Elgin said. “But that’s under heavy debate. Lectures are useful in certain contexts, but you have to engage your mind.”

Polishing raw DNA sequence data

The course “Research Explorations in Genomics” is co-taught by Elgin, Associate Professor of Genetics Elaine Mardis at the Genome Sequencing Center (GSC), and Associate Professor of Computer Sciene and Engineering Jeremy Buhler. In the course, students “finish” gene sequences, a task usually reserved for professional finishers.

In the course, each student receives their own “fosmid,” or chunk of unfinished DNA sequence, which is generated by highly automated gene sequencing done by the GSC. Such sequences contain gaps, errors and ambiguities, and students must use a computer program to fix each genomic problem.

Once the quality of the data is improved, the students use computer programs to label the genes interspersed among the “junk DNA.” Elgin compares this to being handed a copy of “Moby Dick” in 20 volumes, with the real text of the book interspersed at random with gibberish, and then parsing out the original text.

“You know what words look like. You can look for capital letters and periods,” Elgin said, describing how students must search for the predictable DNA sequences marking the beginning and end of genes.

Together, past classes have already finished a small chromosome from a species of fruit fly, Drosophila virilis, which is of interest to evolutionary biologists. Class results were published for the first time in February 2006 in Genome Biology.

Students who took the class praised the efficacy of its teaching methods.

“Even though we’re using computers, I think the hands-on experience we got and the fact that we’re contributing to scientific results motivates you to participate more,” senior Ryan Lee said.

Another said that genomics got her interested in computer science.

“I’ve never been this motivated through a class,” senior Sarah Spencer said. “I never even considered computer science, mathematics and bioinformatics before, but now I’m thinking about how useful it is.”

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