School: Meadowdale Middle School
City: Lynnwood, WA
Grades taught: 8 (Physical Science, Honors Biology)

Principle Investigator: Debbie Nickerson, Ph.D.
Department: Genome Sciences, School of Medicine
Institution: University of Washington

Project Description
This summer I worked on computational biology in the field of bioinformatics. The Nickerson lab focuses on large scale DNA sequencing. The EGP, or environmenetal genome project, looks at genes that are involved in cell cycle control and DNA repair mechanisms as well as DNA replication, apoptosis, and detoxification. A standard panel of 90 individuals have been sequenced that represent ethnically diverse populations. Added to this are six primate species including chimpanzees, gorillas, and orangutans.The samples undergo PCR amplication , are purified, and then sequenced using BigDye Terminator Cycle Sequencing and run on an ABI Prism 3700 automated DNA sequencer.  Once the chromatograms come off of the  sequencers, then a number of computer programs are used to analyze the data. Phred calls the bases by looking at peak quality in the chromatograms. Phrap assembles the input sequences into one or more contigs and then Refcomp takes the alignment data files produced by Phrap and identifies sites in the consensus sequence which differs from a defined sequence. Consed visually reviews the Refcomp output.

My job was to learn how to assemble primate sequences with these programs using a human sequence as the defined reference . I ran Polyphred and Refcomp to look at fixed base pair differences and then ran a program called HiQual which kept track of the number of high quality sequences that were seen. If the contigs were poor, or the alignment data seemed mismatched, or the primer numbers seemed out of sequence, I either edited the contigs or removed them from the assembly. I visually inspected all of the 164 genes in the EGP project for both chimpanzees and gorillas in the primate panel. (All of the sequencing procedures were optimized for human DNA and it is possible that some of the poor data seen  could represent a mismatch in temperatures or timing in the protocol). A program was written that would keep track of the ratio of the number of fixed base differences between primate DNA and the HiQual number as compared to human DNA. It was expected that the ratio would be lower in chimpanzees than in gorillas indicating fewer differences between human and chimp DNA. This would  confirm the closer evolutionary relationship between the two. But we were especially interested in whether or not there were any genes where there seemed to be a closer relationship between human and gorilla than human and chimp.

In analyzing the data, for the most part, the expected result was confirmed. Overall, there were fewer significant differences between the chimps and the human DNA; however, there were some cases where the ratio was closer between human and gorilla.

Some of these represented highly conserved genes, but there were a few that raise some interesting questions and warrant further study even though the statistical significance was small. Given more time, I would like to go into greater depth on these candidate genes and perhaps repeat some of the sequencing protocols optimized for these primates to obtain better quality data. I also did not have time to go to the more distantly related orangutans and subject them to the same analysis that was done on the chimpanzees and gorillas; this would have been an interesting addition to the study since the time of divergence from a common ancestor is longer.

In my own classroom, this experience has given me new insights as to how to approach hominid evolution at the molecular le vel. Traditionally, a lot of work is done on comparative anatomy, particularly in looking at cranial measurements. This bioinformatic approach is much more sophisticated and I think that it could be simplified and easily adaptable to some classroom exercises. It also gave me a tremendous appreciation for the importance of computer literarcy, especially programming skills and statistical analysis, which I will pass on to my students.

 I would like to express my appreciation to Drs. Nickerson and Rieder for giving me this opportunity, the staff at the Nickerson lab, and especially to my expert programmer and guide in this project,  Rachel Mackelrprang