School: Mundelein High School
City: Mundelein, IL
Classes: Grades 9-12 (Biology, Biology 2, AP Biology, Chemistry)

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

Project Description
Over the summer I had the opportunity to work in the lab of Debbie Nickerson on the campus of the University of Washington. My project involved preparing and sequencing DNA samples from numerous people in an attempt to find SNP's (Single Nucleotide Polymorphisms) in TA2R1, a candidate gene for the ability to taste PTC. If we could locate a SNP in the coding region of the gene, it would give the researchers reason to proceed on to sequencing samples which had been phenotyped so as to determine which version of the SNP produced tasters and which produced non-tasters. With any luck, these SNP's would correlate to the ability to taste PTC, which would provide more evidence to support the idea that this candidate gene was, in fact, the gene responsible for PTC tasting.

To do this, I first needed to do PCR (Polymerase Chain Reaction) on the samples of DNA to amplify the area of DNA that we were looking at. We did not sequence the entire gene because it is fairly large, but rather we chose several small areas to concentrate on, three of which were in a coding region. These small areas were isolated through the use of primers that allowed us to sequence certain areas of the DNA strand very specifically. After the PCR was complete and it had been shown to be accurate, we placed the samples into one of 2 high speed computerized sequencing machines which ran the samples and left us with a database file containing the base sequence of the area we were looking at. Finally, we ran this database file through several programs which produced an image file that we could view. This image file was then scanned for any possible SNP's which were then reported. As it turns out, there were several possible SNP's found in the coding region, but further analysis is needed along with more samples to be sure of the results.

At the time I left, more sequencing needed to be done to clean up some of the areas that had many errors in the base sequences. In addition to this, further analysis needs to be done to determine if the SNP's that were found produce an amino acid change, and if so, is it enough of a change to alter the functioning of the protein that is produced by this gene.