School: Interlake High School
City: Bellevue, WA
Grades taught: 9-12 (Biology, IB Biology)

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

Project Description
The laboratory of Debbie Nickerson focuses on large-scale genomic analyses of single nucleotide polymorphisms (SNPs).  SNPs are small DNA sequence variations in the genome that occur at specific locations, typically at one nucleotide.  Some of these small genetic variations account for the large differences in observable characteristics between people.  Of particular interest to the Nickerson lab are SNPs in genes that may correlate with predisposition to disease.

PTC (phenylthiocarbamide) is a compound that tastes bitter to some individuals and is tasteless to others.  The variation in tasting ability between individuals makes this trait a useful model for the study of genetics.  A harmless PTC taste test is widely performed in middle school and high school classrooms as a simple example to educate students about basic genetic principles such as variation of phenotypes within a population, inheritance of phenotypes, and the relationship between genotype and phenotype.  Although initially thought to be inherited in a simple recessive manner, the genetics of the trait are now known to be more complicated.

The purpose of the project is to examine the genetics of PTC tasting ability by determining whether SNPs in the candidate genes for PTC taste perception associate with the ability to taste PTC.  Previously in the lab, SNPs in a candidate PTC taste receptor gene (T2R1) were identified by determining differences between DNA sequences in a large population of individuals.

Over the course of the summer, Dan used the following approaches to address the research purpose:

• To discover correlations between specific SNPs and the ability to taste PTC, Dan compared the frequency of identified SNPs to the frequency of “tasters” and “non-tasters” in the sequenced population.
• To identify sequence characteristics that correlate with the ability to taste PTC, Dan sequenced the T2R1 gene in primate species that do or do not taste PTC and compared differences between the sequences.
• To determine whether particular SNPs might affect an individual’s ability to taste PTC, Dan characterized the contexts and predicted effects of the amino acid changes on T2R1 protein structure and function.
• To discover other SNPs that may associate with the ability to taste PTC, Dan sequenced a second candidate PTC taste receptor gene (T2R16) in a large population and identified SNPs in this gene.
• To prepare for determining more directly whether any of the candidate SNPs confer the ability to taste PTC, Dan wrote an application for Human Subjects Approval at the University of Washington to perform an association study.

Following IRB approval, the Nickerson lab plans to conduct an association study where individuals will perform a PTC taste test and supply a sample of their DNA.  Candidate SNPs for the ability to taste PTC will be analyzed, and any correlations between these SNPs and the ability to taste PTC will be identified. 

Acknowledgements
Dan is very grateful for the experience in the Nickerson lab and would like to thank Dr. Debbie Nickerson, Dr. Mark Rieder, Suzanne da Ponte, Emily Toth, and many other helpful, friendly people in the Nickerson lab.