GENOMICS TERM PROJECT

Assessment of Significance in a SNP

Term Project

• For a gene of your choice (let me know which gene you have chosen) find a polymorphism/mutation with potential functional importance and association with a disease. Furthermore, test whether this SNP is in HWE in normal populations (HapMap or SNP500 data). Also show whether different populations have different allele distributions for this SNP. Finally design an experiment in which you test the association with disease of this SNP.

Project

• INTRODUCTION: Provide background information about your gene of interest based on literature. Is there any known disease associated with this gene? Make sure you cite 2 or more articles. (maximum half a page).

• METHODS: Briefly describe your strategy of finding a potentially functionally important candidate SNP in your gene of interest. Also describe which statistical tests you used for testing whether the SNP is in HWE and whether the allele frequencies of the SNP vary among different populations. (maximum half a page).

Project

• RESULTS1: Create a table with the following information:– a table that summarizes the allele frequencies

(minor allele freq vs. major allele freq. for the populations considered) for the SNP you have chosen. In this table make sure that you also indicate the genotypic frequencies and whether they are in HWE (test, and report a X2 and p-value) using either the HapMap (dbSNP in NCBI) or SNP500 Cancer databases.

Project

• RESULT 2: Explain and provide data why the SNP you have chosen might be functionally important (Hint: Use SNPSeek and Panther).

Project

• RESULTS 3: Does the SNP that differ in allele counts across different populations? Do a statistical test and briefly explain (e.g., caucasian vs. hispanic, caucasian vs. african american).

• DISCUSSION: Briefly evaluate your results 1-3.

Project

• FUTURE PERSPECTIVES: Design an experiment (including selection of the case and control populations, or families, molecular methods that you will use, and how to interpret the results) to study this SNP to find out whether it could be involved in initiation or progression of a specific type of disease.

HELPFUL LINKS AND CALCULATIONS

• dbSNP-HapMap Data– http://www.ncbi.nlm.nih.gov/SNP/

• SNP500 Cancer– http://snp500cancer.nci.nih.gov

ATM

http://snp500cancer.nci.nih.gov/

Test whether subpopulations are different?

Compare Caucasian vs. Afr. American

Compare Caucasian vs. Hispanic

Test whether a population genotypic frequency is in HWE

HWE X2 TESTS

HWE Tests

HWE

Hispanics

HWE Tests