GENOMICS TERM PROJECT

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GENOMICS TERM PROJECT

• Assessment of Significance in a SNP

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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.

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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).

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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.

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Project

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

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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.

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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.

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HELPFUL LINKS AND CALCULATIONS

• dbSNP-HapMap Data
• http//www.ncbi.nlm.nih.gov/SNP/
• SNP500 Cancer
• http//snp500cancer.nci.nih.gov

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ATM
http//snp500cancer.nci.nih.gov/
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Test whether subpopulations are different?
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Compare Caucasian vs. Afr. American
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Compare Caucasian vs. Hispanic
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Test whether a population genotypic frequency is
in HWE
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HWE X2 TESTS
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HWE Tests
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HWE
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Hispanics
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HWE Tests