FINAL EXAM TAKE-HOME期末考试take-home.pptVIP

FINAL EXAM: TAKE-HOME Assessment of Significance in Cancer Gene SNPs AIM By using SNP information in Cancer Genome Anatomy Project SNP500Cancer Database learn to read SNP data, analyze allelic and genotypic frequencies, test whether different populations differ in their allele frequencies from each other; and evaluate your findings and propose a case/control study for a cancer SNP. ATM Compare Cancer500 and HDP Test If Two Sources of SNP info Differ 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 TAKE-HOME EXAM INTRODUCTION: Provide background information about your gene of interest based on literature. Make sure you cite 2 or more articles. RESULT 1: Create a table with the following information: a table that summarizes the allele frequencies (minor allele freq vs. major allele freq. for the total population considered) for about 8 or more SNPs. 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). TAKE-HOME EXAM RESULT 2a: Answer the following question: Do non-synonymous SNPs generally have lower frequencies when compared to synonymous and/or intronic or regulatory region SNPs? Explain based on your findings, and discuss why or why not would that be so. RESULT 2b: Select a nonsynonymous SNP from your table and locate this SNP on the cDNA sequence. What might be the implications of this amino acid change (e.g., does it correspond to a specific domain?). Is this specific nucleotide highly conserved across different organisms (e.g., among mouse, rat, and humans). Align sequences from three different organisms find this specific amino acid change due to SNP, and assess how conserved this amino acid is when compared to the rest of the sequence. TAKE-HOME EXAM RESULTS 3: Investigate a few SNPs (nonsynonymous, synonymous, a