These Discovery Questions expose you to the richness of The SNP Consortium (TSC).
1) You have to use a browser that works with the Java applet that is supported only by IE on the Macintosh platform. Click on the SNP search button at the top of the page and enter SNP ID# “19265”. Click on the hyperlink text "TSC0019265" and use the key to determine which bases have been found at this location.
2) Click on “View screening details ” and you will see the chromatograms for the three alleles that have been sequenced for this SNP. Be patient and allow the applet to fully load. Do these data agree with what you found in the initial search? Explain your answer.
3) Go back to the TSC0019265 page, click on the link called rs1806509. Scroll down and determine the frequency of the two bases.
4) Go back to the TSC0019265 page, scroll to the top of the page and click on “ss2669205”. This will take you to the NCBI page with information about this particular SNP. In the far left column, under the heading of “search”, click on the link that says “Detail”. Search the “submitter population id” from the menu and enter “MDECODE-3” in the blank box. The result will give you a description of the population from which this SNP was isolated. Based on what is known about human evolution, would you predict there will be many or few SNPs in this population compared to the reference genome?
5) Click on the hyperlink MDECODE-3, then on “MDECODE-3 APOE SNP” then on “detail” to the right of MDECODE-3 out of the list of 1-4 MDECODE options. Scroll down and click on the link "ss870154" about half way down the list of SNPs.Is this SNP an uncommon SNP or a more common one for the population MDECODE-3. Apolipoprotein E is a gene that has been associated with early onset Alzheimer’s disease. SNP ss870154/ae1163 is a coding SNP and therefore of special interest. Under the heading of Allele Frequency Information:, notice the frequency of the different bases for each of the four populations (e.g. 21% of MDECODE-3 have a C at this position). Click on the links for MDECODE 1 –4 and correlate the frequency of this SNP with all four populations. What did you learn about populations and frequency of SNPs?
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