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PV92 PCR/Informatics Kit

PV92 PCR/Informatics Kit. Population Genetics and Informatics. To estimate frequency of Alu within a population:. Amplify Alu insert from representative sample population Calculate the expected allelic and genotypic frequencies Perform Chi-squared Test. Alu and Population Genetics.

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PV92 PCR/Informatics Kit

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  1. PV92 PCR/Informatics Kit Population Genetics and Informatics

  2. To estimate frequency of Alu within a population: • Amplify Alu insert from representative sample population • Calculate the expected allelic and genotypic frequencies • Perform Chi-squared Test

  3. Alu and Population Genetics Hardy-Weinberg Equilibrium p2 + 2pq + q2 = 1 q p pp pq p +/+ = p2 +/- = 2pq -/- = q2 q pq qq

  4. Calculating Observed Genotypic Frequencies Genotype+/+ (p2)+/- (2pq)-/-(q2)Total (N) # of people25 5 8 38 Observed frequency 0.65 0.13 0.21 1.00 Calculation: +/+ genotypic frequency =# with genotype total number of people (N) =25/38 = .65

  5. Calculating Allelic Frequencies • Frequency of p = number of p alleles = 55 = 0.72 total alleles 76 • Number of p alleles = +/+ = 25 with two + alleles = 50 + alleles +/- = 5 with one + alleles = 5 + alleles Total = 55 + alleles • Total number of alleles = 2N = 2(38) = 76

  6. Using Hardy-Weinberg • Determine p2,2pq, and q2 values= Expected genotypic frequencies • p = 0.72 , so q = 0.28 since p + q = 1p2 + 2pq + q2 = 1 (0.72)2 + 2 (0.72)(0.28) + (0.28)2 = 1 0.52 + 0.40 + 0.08 = 1 • p2 = 0.52 • 2pq = 0.40 • q2 = 0.08

  7. Calculate Expected Number of Genotypes Expected number of genotype = Genotypic frequency x population number (N) GenotypeExpected number +/+ 0.52 x 38 = 20 +/- 0.40 x 38 = 15 -/- 0.08 x 38 = 3

  8. Chi Squared Test Observed Expected(O-E)2 E +/+ 25 20 1.25 +/- 5 15 6.66 -/- 8 3 8.33 Total 16.21 X2 Critical Value (from statistics table) = 5.9 13.21 is above 5.9 so the ratio is not accepted.

  9. Allele Server Cold Spring Harbor Lab DNA Learning Center

  10. http:// vector.cshl.org Click on Resources

  11. Click on Bioservers Click on Bioservers

  12. Enter the Allele Server

  13. Allele Server Click on Manage Groups

  14. Select Type of Data Select Group

  15. Your Group Scroll down to “Your Group”

  16. Click on Add Group Click on Add Group

  17. Fill Out Form

  18. Click on Edit Group Click on Edit Group

  19. Fill out Completely

  20. Click on Individuals Tab Click on Individuals Tab

  21. Add Each Student With Information • Add as much info as you can • Genotype ( +/+, +/-, -/- ) • Gender • Personal Info

  22. Click on Done Done

  23. Select Your Group Select and then press OK

  24. Click to Analyze Then Click Here Click Here

  25. Then Look at the Terse and Verbose Tabs

  26. Extensions • Add each class separately and compare each to see if each is different from each other. • Compare your group to other existing groups. • Have students do manual calculations first and then compare to the computer generated version.

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