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 Amplify Alu insert from representative sample population Calculate the expected allelic and genotypic frequencies Calculate the expected allelic and genotypic frequencies Perform Chi-squared Test Perform Chi-squared Test

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

4. Calculating Observed Genotypic Frequencies Genotype (p2)(2pq)(q2)Total (N) Genotype +/+ (p2) +/- (2pq) -/- (q2) Total (N) # of people 25 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 = 25/38 =.65

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

6. Using Hardy-Weinberg Determine p 2, 2pq, and q 2 values= Determine p 2, 2pq, and q 2 values= Expected genotypic frequencies p = 0.72, so q = 0.28 since p + q = 1 p 2 +2pq+ q 2 = 1 p = 0.72, so q = 0.28 since p + q = 1 p 2 +2pq+ q 2 = 1 (0.72) 2 + 2 (0.72)(0.28)+ (0.28) 2 = 1 (0.72) 2 + 2 (0.72)(0.28)+ (0.28) 2 = 1 0.52+0.40+ 0.08= 1 0.52+0.40+ 0.08= 1 p2 = 0.52 p2 = 0.52 2pq = 0.40 2pq = 0.40 q2 = 0.08 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 - / - 0.08 x 38 = 3

8. Chi Squared Test Observed Expected (O-E)2 E E +/+ 25 201.25 +/- 5 156.66 -/- 8 38.33 Total 16.21 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

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

17. Fill Out Form

18. Click on Edit Group

19. Fill out Completely

20. Click on Individuals Tab

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

22. Click on Done Done

23. Select Your Group Select and then press OK

24. Click to Analyze Click Here Then 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. Add each class separately and compare each to see if each is different from each other. Compare your group to other existing groups. Compare your group to other existing groups. Have students do manual calculations first and then compare to the computer generated version. Have students do manual calculations first and then compare to the computer generated version.