PV92 PCR/Informatics Kit Population Genetics and Informatics

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

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

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

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

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) (0.72)(0.28)+ (0.28) 2 = 1 (0.72) (0.72)(0.28)+ (0.28) 2 = = = 1 p2 = 0.52 p2 = pq = pq = 0.40 q2 = 0.08 q2 = 0.08

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

Chi Squared Test Observed Expected (O-E)2 E E +/ / / Total Total X2 Critical Value (from statistics table) = is above 5.9 so the ratio is not accepted.

Allele Server Cold Spring Harbor Lab DNA Learning Center

vector.cshl.org Click on Resources

Click on Bioservers

Enter the Allele Server

Allele Server Click on Manage Groups

Select Type of Data Select Group

Your Group Scroll down to “Your Group”

Click on Add Group

Fill Out Form

Click on Edit Group

Fill out Completely

Click on Individuals Tab

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

Click on Done Done

Select Your Group Select and then press OK

Click to Analyze Click Here Then Click Here

Then Look at the Terse and Verbose Tabs

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.