PV92 PCR/Informatics KitPV92 PCR/Informatics Kit

Population Genetics and Population Genetics and InformaticsInformatics

To estimate frequency of To estimate frequency of Alu Alu

within a population:within a population:

Amplify Amplify Alu Alu insert from insert from representative sample populationrepresentative sample population

Calculate the expected allelic and Calculate the expected allelic and genotypic frequenciesgenotypic frequencies

Perform Chi-squared TestPerform Chi-squared Test

Alu and Population GeneticsAlu and Population GeneticsHardy-Weinberg EquilibriumHardy-Weinberg Equilibrium

pp22 + 2pq + q + 2pq + q22 = 1 = 1

+/+ = p+/+ = p22

+/- = 2pq+/- = 2pq-/- = q-/- = q22

pppp pqpq

qqqqpqpq

p p

pp

qq

qq

Calculating Observed Calculating Observed Genotypic FrequenciesGenotypic Frequencies

GenotypeGenotype +/+ (p2)(p2) +/- (2pq)(2pq) -/- (q2)(q2) TotalTotal (N) (N)

# of people# of people 25 5 825 5 8 38 38

Observed frequencyObserved frequency 0.65 0.13 0.21 0.65 0.13 0.21 1.001.00

Calculation:Calculation:+/+ genotypic frequency == # with genotype

total number of people (N)total number of people (N)

== 25/3825/38 = .65= .65

Calculating Allelic Calculating Allelic FrequenciesFrequencies

Frequency of p Frequency of p = = number of p allelesnumber of p alleles = = 55 55 = = 0.720.72 total alleles total alleles 7676

Number of p alleles =Number of p alleles = +/++/+ == 25 with two 25 with two + + alleles alleles = 50 + = 50 +

allelesalleles +/-+/- = = 5 with one 5 with one + + allelesalleles = 5 + = 5 + allelesalleles TotalTotal = = 55 + 55 + allelesalleles

Total number of alleles = 2N = Total number of alleles = 2N = 2(38)2(38) = 76 = 76

Using Hardy-WeinbergUsing Hardy-Weinberg

Determine Determine pp22,, 2pq, and q2pq, and q22 values= values= Expected genotypic frequenciesExpected genotypic frequencies

p = 0.72 , so q = 0.28p = 0.72 , so q = 0.28 since since p + q = 1p + q = 1 pp22 ++ 2pq2pq + q+ q22 = 1= 1

(0.72)(0.72)22 + 2 (0.72)(0.28)+ 2 (0.72)(0.28) + (0.28)+ (0.28)22 = 1= 1 0.520.52 ++ 0.400.40 + + 0.080.08 = 1= 1

p2 = 0.52p2 = 0.52 2pq = 0.402pq = 0.40 q2 = 0.08q2 = 0.08

Calculate Expected Number of Calculate Expected Number of GenotypesGenotypes

Expected number of genotype =Expected number of genotype =

Genotypic frequency x population Genotypic frequency x population number (N)number (N)

GenotypeGenotype Expected Expected numbernumber+/+ +/+ 0.52 x 38 = 0.52 x 38 = 2020+/+/- - 0.40 x 38 = 0.40 x 38 = 1515

--//- - 0.08 x 38 = 0.08 x 38 = 33

Chi SquaredChi Squared Test Test

E

EOX

22

Observed Observed Expected Expected (O-E)2(O-E)2

EE+/+ +/+ 2525 20 20 1.251.25 +/- +/- 55 15 15 6.666.66-/- -/- 88 3 3 8.338.33

Total Total 16.2116.21

X2 Critical Value (from statistics table) = 5.9X2 Critical Value (from statistics table) = 5.9

13.21 is above 5.9 so the ratio is not accepted.13.21 is above 5.9 so the ratio is not accepted.

Allele ServerAllele Server

Cold Spring Harbor LabCold Spring Harbor Lab

DNA Learning CenterDNA Learning Center

http:// vector.cshl.orghttp:// vector.cshl.org

Click on Resources

Click on BioserversClick on Bioservers

Click on Bioservers

Enter the Allele ServerEnter the Allele Server

Allele ServerAllele Server

Click on Manage Groups

Select Type of DataSelect Type of Data

Select Group

Your GroupYour Group

Scroll down to “Your Group”

Click on Add GroupClick on Add Group

Click on Add Group

Fill Out FormFill Out Form

Click on Edit GroupClick on Edit Group

Click on Edit Group

Fill out CompletelyFill out Completely

Click on Individuals TabClick on Individuals Tab

Click on Individuals Tab

Add Each Student With Add Each Student With InformationInformation

Add as much info as you canAdd as much info as you can Genotype ( +/+, +/-, -/- )Genotype ( +/+, +/-, -/- ) GenderGender Personal InfoPersonal Info

Click on DoneClick on Done

Done

Select Your GroupSelect Your Group

Select and then press OK

Click to AnalyzeClick to Analyze

Click Here

Then Click Here

Then Look at the Terse and Then Look at the Terse and Verbose TabsVerbose Tabs

ExtensionsExtensions

Add each class separately and Add each class separately and compare each to see if each is compare each to see if each is different from each other.different from each other.

Compare your group to other existing Compare your group to other existing groups.groups.

Have students do manual Have students do manual calculations first and then compare calculations first and then compare to the computer generated version.to the computer generated version.