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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. - PowerPoint PPT Presentation
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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
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.