PV92 PCR Informatics Kit: Where did you get those GENES?
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Transcript of PV92 PCR Informatics Kit: Where did you get those GENES?
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PV92 PCR Informatics Kit: Where did you get those GENES?
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Chromosome 16: PV92 PCR Informatics Kit
Instructors
Stan HitomiCoordinator – Math & ScienceSan Ramon Valley Unified School DistrictDanville, CA
Kirk BrownLead Instructor, Edward Teller Education CenterScience Chair, Tracy High School and Delta College, Tracy, CA
Sherri Andrews, Ph.D.Curriculum and Training SpecialistBio-Rad Laboratories
Essy Levy, M.Sc.Curriculum and Training SpecialistBio-Rad Laboratories
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Why Teach Polymerase Chain Reaction (PCR)? • Powerful teaching tool
• Real-world connections
• Link to careers and industry
• Tangible results
• Laboratory extensions
• Standards-based
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• Aligns with AP Biology AP Lab 8
• Extract genomic DNA and amplify student samples
• Introduce the polymerase chain reaction (PCR)
• Apply PCR to population genetics
• Directly measure human diversity at the molecular level
• Compare results to online data
• Sufficient materials for 8 student workstations
• Complete activity in three 45 minute sessions
Chromosome 16: PV92 PCR Informatics
Kit Advantages
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Chromosome 16: PV92 PCR Informatics KitWorkshop Timeline
• Introduction
• Extract genomic DNA and prepare samples for PCR
• Cycle samples
• Agarose gel analysis
• Hardy-Weinberg analysis
• Bioinformatics
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Chromosome 16 PV92 PCR Procedure Overview
Day 2
Day 1
Day 3
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What Is PCR?
• DNA replication gone crazy in a test tube!
• Makes millions of copies of a target sequence from template DNA
• Uses heat-resistant Taq polymerase from Thermus aquaticus
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LaboratoryQuick Guide
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Micropipet Use
1. Twist dial to desired volume
2. Pick up pipet tip
3. Press plunger to first, soft stop
4. Insert pipet tip into solution to be transferred
5. Slowly release plunger to retrieve liquid
6. Move pipet tip into desired tube
7. Press plunger past first stop to second, hard stop to transfer liquid
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Protocol Highlights Genomic DNA Extraction
• InstaGene™ - Chelex® cation exchange resin; binds cellular magnesium ions
• 56°C - loosens connective tissue and inactivates DNAses
• 100°C - ruptures cell membranes and denatures proteins
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InstaGene Extraction
Mg++
Mg++
Mg++
Mg++
Mg++
Mg++
Nuclear membrane
Cell membrane
Heat disrupts membranes
InstaGene matrix binds released cellular Mg++
Genomic DNA
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What Is Needed for PCR?
• Template (the DNA you want to amplify for the study)
• Sequence-specific primers flanking the target sequence:
• Nucleotides (dATP, dCTP, dGTP, dTTP)
• Magnesium ions (enzyme cofactor)
• Buffer, containing salt
• Taq polymerase
3’
5’
5’
3’
3’ 5’
3’5’
Forward primer Reverse primer
Target sequence
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How Does PCR Work?
• Heat (94°C) to denature DNA strands
• Cool (60°C) to anneal primers to template
• Warm (72°C) to activate Taq polymerase, which extends primers and replicates DNA
• Repeat multiple cycles
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Denaturing Template DNA
3’
5’
5’
3’
5’
3’
3’
5’
Heat causes DNA strands to separate
Denaturation of DNA at 94°C
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Annealing Primers
3’
5’
5’
3’
3’
5’
5’
3’3’ 5’3’5’
• Primers bind to the template sequence• Taq polymerase binds to double-stranded substrate
Primers anneal at 60°C
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Taq Polymerase Extends…
• Taq polymerase extends primer• DNA is replicated
Extends at 72°C
3’
5’3’ 5’3’5’
3’
5’3’ 5’3’5’
5’
3’
5’
3’
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Exact-length Target Product is Made in the Third Cycle
3’
5’3’5’3’5’
5’
3’
3’
5’5’
3’
5’
3’
5’3’
3’
3’3’
3’5’
5’
5’
5’
Cycle 1
Cycle 2
Cycle 3
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The Target Sequence
5’5’ 3’3’Alu
Amplified RegionAmplified Region
• PV92 Alu insertion• Located on Chromosome 16
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PV92 Alu Insertion
• A member of Alu repeat family• Human-specific Alu insertion• Found in a non-coding region of your DNA• Not diagnostic for any disease or disorder
5’5’ 3’3’Alu
Amplified RegionAmplified Region
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PCR Results
• The PV92 Alu is dimorphic so there are two possible PCR products: 641 bp and 941 bp
No insertion: 641 bpNo insertion: 641 bp
300 bp Alu insert
641 bp 641 bp
With Alu: 941 bp With Alu: 941 bp
5’5’ 3’3’Alu
Amplified RegionAmplified Region
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Actual Alu PCR Results
941 bp941 bp641 bp641 bp
-- +/-+/-++
++ -- +/-+/-
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Alu Repeats
• Classified as SINEs (Short Interspersed Repetitive Element)
• Mobilized by an RNA polymerase-derived intermediate (retroposition)
• Approx. 500,000 Alu copies per haploid genome, representing about 5% of the genome
• Named for the Alu I restriction site within the element
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Evolutionary Significance of PV92 Alu Inserts
• Highly conserved
• Inserted in the last 1,000,000 years
• Genotypes (+/+, +/–, –/–)
• Used in population genetics, paternity analysis, and forensics
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Determination and analysis of Alu Frequency in a population
• Amplify Alu insert from representative sample population
• Calculate the expected allelic and genotypic frequencies
• Perform Chi-square test
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Calculating Observed Genotypic Frequencies
Genotype +/+ +/– -/- Total (N)
# of People 25 5 8 38
Observed 0.66 0.13 0.21 1.00Frequency
+/+ Genotypic frequency
Number with genotypePopulation total (N)=
2538
.66
==
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Calculating Allelic Frequencies
Number of + alleles
25 individuals with two + alleles = 50 + alleles 5 individuals with one + allele = 5 + alleles
Total = 55 + alleles
Total number of alleles
2N = 2(38) = 76
p Frequency of + alleles
Number of + allelesTotal number alleles= 55
76= 0.72==
p = 0.72; therefore q = 0.28 since p + q = 1.00
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Alu and Population Genetics +/+ = p+/+ = p22
+/- = +/- = 2pq2pq -/- = q-/- = q22
pppp pqpq
qqqqpqpq
p p
pp
Hardy-Weinberg Equation pp22 + 2pq + q + 2pq + q22 = 1 = 1
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Using theHardy-Weinberg Equation to Determine Expected Genotypic Frequencies (p2, 2pq, q2 values)
p2 + 1.00=2pq + q2
(0.72)2+ 1.00=2(0.72)(0.28)+(0.28)2
0.52 + 1.00=0.40 + 0.08
p2 = 0.52 2pq = 0.40 q2 = 0.08
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Calculate Expected Numbers for Each Genotype
+/+ (p2)
+/– (2pq)
–/– (q2)
0.52
Genotype frequency x =Populationt
otal (N)Expected number
x =x =x =
38 20
0.40 38 15
0.08 38 3
Genoty
pe
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Chi-Square Test X2 critical value (from statistics table) = 5.9
+/+
+/–
–/–
25 20 1.25
5 15 6.67
8 3 8.33G
enoty
pe
X2 = ∑ (Observed – Expected)2
Expected
Observed Expected(O–E)2
E16.25 is above 5.9 so the observedgenotypic frequencies are not in genetic equilibrium X2 = 16.25
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Allele Server(1 of 17)
Cold Springs Harbor Laboratory DNA Learning Center
Web site:http://www.dnalc.org/
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Allele Server(2 of 17)
Scroll through DNALC internet sitesuntil BioServers Link appears
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Allele Server(3 of 17)
Click on Bioservers
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Allele Server(4 of 17)
Enter the Allele Server
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Allele Server(5 of 17)
Click on Manage Groups
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Allele ServerType of Data(6 of 17)
Select Group
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Allele Server(7 of 17)
Scroll Down to Select “Your Group”
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Allele Server(9 of 17)
Fill Out Form
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Allele Server(10 of 17)
Click on Edit Group
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Allele Server(11 of 17)
Edit Your Group Information
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Allele Server(12 of 17)
Click on Individuals Tab
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Allele Server(13 of 17)
Add Each Student’s Information
Add as much information as possible:
• Genotype (+/+, +/–. –/–)• Gender• Personal Information
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Allele Server(14 of 17)
Click on Done
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Allele Server(15 of 17)
Select and then Click OK
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Allele Server(16 of 17)
Analyze Data
2: Then Click Here
1: Click Here First
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Allele Server(17 of 17)
Click on the Terse and Verbose Tabs to Review Data Results
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Extensions
• Add each class separately and compare to see if the classes 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