Title: PV92 PCR/Informatics Kit
1PV92 PCR/Informatics Kit
- Population Genetics and Informatics
2To 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
3Calculating Allelic and Genotypic Frequencies
- Within your class, how unique is your particular
combination of Alu alleles? By calculating an
allele frequency, you can begin to answer this
question. An allele frequency is the percentage
of a particular allele within a population of
alleles. It is expressed as a decimal. You can
calculate an allele frequency for the Alu PV92
insertion in your class by combining all your
data. For example, imagine that there are 38
students in your class and the genotype
distribution within the class is as follows
Genotype / /- -/-
Total (N) of people 25
5 8 38
4Calculating Allelic Frequencies allele
- Total number of alleles 2N 2(38) 76
- Number of alleles
- / 25 with two alleles 50
alleles - /- 5 with one alleles 5
alleles - Total 55 alleles
- Frequency of number of alleles 55
0.72 - total alleles
76 - Calculation for the alleles would be similar,
and the result would be .28 - Notice ( allele) (- allele) 1.0
5Calculating Genotypic Frequencies
- How does the distribution of Alu genotypes in
your class compare with the distribution in other
populations? For this analysis, you need to
calculate a genotype frequency, the percentage of
individuals within a population having a
particular genotype. Remember that the term
allele refers to one of several different forms
of a particular genetic site whereas the term
genotype refers to the specific alleles that an
organism carries. You can calculate the frequency
of each genotype in your class by counting how
many students have a particular genotype and
dividing that number by the total number of
students. - Given the ethnic makeup of your class, might you
expect something different? - How can you estimate what the expected frequency
should be?
6Calculating Observed Genotypic Frequencies
- Genotype / (p2) /- (2pq)
-/- (q2) Total (N) -
- of people 25 5
8 38 - Observed 0.66 0.13
0.21 1.00 - frequency
- Calculation
- / genotypic frequency with genotype
- total number of people (N)
- 25/38
- .66
7Alu and Population Genetics
- If within an infinitely large population no
mutations are acquired, no genotypes are lost or
gained, mating is random, and all genotypes are
equally viable, then that population is said to
be in Hardy-Weinberg equilibrium. In such
populations, the allele frequencies will remain
constant generation after generation. Genotype
frequencies within this population can then be
calculated from allele frequencies by using the
equation - p2 2pq q2 1.0
- p and q are the allele frequencies for two
alternate forms of a genetic site. The genotype
frequency of the homozygous condition is either
p2 or q2 (depending on which allele you assign to
p and which to q). The heterozygous genotype
frequency is 2pq.
8Alu and Population Genetics
- Hardy-Weinberg Equilibrium
p2 2pq q2 1
p
q
pp
pq
p
/ p2 /- 2pq -/- q2
q
pq
qq
9Using Hardy-Weinberg
- Determine p2, 2pq, and q2 values
- Expected genotypic frequencies
- p 0.72 , so q 0.28 since p q 1
p2 2pq q2 1 - (0.72)2 2 (0.72)(0.28) (0.28)2
1 - 0.52 0.40 0.08 1
- p2 0.52
- 2pq 0.40
- q2 0.08
10Calculate Expected Number of Genotypes
- Expected number of genotype
- Genotypic frequency x population number (N)
- Genotype Expected number
- / 0.52 x 38 20
- /- 0.40 x 38 15
- -/- 0.08 x 38 3
11Chi Squared Test
- Chi-square, a statistical test used for comparing
observed frequencies with expected frequencies.
The larger the chi-square value, the greater is
the difference between the observed and the
expected values. - When using the Chi-square analysis, we test the
null hypothesis that there is no difference
between samples (observed and expected) and we
assume that if there is any difference, then it
arose simply by chance and is not real. - Our null hypothesis is that your class is in
Hardy-Weinberg equilibrium. Whether or not we can
accept the null hypothesis is given by a p-value.
- If the calculated p-value is less than 0.05, the
null hypothesis is disproved the population is
not in Hardy-Weinberg equilibrium. - If the p-value is greater than 0.05, the
population may be in Hardy-Weinberg equilibrium
we can not prove that it is not in Hardy-Weinberg
equilibrium.
12Chi Squared Test
- As an example, lets say that Chi-square analysis
of some data gives a p-value of 0.17. This means
that there is a 17 probability that the
difference between the observed and the expected
values is due to chance. It also means that there
is an 83 (100 - 17 83) probability that the
difference is not due to chance the difference
is real.
13Chi Squared Test
Observed Expected
(O-E)2
E / 25 20 1.25
/- 5 15 6.66 -/-
8 3 8.33
Total 17.12 X2
Critical Value (from statistics table)
5.9 17.12 is above 5.9 so the ratio is not
accepted.
14Allele Server
- Cold Spring Harbor Lab
- DNA Learning Center
15http// vector.cshl.org
Click on Resources
16Click on Bioservers
Click on Bioservers
17Enter the Allele Server
18Allele Server
Click on Manage Groups
19Select Type of Data
Select Group
20Your Group
Scroll down to Your Group
21Click on Add Group
Click on Add Group
22Fill Out Form
23Click on Edit Group
Click on Edit Group
24Fill out Completely
25Click on Individuals Tab
Click on Individuals Tab
26Add Each Student With Information
- Add as much info as you can
- Genotype ( /, /-, -/- )
- Gender
- Personal Info
27Click on Done
Done
28Select Your Group
Select and then press OK
29Click to Analyze
Then Click Here
Click Here
30Then Look at the Terse and Verbose Tabs
31Extensions
- Is your class in Hardy-Weinberg Equilibrium?
- Compare your group to other existing groups.
- Form an explanation for the origination of Alu
and how it spread throughout different
populations. - Have students do manual calculations first and
then compare to the computer generated version.
32Plotting Alu PV92 on a World Map
- The Alu element first appeared tens of millions
of years ago and since that time, it has been
increasing within our genome at the rate of about
one copy every 100 years. - It is difficult to tell how Alu arose. It shows a
striking similarity to a gene (called 7SL RNA)
that performs a vital function in our metabolism.
But Alu , it seems, has no function. It is
self-serving and, like a parasite, takes
advantage of us for its own replication without
providing us any advantage to our own survival. - Most Alu elements are fixed they are found at
the same chromosomal site in every person on the
planet. Fixed Alu elements must have arose very
early in our evolution, well before Homo sapiens
appeared. When modern humans did arise some
200,000 years ago, the vast majority of our Alu
insertions came to us already intact in our DNA. - The Alu PV92 insertion, however, is not fixed.
This insertion may or may not be present on one
or both of a persons number 16 chromosomes.
Since not everyone has the Alu PV92 element, it
must have arisen after the initial human
population began growing. - It is a widely held belief that modern humans
originated in Africa and then disseminated across
the planet. Did the Alu PV92 insert arise in
Africa or on some other continent during our
spread across the globe? - In the following exercise, you will plot the
allele frequencies for various populations on a
world map and make some determination as to where
this Alu arose and how it might have spread
across continents.
33.18
.20
.12
.18
.86
.53
.30
.52
.09
.26
.35
.96
.15
34Classroom How To
- We have worksheets for calculating allelic and
genotypic frequencies for your class - BABEC has the materials for the world population
data