week 16 of SIP
Hi everyone =) 16 weeks have passed and we are one month away from the end of attachment. Hope you guys are doing fine.
It's my turn to tell you guys more about what I'm doing in the lab I'm in and what my project is about.
As mentioned peviously, I am in a lab that mostly deals with pharmacogenetics. That is how genetic variation affects the drug metabolism. So, bascially everyday I'm doing PCR, gel electrohporesis, purification and sequencing. In school, we were only taught the basics but in my lab, I got all hands-on.
In my previous post, I discussed about how genptyping is done and it's significance. This week, my last post of the whole SIP, I will teach you guys an euqilibrium that most labs dealing with genetic population studies use. It is known as the Hardy-Weinberg Equilibrium, short-form HWE.
Hardy-Weinberg Equilibrium
In population genetics, the HWE principle states that genotypic/ allelic frequencies in a population remain constant from generation to generation unless specific factor are changed.
In HWE, there is 5 assumption.
1. Larger Population Size: The population must be large to minimise random sampling errors. With a large population, the number of changes that occur by chances alone becomes insignificant.
2. Random Mating: There musn't be any mating preference. For example, an AA male does not prefer an aa female.
3. No Mutation: There shouldn't be any mutationthat will result in a change in the alleles. This is because mutation is the source of genetic variation.
4. No Migration: This means that there shouldn't be any exchange of genes between a population and another population. A migration of gnees from a population to another will result in a change in the population's genetic frenquency.
5. No Natural Selection: No alleles are being selected over other alleles. If selection were to occur, the specific alleles selected will tend to be more common.
HWE equation
It is an equation used to estimate and determine the allelic and genotypic frequencies in different populations. This is done after all the genotypes of all subjects on all the SNPs are done. It can also be known as statistical analysis.
HWE equation:
p2 + 2pq + q2 = 1
where, p= frequency of the dominant allele (eg: A)
q= frequency of the recessive allele (eg: a)
For a population to be in genetic equilibrium, p+q must be equal to 1.0 (ie.: the sum of the frequencies of both alleles is 100%)
So, (p+q)2=1
=> p2 + 2pq + q2 = 1
p2 denotes the frequency of homozygous dominant (AA).
2pq denotes the frequency of heterozygous (Aa).
q2 denotes the frequency of homozygous recessive (aa).
Here is one website that I kind that it's quite good at explaining HWE.
Website: http://www.phschool.com/science/biology_place/labbench/lab8/intro.html
That's all on HWE. Hope you guys understand my explaination. Take cares everyone. =)
Lyn
0611027D
TG02
posted by THE CODEC 5 @ 10:38 PM
6 Comments:
Hi Lyn,
The values of A and a are obtained from the population correct? Can you show an example of how you calculate it?
thanks.
Yvonne Teo
0605109H
hihi lyn,
what is the significant of doing HWE ?
and how is HWE related to your project?
what will the HWE result show ?
as in the HWE result means ? to show the patient is recessive or dominant of the particular drugs or other factors ?
tingjie
tg02
0608495h
Oei! We are 1 month away! Not 1 week away from end of SIP!
Haha, Lloyd TG02
To Tingjie,
As I'm dealing with polymorphsisms in a gene in a population, it means genetic population studies. That is studying of the frequency of having certain genetic variation in populations. HWE is used to estimate and determine the allelic and genotypic frequencies in different populations. It is also a form of statistical analysis.
HWE enables us to determine to allelic or genotypic of the various polymorphisms in the population we are studying it. BY using HWE, we are ablt to get the results for the allelic and genotypic frequencies for different polymorphisms in each population studied.
Nope. The result of HWE does not show if the patient is recessive or dominant of a particular drugs or other factors. That requires further studies and research.
By doing statiscal analysis, one is also able to determine if polymorphisms are in complete linkage disequilibrium. For this, it is explained in my previous post.
Hope I have answered your questions.
Lyn
TG02
Haha .. Thanks. typo error. changed already.
Lyn
TG02
Hi Yvonne.
Hmm .. Take for example,
For a gene XYZ, it has this one polymorphism 'A>G'.
As the HWE equation states that p2+2pq+q2=1 and p represents the dominant allele and q represents the recessive allele, in this case, A is the dominant allele while G is the recessive allele.
This is because it's either you get an A or a G at the allele.
Ok. So let's say the number of AA:AG:GG in a particular population is 10:8:9.
As AA, AG and GG are known as the genotypes, an AA genotype has 2 A alleles. Thus is total there are 3 A alleles and 3 G alleles.
So, since the number of AA is 10, we have to multiply by 2 'cause there's 2 A's in an AA. Also, do not forget that AG also has an A in it. So now,the allelic number for A is 28.
To get allelic frequency, you have to divide the number with all the alleles present. So it is 28/54 and the answer is usually expressed in decimals,which is ~0.52.
Hope I have explained clearly and you understand. =)
Lyn
TG02
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