Welcome to the Personalized Medicine Project page. I am Rui, a first year graduate student of ACCESS program, an umbrella biological program.
Project Description
This Project is to help doctor decide which SNPs are worth measuring for a certain type of diseases.
There are two webpages that relate to this project which can help us know more about this project:
http://www.navigenics.com/campaigns/prevention?s_kwcid=navigenics.%7C3883443815
Goal for the quarter
Build up a model that could help doctors choose the SNP that worthy measuring based on the prevalence and risks of the diseases.
Weekly Schedule
Week1 4/23
background learning
Week2 4/30
I have calculated the Var(r)(variance of risk increased by the SNP) for one single SNP based on the prevalence F and the probability of the SNP.
I problem I met was firstly I used case study way to try to find the distribution of r. It is difficult. When I switch this way to do the derivation, it's much easier. But new problem comes, the formula of Var(r) contains r itself. If I want to use this formula to real data, either I should know the r in advance or I have to estimate the r by samples. It is also like a case study then.
(1)The goal for the next step is to calculate the Var(r) for multiple SNPs, then code them in R.
I grade A for myself this week.
Week3 5/7
I tried to get the formula for multi-SNPs.
Assume there are 3 SNPs related to the disease:then there will be 8 situations of prevalence.
Assume SNPs are A,B,C;
The relative risk are:$\gamma_{A},\gamma_{B},\gamma_{C}$
The disease prevalence under every condition is following:
Under this condition, the formula for variance is very complex.
The plan to next step is to move to R coding for the model. Also, find a way to summary the variance for N SNPs.
I grade myself A this week.
Week4 5/14
After the discussion in class, I got the formula for multiple SNPs. I find to use different cases to explain the formula.
I simulate the data and create the SNP matrix using R code and calculate the expectation and variance.
I gave the presentation the first Friday.
I grade myself A- this week.
Week5 5/22
I prepared the presentation report for this project.
I also think out another way to measure the variance of disease prevalence.
Besides using the criteria, I think out anther way to measure, that is to use:
I grade myself A+ this week.