Personalized Medicine

Project Member
Nathaniel Dang

Motivation
There are many factors that must be taken into account when we calculate disease risk – including environmental and genetic factors, as well as occasional chance factors. If we are able to effectively approximate an individual’s increased disease risk factor due to genetic variation, there are several actions we can take (assuming that other risk factors can be affected by such actions). These actions include more frequent and earlier screening for disease, pre-symptomatic medication aimed at reducing one or more risk factors, and focusing on reducing environmental risk factors, including making lifestyle changes. We can also use the information from the genetic study to study variations in more depth, to find correlated SNPs, and to further study the proteins encoded by the genes – which leads to a greater understanding of the overall genetic contribution to disease. There are several companies that offer a genetic “pre-screening” for disease risk, such as 23andMe and Navigenics, which take a similar approach.

Goals
We wish to be able to calculate an individual’s risk for a certain disease given a baseline risk level, the presence or absence of several mutations, and the relative risks of the mutations. We also wish to be able to calculate the overall prevalence of a disease, as well the total genetic contribution to disease risk, given the minor allele frequencies and relative risks of mutations. Finally, we hope to study not only how to calculate the total genetic contribution to risk, but how much each factor affects this risk. For example, what has more of a genetic effect on overall risk – to have more SNPs of lower relative risk or probability, or to have fewer SNPs with a higher relative risk or probability?

Related Files:
Project Documentation (PDF)
Project Slides (PPT)
Project Source Code (.R)

Schedule
Week 1: Select Topic, create wiki
Week 2: Research, Further define problem, outline
Week 3: Begin work on R Program
Week 4: Continue work on R-Program
Week 5: Testing, Example cases using real data

Progress

April 25, 2008
What I did this week: Selected topic, created Wiki
What I plan to do next week: Research and outline
How did what you did compare with what you planned to do: Very well
What grade do you think you deserve: A+

May 1, 2008
What I did this week: Further defined the problem, did some basic research, outline, expanded description
How did what you did compare with what you planned to do: Well
What grade for this week: A

May 9, 2008
What I did this week: Due to Midterms, just a little work on the R program
How what I did compared with planned: Decently
Grade for the week: B

May 15, 2008
What I did this week: I wrote a working beta version of the code.
How what I did compared with planned: Well
Grade for the week: A-
What I plan to do next week: Tweak code, gather feedback, try some sample data

May 20, 2008
What I did this week: Tweaking, same as last week
How what I did compared: ok
Grade for week: B+
What I plan to do: Last minute changes.

May 27, 2008
What I did this week: Prepared Presentation, Analysis of results
How what I did compared: ok
Grade for week: A
What I plan to do:

June 6, 2008
What I did this week: Writeup, further analysis, Presentation/Slides
Grade for week: A

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