Disease Models

Project Member

Nicolas Widman

Introduction

There are several different models of how a mutation occurs on the two chromosomes. Dominant, Recessive, and Additive are 3 such models. The objective of this project is to implement and compare the association power statistics for several diploid (two chromosome) models for different ways SNPs result in a disease phenotype. These models use a relative risk factor to determine the probability of the occurrence of a disease given the probability of the responsible SNP. However, the relative risk model briefly covered in class assumes a haploid model where exactly zero or one copy of the associated SNP is inherited and is directly responsible for the increased risk for the disease. In a diploid model of inheritance, two copies of the SNP are inherited and as a result one, two, or neither of the SNPs may be the disease-associated version of the SNP.

dom_72.tifrec_72.tifadd_72.tif

Presentation

Project Presentation- Powerpoint

Description

Project Description- MS Word

The goal of this quarter

Develop a model for recessive, dominant, and additive effects for SNPs between 2 chromosomes and evaluate the association power for these models.

Schedule for the quarter

Week 4: Choose a project, set up wiki for project
Week 5-6: Learn more about disease models and their interaction with mutations
Week 7: Derive models for recessive and dominant SNPs
Week 8: Implementation of models, work on additive model
Week 9: Make sure models are correct, implement models in code, plot association power trends
Week 10: Present project in class

April 21-27

What I did this week: Chose topic, set up wiki, planned schedule
What I plan to do next week: Find out how disease models can be evaluated within the data provided by the HapMap, outline high level technical details of project.
How what I did compares to what I planned: Decided on project, created wiki page with necessary information in the proper format; everything for week 4 complete.
Week 4 grade: A

April 28-May 4

What I did this week: Found out more about the topic, discussed general details of project.
What I plan to do next week: Represent each disease model (dominant and recessive) as a virtual SNP with relative risk model, have an overall structure for the project.
How what I did compares to what I planned: I have a better idea of the nature of the project and what to work on.
Week 5 grade: A

May 5-11

What I did this week: Gained a better understanding of the derivation of the relative risk model to accommodate disease models.
What I plan to do next week: Have an outline of the project and begin coding. Obtain data that can be used with the project.
How what I did compares to what I planned: Gained a better understanding of underlying mathematics, made conceptual progress. However, overall design idea for project is still vague.
Week 6 grade: A-

May 12-18

What I did this week: Determined formulas for dominant and recessive SNP models, tested these models
What I plan to do next week: Work on additive SNP model, plot association power trends
How what I did compares to what I planned: Made progress, some implementation
Week 7 grade: A

May 19-25

What I did this week: Asked about additive SNPs
What I plan to do next week: Work on additive SNP model, plot association power trends, finish project
How what I did compares to what I planned: Unfortunately, not too much progress this week.
Week 8 grade: B+

May 26-June 1

What I did this week: Implemented additive SNP model, all three models coded, some association power data plotted
What I plan to do next week: Wrap up project, write up presentation
How what I did compares to what I planned: Made a lot of progress, but not finished. Coding done, but no detailed plan on how to present the project.
Week 9 grade: A-

June 2-June 6

What I did this week: Finished project, made presentation, presented project
How what I did compares to what I planned: Everything as planned, although schedule was a bit tight towards the end
Week 10 grade: A

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