Angela A. Garibaldi Week 5
Background
Looking at annual rate of CD4 T cell decline of subjects 7,6 (moderate progressors), subject 10 or 11 (Rapid progressors), and Subject 13 (Non progressor).
- We noticed that subject 7 has a similar rate of decline to the Rapid Progressors (10,11).
- We noticed that subject 6 has a similar rate of decline to Non Progressors (13)
- We want to compare the divergence and diversity with a focus on divergence of 7 and 10/11, 6 and 13 to see if the sequences of these subjects are more similar to one another in comparison with 6 and 7 to compare two currently labeled Moderate progressors.
- Basically, we are questioning the methods of categorizing subjects' progressor status
Other Previously Published Work:
Question
Reevaluating the standards of categorizing HIV progressors based on CD4 T cell decline rates by examining divergence and diversity in HIV-1 env sequences.
Hypothesis
We predict that subject 7 (moderate progressor), who has a similar CD4 T cell decline rate to subject 10/11( Rapid progressor), will have similar patterns of diversity and divergence based on sequence analysis. We also predict that subject 6 (Moderate progressor), with a similar decline in CD4 T cell decline rate to Subject 13 (Non progressor), will be similar in the same analyses. Lastly, we predict that Subjects 7 and 6, both Moderate Progressors, will be significantly more divergent from one another. Subject 7 will be less divergent and more closely related to Subject 10/11. Subject 6 will be less divergent and more closely related to Subject 13.
Procedure:
- Upload approximately 30 sequences from each subject from Visit xx.
- Conduct Clustdist multiple sequence alignment between the following pairs and generate phylogenetic trees:
7:10 6:13 7:6
- Calculate S, Theta, and the Minimum and Maximum
- Interpret phylogenetic trees and statistical data
