Samantha M. Hurndon Week 5
Markham’s paper on CDT 4 cell decline in HIV-1 subjects left us with some lingering questions. IT was said that of the 15 subjects in the research, 10 of them showed no evidence of a predominant strain. However, they did not go into detail of the other five subjects who could have possibly showed evidence of a predominant strain. Therefore, my colleague and I wanted to investigate exactly who those five subjects are and if they share certain characteristics that we cause them to be more susceptible to a predominant viral strain. It is predicted that the five subjects that show evidence of a predominant strain fall under the same grouping of progressesors. .
- Subjects 2, 3, 4, 6, 12 and 13 will be further looked at. We will use the database for these that gives the number of sequences and number of distinct sequences (taken from http://bioquest.org/bedrock/problem_spaces/hiv/nucleotide_sequences.php).
- Taking the total number of sequences and total number of distinct sequences from the subjects we will them use their ratios to identify which fall under 0.5 (indicating that they are significant to our study)
- Now that we have the subjects that could possibly be the five subjects with evidence of a predominant strain we will then build phylogenetic trees based of their visits and clones and analyze these better understand why they are different from the other subjects.
- Data can be seen below:
- based of the ratios of unique: total sequences (taken from http://bioquest.org/bedrock/problem_spaces/hiv/nucleotide_sequences.php) 6 subjects proved to be possible candidates of the 5 from the 15 that were not included in not showing evidence of a predominant strain.
- Trees for these six individuals were made in hopes of narrowing down the 5 subjects.
- Subject five, which was not part of our study, also had a phylogenetic tree made for reassurance that the trees provided from Markhams study matched the trees we were building. Subject five passed our comparison tested and allowed us to move forward.
We predicted that our five subjects found would show some similarity based of its grouping of progressors. However, it turned out that the five subjects were split between non progressors, rapid progressors and moderate progressors. What can be said though, is that three of the five subjects were non progressors, therefore all non progressors possibly showed evidence of a predominant strain.
Bioinformatics Individual Journal Entries
Week 5: Group project