What I Did
As part of the analysis, I worked on locating and analyzing the dataset for the healthy patients from the Human Microbiome Project. After all the analyses were run, I also wrote the discussion portion based on my team member’s ideas on what happened in the results.
How You Can Help
I also noted in the future research portion that taking the AMRs of patients pre- and post-treatment would be useful, in order to see change over time. It is difficult to compare patients pre- and post-treatment, especially when they are considered different samples.
What I Did
For this project, I helped develop the workflows, and also concatenated the 10 indiv samples of the the HNC dataset together to have one larger representative data set. I then completed the analysis on this concatenated dataset, as well as the analysis on the Zymo Fecal Reference, and Breast Cancer sample, and reflected these results in Figures 3 and 6.
How You Can Help
One area of further research to continue this project would be to actually size down the samples to see if the graphed relationship in figure 6 is accurate. Furthermore, I would try and understand why the concatenated HNC dataset only 2 AMRs, as I would imagine given it was 10 pts there would be more.
What I Did
I analyzed the Illumina dataset for our head and neck cancer patients in order to have a direct comparison with the healthy controls that were also sequenced with Illumina. The most surprising result for me was that less AMRs were found in the dataset with all 10 head and neck cancer patients together than in the Illumina reads for one individual.
How You Can Help
A future direction could be to look into specific AMRs that may be common for the environment the individuals are in like a hospital for example. This could further explain if any changes in the AMRs present occurs beyond if there are more or less of them in our datasets.