During the last five years as a student, I have worked on completing my dissertation titled "Genetically informative designs for the study of aging and health associated biomarkers." This resulted in publishing the following manuscripts:
- https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-019-1602-8
- https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170765
- https://www.cambridge.org/core/journals/twin-research-and-human-genetics/article/metataxonomic-analysis-of-individuals-at-bmi-extremes-and-monozygotic-twins-discordant-for-bmi/50D8B81B2D15D5E9AE8824234F7F96D3
Although not a traditional programming project, the analysis for these projects used combinations of makefiles, bash, R, Python, and many bioinformatics-specific tools.
Dissertation Abstract:
Genetically informative study designs have long been of great importance for helping to determine the role the environment and genetic susceptibility play in several human phenotypes. Of such designs, one of the most well-known is the classical twin design, including both monozygotic (MZ) and dizygotic (DZ) participants. In addition to the comparison of MZ and DZ twin pairs, studies focused on MZ twin pairs discordant for a specific phenotype allow for researchers to better understand how environmental influences impact a trait while controlling for the host genomic profile. Beyond the use of twin derived samples, with information on the genomic content of unrelated individuals, it is possible to create genetically informative designs aimed at understanding many biological phenomena.
In this project, genetically informative study designs are used to investigate human aging and health-associated phenotypes. The first study utilizes blood and buccal derived DNA samples collected simultaneously in order to investigate telomere repeat mass (TRM) in both tissue types. These samples were collected from MZ and DZ twin pairs and thus will allow exploration into the heritability of TRM in both tissue types as well as the suitability of buccal derived DNA for TRM measurement. The second study focuses on using multiple genetically informative designs to understand the relationship between the gut microbiota and the host obesity-associated measures. These studies include the use of samples collected from body mass index (BMI) discordant MZ twin pairs and the four-corners study design, with individuals at high/low extremes for both genetic risk for obesity and actual BMI. The final study within this project is aimed at determining the role of cohabitation on the gut microbiota composition. Samples collected from MZ twin pairs who cohabitate and those that do not, in addition to spouse pairs, allows a unique view into the role of cohabitation as an important environmental modulator of the gut microbiota. Microbes that are particularly influenced by cohabitation are further explored to determine relationships between host cardiometabolic and disease burden.
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