Genetics and Genomics Commons^™

Leveraging Dna Methylation Profiling And Microrna Sequencing To Characterize The Epigenomic Landscape Of Major Depressive Disorder Disease Trajectory, Jan Dahrendorff

USF Tampa Graduate Theses and Dissertations

Major depressive disorder (MDD) is a common and debilitating mental disorder associated with a significant disease burden and economic cost. Despite ample evidence documenting the efficacy of a diverse array of established MDD therapies, a large proportion of patients are inadequately responsive to initial treatment attempts, with first-line treatments leading to remission in only ~30% of the patients. Importantly, about a third of patients even fail to achieve symptom improvement after two or more antidepressant trials, resulting in what is commonly defined as treatment-resistant depression (TRD). The ability to identify which treatments are most likely to elicit a positive response …

Using Rattlesnake Venom To Model Complex Trait Evolution Across Ecological And Evolutionary Scales, Samuel R. Hirst

USF Tampa Graduate Theses and Dissertations

A central challenge in evolutionary biology is understanding how genetic variation leads to phenotypicdiversity, particularly for complex traits that strongly influence fitness. Traits form the substrate of natural selection, but it is genes, that are inherited across generations. To fully understand the evolutionary process, we must therefore connect the molecular basis of trait variation with the evolutionary outcomes of such traits.

For relatively simple traits, the genotype–phenotype relationship is well understood. Classic systems, such as coat color in beach mice or toxin resistance in garter snakes, have provided effective examples of how relatively few loci underlie conspicuous adaptive differences across …

Changes In Immune-Regulated Gene Methylation Over Time In Women Who Do And Do Not Develop Breast Cancer, Kyle Laney

USF Tampa Graduate Theses and Dissertations

Breast cancer survivors face elevated risks of chronic inflammatory conditions and immunedysfunction compared to the general population. These elevated health risks in survivors are well-documented but mechanistically poorly understood. This study aimed to characterize longitudinal changes in DNA methylation patterns of immune-regulatory genes in women who developed breast cancer compared to cancer-free controls. We conducted an EWAS using Sister Study cohort data, analyzing longitudinal changes in DNA methylation by comparing the difference in beta values between pre- and post-diagnosis time points in breast cancer cases versus changes over the same period in cancer-free controls. The analysis included 414 participants: 189 …

Exploring Religious Leaders’ Perspectives On Genetic Counseling, Testing, And Related Technologies, Kristina M. Wittenburg

USF Tampa Graduate Theses and Dissertations

Religion significantly influences healthcare decisions, including those related to genetic testing, by shaping ethical and emotional considerations. While some religious groups provide formal stances on genetic testing, others lack clear guidelines, leaving both patients and healthcare providers without consistent resources for navigating faith-informed decisions. Understanding religious leaders’ perspectives is critical to bridging this gap and supporting diverse patient needs. This study aimed to examine religious leaders’ perspectives on genetic testing, genetic counseling, in vitro fertilization (IVF), gene therapy, stem cell research, and abortion. These topics were explored to understand the role of religious beliefs in healthcare decisions, and to develop …

Identifying Racial Disparities In Patient Activation Outcomes In Genetic Counseling Sessions, Moriah M. Melhado

USF Tampa Graduate Theses and Dissertations

Patient empowerment and activation are critical determinants of health outcomes, fostering patients’ confidence, knowledge, and engagement in their care. While the influence of race and ethnicity on patient activation has been extensively studied with other healthcare providers such as physicians and nurses, limited research has explored this dynamic within genetic counseling (GC). This study combines a systematic literature review, following PRISMA guidelines, a secondary data analysis , and an exploratory qualitative analysis of patient interviews post-session to examine relationships between race, ethnicity, and patient activation or empowerment in GC. Search terms identified 536 peer-reviewed articles, of which 44 met inclusion …

Genetic Counseling Student Anxiety, Self-Efficacy, And Study Strategy Use For The Genetic Counseling Board Certification Exam., Teagan E. Nunnery

USF Tampa Graduate Theses and Dissertations

With a 76% pass rate for the 2024 American Board of Genetic Counseling (ABGC) certification exam, it's crucial to evaluate the study strategies used by candidates and their alignment with evidence-based practices. This study surveyed 84 genetic counseling students and graduates from 35 U.S. and Canadian training programs, focusing on demographic data, study strategy usage, anxiety, and self-efficacy. Study strategies were categorized into one of three groups: 1) active strategies, which promote recall and understanding, 2) passive strategies, and 3) hybrid, for strategies that involve both active and passive engagement as well as three metacognitive strategies: regulating learning, monitoring learning, …

Evaluating And Improving The Serious Game Life With Hereditary Cancer, Jenna K. Peterson

USF Tampa Graduate Theses and Dissertations

Hereditary cancer syndromes increase cancer risks for individuals with pathogenic variants and their family members, yet many at-risk individuals do not pursue genetic testing due to barriers in family communication. Serious games—interactive tools designed to educate through gameplay—offer a promising approach to addressing these barriers by engaging users and creating supportive learning environments. LIFE with Hereditary Cancer is a serious game designed to improve genetic literacy, promote informed decision-making, and encourage family conversations about hereditary cancer risks and genetic testing. This evaluation used a mixed-methods approach to assess participant emotions, perceptions, and experiences with LIFE with Hereditary Cancer and identify …

Analyzing And Extending Machine Learning Frameworks On High Risk Domains, Chengbin Hu

USF Tampa Graduate Theses and Dissertations

Machine learning (ML) has become a transformative force in high-risk domains such as genomics and cybersecurity, where accurate predictions and robust defenses are essential. This dissertation advances ML frameworks in these areas by developing methods to enhance predictive power in health applications and assess vulnerabilities in machine learning systems.

In the genomics field, the work addresses challenges in Non-Invasive Prenatal Testing (NIPT) of monogenic disorders by proposing a deep learning model that reconstructs the fetal genome using maternal plasma cell-free DNA (cfDNA) and parental whole-genome sequencing (WGS) data. This model achieves high accuracy in single nucleotide variation (SNV) prediction, surpassing …

Unravelling The Impact Of Blood Metabolites, And Lifestyle Factors On Periodontal Disease Using Mendelian Randomization, Rhea Charles

USF Tampa Graduate Theses and Dissertations

Periodontal disease remains a global public health concern. Despite the availability of preventive and therapeutic strategies, the multifactorial nature of periodontitis complicates its understanding and management. Periodontal disease is associated with an increased risk of chronic conditions, including ischemic heart disease (IHD), gestational hypertension, respiratory diseases such as COPD and bronchitis, and various cancers, including kidney and pancreatic cancers. Moreover, individuals with diabetes, autoimmune diseases like lupus and Crohn’s disease, and osteoporosis are more likely to develop periodontitis. The ambiguity in the direction of causality between periodontal disease and its associated conditions poses challenges for effective treatment. Mendelian randomization offers …

The Influence Of Childhood Trauma On Dna Methylation Patterns And Sex-Specific Cortisol Stress Reactivity: A Secondary Analysis, Isabella F. Correia

USF Tampa Graduate Theses and Dissertations

Childhood trauma has been shown to significantly impact physical and mental health outcomes, leading to conditions such as heart disease, diabetes, depression, and difficulties in decision-making and maintaining relationships. Exposure to such trauma has the potential to dysregulate an individual’s stress response system, resulting in abnormal cortisol levels. Many studies suggest a lasting impact of early-life stress on DNA methylation patterns and, separately, cortisol stress reactivity. In addition, there are known sex differences in exposure to childhood trauma and cortisol reactivity; yet studies to date have not investigated whether there is an association to DNA methylation. This study utilized a …

Porphyrin Overdrive In Cancer: Unraveling The Mechanisms And Therapeutic Potential, Pravin D. Meshram

USF Tampa Graduate Theses and Dissertations

The increased understanding of cancer cell metabolism has shown options for novel treatment strategies. This thesis looks at the role of heme metabolism, specifically "porphyrin overdrive," in cancer progression and treatment. Cancer cells are hypermetabolic and rely on heme synthesis. When treated with δ-aminolevulinic acid (ALA), they abnormally accumulate heme intermediates. This metabolic weakness presents an opportunity to exploit heme synthesis in targeted cancer therapy. In this study, we suggest a "Bait and Kill" technique that uses exogenous ALA to induce protoporphyrin IX (PpIX) buildup in cancer cells, making them more susceptible to oxidative stress. We investigate the possibility of …

Assessing Roman Catholics’ Modern Beliefs And Behaviors Surrounding Genetics Counseling Services, Mary S. Shinaberry

USF Tampa Graduate Theses and Dissertations

Currently, there is limited knowledge about the contemporary beliefs of Roman Catholics regarding genetic healthcare, and concerns exist that they may be less comfortable accessing genetic counseling services. To better meet the needs of this population, we interviewed 18 adult Roman Catholics living in the United States. A novel method of thematic analysis was utilized, combining traditional qualitative techniques with the assistance of ChatGPT-4, following best practices proposed to improve the trustworthiness of AI-assisted qualitative analysis. The majority of participants were college-educated women aged 25-40, none of whom had seen a genetic counselor. Most participants associated the term “genetic counseling” …

Linking Shared Decision Making To Outcomes In Simulated Prenatal Genetic Counseling Sessions, Raquel C. Chavarria

USF Tampa Graduate Theses and Dissertations

Shared decision-making (SDM), defined as the collaborative process between patient and healthcare provider to arrive at a values-based clinical decision, may be valuable in genetic counseling (GC) given that patients are often faced with various options. Four published studies have measured or made conclusions about the use of SDM skills in GC settings, but only one study evaluated relationships between third-party observations of SDM in recorded GC sessions and patient-reported outcomes (i.e., anxiety and decisional conflict) and found no correlations between these measures. The purpose of this study was to evaluate relationships between SDM and measures of patient-reported experience (i.e., …

Evaluation Of Pediatric Genetics Clinics’ Workflows, Efficiencies, & Genetic Counselor Job Satisfaction, Ashlyn M. Keziah

USF Tampa Graduate Theses and Dissertations

The organizational structures and workflows of pediatric/general genetics clinics exhibit significant variability across institutions. However, there is a notable lack of studies exploring which structural components within pediatric clinics contribute to increased patient volumes, while concurrently upholding genetic counselor work satisfaction and mitigating burnout risks. To address this gap, this multiple case study delves into the operational dynamics of several pediatric genetics clinics located throughout the state of Florida. We employed surveys and interviews to identify shared patterns and distinctions in clinic workflows and structures, subsequently evaluating efficiency and genetic counselor job satisfaction/burnout at each site. This study includes survey …

Analyzing The Relationship Between Preeclamptic Severity And Placental Methylation, Mackenzie C. Maggio

USF Tampa Graduate Theses and Dissertations

Preeclampsia (PE) is a life-threatening hypertensive disorder in pregnancy (HDP) characterized by high blood pressure and proteinuria after 20 weeks of gestation. PE poses significant risks to both maternal and child health. An incomplete etiopathogenesis, diverse disease heterogeneity, and limited intervention and detection strategies further exacerbate and perpetuate PE as a major public health concern. By assessing symptom severity of placental tissues from PE pregnancies and analyzing the DNA methylation differences, this thesis aimed to identify epigenetic variations contributing to disease heterogeneity. Using the publicly available dataset GSE 98224, differentially methylated region (DMR) analysis on placental samples (n=48) revealed increasing …

A Differentially Methylated Region Analysis Between Three Disease States Of Major Depressive Disorder In Primarily African-American Cohorts, Lanie Katelynn Mullins

USF Tampa Graduate Theses and Dissertations

Major depressive disorder (MDD) is a common and debilitating disorder that affects millions of people worldwide. MDD is a multifactorial disease with no established mechanism currently able to explain all facets of the disease or its etiology. Feedback loop mechanisms have been posited to explain the interactions of psychological and physical components of the disease etiology. Epigenetics, specifically DNA-methylation analyses, can shed light on the interaction between the within-person environment resulting from MDD symptomology, the persistence of the disease, and factors influencing remission. Here, a differentially methylated region analysis was conducted using samples derived from whole blood to interrogate the …

Factors Impacting Genetic Test Result Recall And Adherence To Cancer Risk Management Recommendations Among Patients With Germline Pathogenic Variants, Karishma Prakash Bharwani

USF Tampa Graduate Theses and Dissertations

Only 20-60% of information from medical appointments is estimated to be retained of which about half is recalled accurately; however there remains limited information about recall following disclosure of inherited cancer genetic test results (GTR). We sought to evaluate recall of GTRs and the association of recall with adherence to recommended cancer risk management (CRM). Study participants were consented individuals with a confirmed germline pathogenic or likely pathogenic variant (GPV) in an inherited cancer predisposing genes for which there are CRM guidelines per the National Comprehensive Cancer Network (NCCN). Through information collected through self-reported surveys, adherence to CRM was defined …

Genetic Counseling Student Self-Efficacy, Exam Anxiety, And Opinions Related To Study Materials For The Genetic Counseling Board Certification Exam., Jessica F. Stanton

USF Tampa Graduate Theses and Dissertations

The Genetic Counseling Board Examination is a critical assessment for clinical practice in the field. However, the relationship between students’ test-related anxiety, confidence in their ability to study (i.e., self-efficacy), and the use of gamification for board examination preparation remains unexplored. This study compared gamification and traditional quiz-style study methods using two randomized groups of students preparing for the Genetic Counseling Board Examination. The primary objectives were to assess for changes in exam-related anxiety and self-efficacy after completing the respective study materials and to evaluate the acceptability and completion rates of these materials. Ninety-eight genetic counseling students or recent graduates …

Novel Genetic Interactions Of The Sgs1 Helicase In The Maintenance Of Genome Integrity, Sonia Vidushi Gupta

USF Tampa Graduate Theses and Dissertations

Mutagenesis and genome instability are characteristics of cancer cells. People afflictedwith Bloom’s syndrome due to mutations in the BLM gene suffer from reduced life expectancy, accelerated aging, sensitivity to sun exposure, immune system abnormalities and increased risk of cancer. The predisposition to cancer is typically due to abnormal DNA repair that results in chromosome breakage and rearrangements. The homologous recombination factor Sgs1, which is a RecQ-like helicase and an ortholog of the human BLM helicase, functions primarily in DNA repair, but has also been implicated in other cellular functions like replication. Several functions of BLM such as its involvement in …

Piloting A Spanish-Language Web-Based Tool For Hereditary Cancer Genetic Testing, Gretter Manso

USF Tampa Graduate Theses and Dissertations

Cancer genetic services (including genetic counseling and testing) help identify patients and families at increased risk of developing cancer so that steps can be taken to reduce risks or find cancers early. Receipt of genetic services in the Hispanic/Latinx population is low due, in part, to a shortage of Spanish-speaking genetic counselors. To address this concern, a 12-minute online tool designed to inform individuals about cancer genetic services was translated into Spanish. The objectives of this pilot study were to determine if the educational tool improves knowledge and informed decision making and to assess usability and appropriateness of the tool …

Identifying Barriers And Facilitators To Family Communication Regarding Genetic Testing For Hereditary Cancer, Andrea K. Shields

USF Tampa Graduate Theses and Dissertations

Cascade testing, whereby at-risk family members are tested for known pathogenic or likely pathogenic (P/LP) variants in high risk cancer genes, provides the opportunity for changes in medical management (e.g., increased surveillance to detect cancer early or preventative surgery to reduce cancer risk). However, the rates of cascade testing are low which suggests that one-time communication may be insufficient to prompt action among family, and an increase in understanding of how to promote ongoing communication about genetic testing within families is needed. We surveyed individuals with P/LP variants in inherited cancer genes and conducted multiple linear regression with forward analysis …

Needs Assessment For A Web-Based Support Resource For Patients With A Pathogenic Variant In Lmna, Dylan M. Allen

USF Tampa Graduate Theses and Dissertations

Pathogenic variants (PV) in the gene LMNA cause autosomal dominant inherited “laminopathies” that can affect multiple different organs, most specifically the heart. Current resources for LMNA patients are sparse and disjointed, leaving a need for a comprehensive resource catering to the wants and needs of the patients. A needs assessment of LMNA support resources was completed through reviewing published literature and existing support resources and conducting 11 semi-structured interviews with individuals who have a PV in LMNA. The Social Support Theoretical Model and thematic analysis of interview transcripts were used to identify discrepancies between the support that affected individuals receive …

Using The Genetic Counseling Skills Checklist To Characterize Prenatal Genetic Counseling, David A. Cline

USF Tampa Graduate Theses and Dissertations

Genetic Counseling relies on communication skills to help patients understand and adapt to a genetic disease or risk. However, little is known about which skills are most commonly used or the extent to which genetic counseling sessions vary. A novel process measure titled the "Genetic Counseling Skills Checklist" (GCSC) was developed in a prior pilot study and includes 8 broad categories each consisting of 5-8 skills. This study is the first to apply the final GCSC to characterize 20 mock prenatal sessions conducted by 5 genetic counselors (GCs) for 2 prenatal indications using 3 trained actors as patients. Two experienced …

Healthcare Decision Makers' Perspectives On Barriers And Facilitators To Hiring Genetic Counselors In Huntington Disease (Hd) Clinic Settings, Bailey Hummel

USF Tampa Graduate Theses and Dissertations

Huntington disease (HD) is a hereditary, neurodegenerative autosomal dominant disorder for which there are currently no effective options to prevent the onset of symptoms. Although meeting with a genetic counselor (GC) is recommended as part of national guidelines for predictive HD genetic testing and a GC is required for Centers of Excellence, not all HD centers have hired a GC. To explore drivers for, valued outcomes of, and barriers to the creation of GC positions in clinics that treat patients with HD, we conducted semi-structured interviews with 11 individuals involved with HD clinics and/or hiring decisions at 8 clinics across …

Evaluation Of A Story-Telling Approach To Educate Minority Populations About Inherited Cancer, Celestyn B. Angot

USF Tampa Graduate Theses and Dissertations

Utilization of hereditary cancer genetic counseling and testing services is substantially lower among minority populations compared to white populations due, in part, to lower levels of awareness and knowledge. To help improve awareness, we designed a 7-minute video that uses storytelling to translate knowledge of genetic testing and hereditary cancer to individuals who have a personal history or family history of cancer. Consented participants were asked baseline questions about hereditary cancer and genetic testing, reviewed the video, and provided feedback on its content, understandability, and visual appeal during semi-structured interviews. Data were coded and analyzed to identify themes and determine …

Lord Of The Z-Rings: Uncovering The Role Of Mraz And Ftsl In Bacillus Subtilis Cell Division, Maria Louise White

USF Tampa Graduate Theses and Dissertations

Cell division is a complex and highly orchestrated process that requires careful coordination. The process of cell division in prokaryotes primarily occurs via binary fission, where one mother cell becomes two genetically identically and equally sized daughter cells. In most bacteria a key protein, FtsZ, forms a FtsZ ring (Z-ring) to mark the division site and recruit proteins involved in cytokinesis. Whilst much has been learned about the contents and assembly of the divisome in model organisms such as Escherichia coli and Bacillus subtilis factors governing the regulation of divisome are much more poorly understood. …

Neural And Cardiac Mechanisms In Friedreich's Ataxia With Patient-Derived Ipscs, Mariana Burgos Angulo

USF Tampa Graduate Theses and Dissertations

Friedreich's ataxia (FA) is an autosomal recessive disease caused, in most cases, by a GAA trinucleotide repeat expansion in the first intron of the frataxin (FXN) gene, which results in transcriptional repression of the encoded protein frataxin. FA is a progressive neurodegenerative disorder, but the primary cause of death is hypertrophic cardiomyopathy, which occurs in 60% of the patients. Several functions of frataxin have been proposed, but none of them can fully explain why its deficiency causes the FA phenotypes nor why the most affected cell types are neurons and cardiomyocytes. It is possible that frataxin affects neural and cardiac …

Population Genomics Of The Giant Caribbean Sea Anemone Condylactis Gigantea (Anthozoa: Actiniidae) In Florida And Across The Caribbean, Nancy E. Sheridan

USF Tampa Graduate Theses and Dissertations

The giant Caribbean sea anemone Condylactis gigantea is a long-lived, conspicuous, and phenotypically diverse species native to the western Atlantic Ocean (from Bermuda to southeast Brazil), Caribbean Sea, and southeastern Gulf of Mexico. This sea anemone is an important benthic community member that provides habitat to numerous species, including cleaner shrimp. This relationship makes these animals desirable to aquarists for both enjoyment and the service provided by the shrimp for the overall health of an aquarium, and which is why they are sought.

The extraction of about 3.3 million C. gigantea individuals in Florida over a 23-year period for the …

Etiology Of Sterile Intra-Amniotic Inflammation: An Exploratory Study, Zoe M. Taylor

USF Tampa Graduate Theses and Dissertations

Preterm birth is the event of spontaneous birth prior to 37 weeks of gestation. In the United States, 1 in 10 babies are born prematurely. Low gestational age has been linked with increased morbidity and mortality. Preterm birth is multifactorial, where a myriad of contributors have been identified to include inflammation, chorioamnionitis, and inflammatory conditions to include hypertension and diabetes. To further explore the role inflammation plays in low gestational age, a literature review was done using PubMed. Two classes of inflammation quickly emerged: Pathogen born intra-amniotic inflammation and Sterile intra-amniotic inflammation. The latter form of inflammation has no identifiable …

Host-Pathogen Coevolution Between Tasmanian Devils (Sarcophilus Harrisii) And Devil Facial Tumor Disease, Dylan Garret Gallinson

USF Tampa Graduate Theses and Dissertations

Coevolution is a driving force of rapid evolution, yet the complexity of coevolutionary interactions has made it difficult to characterize the genomic basis of traits mediating such relationships. Coevolutionary dynamics are especially important in host-pathogen systems where the host and pathogen must constantly adapt to one another. The Tasmanian devil and its species-specific transmissible cancer, devil facial tumor disease (DFTD), provide the rare opportunity to study host-pathogen coevolution in a complex natural system. Extensive spatiotemporal devil sampling, high linkage disequilibrium in devils, and a large selective pressure imposed by DFTD facilitate a system tractable for study. Here, we characterized devil …