Genetics and Genomics Commons^™

The Psychosocial Effects Of Next Generation Sequence Panels For Predictive Testing Of Hereditary Dementias, Dina Green

Human Genetics Theses

The current standard of care in offering predictive genetic testing for neurodegenerative diseases is that individuals wishing to have testing must have a known family mutation or well-documented family history of a specific disease. This model denies testing to individuals in families where the phenotype of the disease is less clear. However, NGS panel testing for many genes with overlapping phenotypes helps alleviate both the cost and tedious nature of a genetic “fishing expedition.” Panel testing increases the risk of receiving variants of unknown significance and, therefore, uncertainty. The goal of this research study is to examine the psychological impact …

Genetic Counselors’ Assessment Of Videos To Augment Whole Exome Sequencing Patient Education, Rebecca Hernan

Human Genetics Theses

Patient education for basic genetics as well as genetic testing options is a key role of a genetic counselor (GC). As whole exome sequencing (WES) becomes more commonly used in clinical care, an increased burden of genetic education is placed on both the GC and the patient due to the complexity of this test. One method to help alleviate this burden is the use of educational tools, these tools need to be assessed for their efficacy. There is a lack of research eliciting GCs’ opinion of educational tools intended for WES. The parents of minor patients evaluated at Columbia University …

Knowledge And Attitudes After Using Videos To Educate A Non-Clinical Cohort About Prenatal Cell-Free Dna Screening, Teresa Cacchione, Safa Yusuf

Human Genetics Theses

Prenatal cell-free DNA (cfDNA) screening is now offered to pregnant women of all risk categories, creating a challenge in providing informed decision-making on a broad scale. Resources to support patient education, such as short educational videos, have been created to help ameliorate this issue but have not been formally evaluated. Thus, we sought to investigate the utility of videos in educating women about prenatal cfDNA screening and whether there were differences in knowledge and/or attitudes after viewing a video created by a non-profit genetics organization (Video A) versus a similar video created by a commercial testing company (Video B). Participants …

Adolescent Perspectives On Genetic Testing For Adult Onset Conditions, Olivia D’Accordo, Erin Davidson, Christina Miller, Yael Weinstein

Human Genetics Theses

The American Society of Human Genetics (ASHG) recommends that testing for adult onset conditions be deferred until adulthood because of the potential for psychological harm combined with lack of medical utility. ASHG’s 2016 DNA Day Essay Contest asked 9- 12th graders to defend or refute this position. 1241 essays were submitted. 572 students defended ASHG’s position statement, while 554 argued against. Essays that addressed Alzheimer’s disease (AD) and BRCA-related Hereditary Breast and Ovarian Cancer syndrome were qualitatively analyzed for themes related to the argued position. 64.4% of students argued for deferred testing of AD, and 46.1% of students argued for …

Dna Unicorn: An N-Of-1 Community Advocacy Resource, Allison Knickle, Taylor Laut, Kari Magnussen, Marianne Vivien

Human Genetics Theses

With the wider use of genetic testing, an increasing number of people are receiving molecular diagnoses of ultra-rare or N-of-1 diseases. The medical and psychosocial challenges of these individuals are compounded by a lack of support and advice from disease-specific communities. A website ( www.dnaunicorn.org) was developed to help N-of-1 families connect with caregivers, researchers, and patients with the same or related medical conditions. The site provides directions and links to resources to facilitate data-sharing through access to databases, and aids in the construction of social media campaigns to connect genotypically- or phenotypically-related patients and families to each other. Furthermore, …

A Retrospective Chart Review Examining The Clinical Utility Of Family Health History, Katherine Dao, Julia Russo

Human Genetics Theses

Family health history (FHH) is a simple and cost-effective clinical tool widely used by genetic professionals. Although the value of FHH for assessing personal and familial health and reproductive risk within a prenatal population has been demonstrated in past studies, its utility within a genetic carrier screening population has not been evaluated. The purpose of this study was to examine the utility of FHH as a clinical screening tool and explore the general outcomes of full FHH evaluations within an expanded carrier screening (ECS) population. A retrospective chart review was conducted for 500 consults, which included 3-generation pedigrees, using data …

Quality Of Life And Psychosocial Impacts Of Persons With A Genetic Predisposition To Thoracic Aortic Dissections Or Aortic Aneurysms, Megan Soucy, Amelia Tahmassi, Nathan Hassel

Human Genetics Theses

BACKGROUND: Thoracic aortic dissections (TAD) and thoracic aortic aneurysms (TAA) can cause significant disabilities and premature sudden deaths. Modern advances in medicine and technology have increased the life expectancy for survivors of TAD or TAA; however, limited studies have measured the quality of life of affected individuals, especially those with genetically triggered aortic diseases. The National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) measured the Health Related Quality of Life (HRQoL) in survivors of a TAD or TAA. Another area of impact on quality of life includes depression. One accurate measurement for depression is the 16-item …

Genetic Counselor Drift: Exploring Contributors To The Recent Growth Of Non-Clinical Genetic Counseling Positions And The Resulting Impact On The Profession., Maki Kaneko, Robert Rigobello

Human Genetics Theses

No abstract provided.

Effects Of Nicotine On The Cyp6a8 Gene Promoter Of Drosophila Melanogaster, Leslie M. Stroud

Chancellor’s Honors Program Projects

No abstract provided.

Characterization Of Myod And Myf5 Double-Knockout Muscle Stem Cells During Muscle Development, Andreea Dinicu

University Scholar Projects

MyoD and Myf5 are transcription factors that regulate myogenesis by promoting satellite cell transcription. The two genes are known to display functional redundancy. Both genes are considered myogenic determination genes and are expressed in satellite cells. The fate of myogenic precursors in the absence of both MyoD and Myf5 remains largely unknown. We aimed to begin attaining this knowledge as part of this project. We utilized a CreLoxP system to control the expression of MyoD in mice lacking Myf5. MyoD was knocked out at embryonic day (E) 11.5 during myogenesis. Limbs were collected from experimental mice following tamoxifen injection. …

Role Of Ime4 And Pho92 Proteins In Pho5 Regulation, Krishna Shah

Senior Honors Theses

In the yeast Saccharomyces cerevisiae, m6A methylation regulates the stability and translation of mRNA. Ime4, which is highly active in meiotic cells, recognizes consensus methyl sites in pre-mRNA and adds methyl groups to a small fraction of adenosine residues, whereas Pho92 binds to such methylated sites and promotes subsequent degradation. PHO5 transcripts expression is upregulated when IME4 and PHO92 are deleted. In the PHO5 transcript, near the stop codon of the open reading frame (ORF), there is a potential consensus methyl site that is predicted to be methylated, based on its location and excellent match to the consensus methylation sequence …

Transcriptomic Effects Of Dispersed Oil In A Non-Model Decapod Crustacean, Hernan Vazquez-Miranda, Brent Thoma, Juliet Wong, Darryl Felder, Keith A. Crandall, Heather Bracken-Grissom

Computational Biology Institute

Background. Oil spills are major environmental disasters. Dispersants help control spills, as they emulsify oil into droplets to speed bioremediation. Although dispersant toxicity is controversial, the genetic consequences and damages of dispersed oil exposure are poorly understood. We used RNA-seq to measure gene expression of flatback mudcrabs (Eurypanopeus depressus, Decapoda, Brachyura, Panopeidae) exposed to dispersed oil.

Methods. Our experimental design included two control types, oil-only, and oil-dispersant treatments with three replicates each. We prepared 100 base pair-ended libraries from total RNA and sequenced them in one Illumina HiSeq2000 lane. We assembled a reference transcriptome with all replicates per treatment, …

Denoising Tandem Mass Spectrometry Data, Felix Offei

Electronic Theses and Dissertations

Protein identification using tandem mass spectrometry (MS/MS) has proven to be an effective way to identify proteins in a biological sample. An observed spectrum is constructed from the data produced by the tandem mass spectrometer. A protein can be identified if the observed spectrum aligns with the theoretical spectrum. However, data generated by the tandem mass spectrometer are affected by errors thus making protein identification challenging in the field of proteomics. Some of these errors include wrong calibration of the instrument, instrument distortion and noise. In this thesis, we present a pre-processing method, which focuses on the removal of noisy …

Investigating The Genetic Basis For Hominoid Taillessness, Samantha M. Tickey-Mccrane, Holly Dunsworth, Johanna E. Wegener

Senior Honors Projects

Investigating the Genetic Basis for Hominoid Taillessness:

A Comparative Genetic Approach Across Ten Catarrhine Taxa

Samantha Tickey-McCrane1,2, Johanna E. Wegener2, and Holly Dunsworth1

Honors Thesis Abstract Written by Samantha Tickey-McCrane, Departments of Anthropology & Biology

Advisor: Dr. Holly Dunsworth, Department of Anthropology

How did hominoid tail loss occur? My goals are to test phylogenetic and adaptive hypotheses for tail length variation among macaques, and use those insights to reconstruct the evolution of hominoid taillessness. Further, I aim to ultimately uncover which candidate genes or pathways may be responsible for catarrhine tail loss, and what other traits may be affected by …

Science, Between The Lines: Rosalind Franklin, Rachael Renzi

Senior Honors Projects

The purpose of this paper is to contrast scientific rhetoric with creative biographical writing style. Both forms of communication rely on specific syntax and styles to describe research findings to the appropriate audiences, but the often passive format of scientific literature excludes the passionate reasonings of the researcher. In order to understand why the scientist is kept separate from his or her published findings, I am going to experiment with the two contrasting forms. Throughout the paper, each form will be tested and used at varying levels. Both scientific and creative writing will be mixed. To emphasize the technically dense …

A Leishmania Secretion System For The Expression Of Major Ampullate Spidroin Mimics, Todd A. Lyda, Elizabeth L. Wagner, Andre X. Bourg, Congyue Peng, Golnaz Najaf Tomaraei, Delphine Dean, Marian S. Kennedy, William R. Marcotte Jr.

Publications

Spider major ampullate silk fibers have been shown to display a unique combination of relatively high fracture strength and toughness compared to other fibers and show potential for tissue engineering scaffolds. While it is not possible to mass produce native spider silks, the potential ability to produce fibers from recombinant spider silk fibers could allow for an increased innovation rate within tissue engineering and regenerative medicine. In this pilot study, we improved upon a prior fabrication route by both changing the expression host and additives to the fiber pulling precursor solution to improve the performance of fibers. The new expression …

Non-Coding Rnas Identify The Intrinsic Molecular Subtypes Of Muscle-Invasive Bladder Cancer, Andrea E. Ochoa

Dissertations & Theses (Open Access)

NON-CODING RNAS IDENTIFY THE INTRINSIC MOLECULAR SUBTYPES OF MUSCLE-INVASIVE BLADDER CANCER

Andrea Elizabeth Ochoa, B.S.

Advisory Professors: David J. McConkey, Ph.D. and Joya Chandra, Ph.D.

There has been a recent explosion of genomics data in muscle-invasive bladder cancer (MIBC) to better understand the underlying biology of the disease that leads to the high amount of heterogeneity that is seen clinically. These studies have identified relatively stable intrinsic molecular subtypes of MIBC that show similarities to the basal and luminal subtypes of breast cancer. However, previous studies have primarily focused on protein-coding genes or DNA mutations/alterations.

There is emerging evidence implicating …

Genetic Polymorphisms Of The Glucocorticoid Receptor And Interleukin-8 Receptor Genes Are Related To Production Traits And Hair Coat Score In Crossbred Cattle, Avery Deaton

Animal Science Undergraduate Honors Theses

The objective of this thesis was to identify polymorphisms in the glucocorticoid receptor (GR) and interleukin-8 receptor (CXCR2) genes and to associate genotypes between the above mentioned polymorphisms and production traits in crossbred cattle. The hypothesis was that polymorphisms will exist for GR and CXCR2 genes and will be linked to production traits. Glucocorticoid receptors have been positively associated with higher milk yields, lactose content, feed intake, and feed conversion rates. Interleukin-8 genes are part of the innate immune response and help with many aspects of female reproduction health, such as protecting the embryo from the maternal immune system during …

Processes On The Emergent Landscapes Of Biochemical Reaction Networks And Heterogeneous Cell Population Dynamics: Differentiation In Living Matters., Sui Huang, Fangting Li, Joseph X Zhou, Hong Qian

Articles, Abstracts, and Reports

The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat. The theory is equally applicable not only to …

Combining Inferred Regulatory And Reconstructed Metabolic Networks Enhances Phenotype Prediction In Yeast., Zhuo Wang, Samuel A Danziger, Benjamin D Heavner, Shuyi Ma, Jennifer J Smith, Song Li, Thurston Herricks, Evangelos Simeonidis, Nitin Baliga, John D Aitchison, Nathan D Price

Articles, Abstracts, and Reports

Gene regulatory and metabolic network models have been used successfully in many organisms, but inherent differences between them make networks difficult to integrate. Probabilistic Regulation Of Metabolism (PROM) provides a partial solution, but it does not incorporate network inference and underperforms in eukaryotes. We present an Integrated Deduced And Metabolism (IDREAM) method that combines statistically inferred Environment and Gene Regulatory Influence Network (EGRIN) models with the PROM framework to create enhanced metabolic-regulatory network models. We used IDREAM to predict phenotypes and genetic interactions between transcription factors and genes encoding metabolic activities in the eukaryote, Saccharomyces cerevisiae. IDREAM models contain many …