Medical Genetics Commons^™

Determinism V. Free Will & Genetic Evidence Of Addiction In Plea Bargaining And Sentence Mitigation: Conversion Of Incarceration To Probation And Rehabilitation Based On Genetic Addiction Risk Severity (Gars) Test, Kenneth Blum, Paul Mullen, Richard Green

St. Mary's Law Journal

In this Article, Dr. Kenneth Blum and his team present the case of a presently abstinent, thirty-five year old alcoholic (“AG”) who has several convictions for DWI. AG has undergone and continues to be engaged in out-patient substance abuse treatment. He entered treatment before adjudication and was mandated by the court to continue treatment to assist in maintaining sobriety. Treatment included the administration of the Genetic Addiction Risk Severity (“GARS”) Test.

AG was facing a probable five-year sentence for his fifth DWI conviction in Bexar County, Texas. However, because AG’s genetic risk results indicated a genetically induced dopamine dysfunction, hypodopaminergia, …

Methods Development In Inflammatory Bowel Disease, Andrew B. Steimke

Theses and Dissertations (ETD)

Inflammatory bowel disease (IBD) is a disease that is classified into two subtypes: ulcerative colitis (UC) and Crohn’s disease (CD). Symptoms can range from mild discomfort to requiring surgical intervention and affects approximately 1-in-200 adults in America alone, with global incidence rates increasing. While many treatments exist for IBD, perhaps the main reason for the lack of a cure is that there are many different pathogeneses that all lead to a very similar expression of symptoms. Over 240 IBD loci have been identified to date, yet the causative allele that drives the association has only been identified in ~60 of …

Identifying And Minimizing Underspecification In Breast Cancer Subtyping, Jonathan Cheuk-Kiu Tang

Master's Theses

In the realm of biomedical technology, both accuracy and consistency are crucial to the development and deployment of these tools. While accuracy is easy to measure, consistency metrics are not so simple to measure, especially in the scope of biomedicine where prediction consistency can be difficult to achieve. Typically, biomedical datasets contain a significantly larger amount of features compared to the amount of samples, which goes against ordinary data mining practices. As a result, predictive models may fail to find valid pathways for prediction during training on such datasets. This concept is known as underspecification.

Underspecification has been more accepted …

A Cloning-Free Recyclable System For Crispr-Cas9 Mediated Mutant And Reversion Construction In Candida Albicans Clinical Isolates, Amanda K. Vogel

Theses and Dissertations (ETD)

Candida albicans is a ubiquitous opportunistic fungal pathogen and one of the most prevalent causes of fungal diseases worldwide. The reference isolate SC5314 is one of the most widely used strains for both experimental and genetic studies, but it is becoming increasingly evident that genetic diversity in clinical isolates plays an important role in antifungal resistance, virulence, and pathogenicity. These recent discoveries highlight the need for genetic tools that are capable of investigating genes in multiple strain backgrounds. Here we build on the SAT1-flipper method and combine it with CRISPR-Cas9 technology to achieve cloning-free homozygous deletion in a single transformation …

North American Genetic Counselors' Approach To Collecting And Using Ancestry In Clinical Practice, Alexandra Hubbel, Elizabeth Hogan, Anne Matthews, Aaron Goldenberg

Student Scholarship

Current guidelines from the National Society of Genetic Counselors (NSGC) recommend that patients' ancestry be obtained when taking a family history. However, no study has explored how consistently genetic counselors obtain or utilize this information. The goals of this study included assessing how genetic counselors collect their patients' ancestry, what factors influence this decision, and how they view the utility of this information. Genetic counselors working in a direct patient care setting in the US or Canada were recruited to participate in an anonymous survey via an NSGC email blast. Most participants (n = 115) obtain information about their patients' …

Editorial: Epigenetics And Molecular Genetics Of Rare Tumors, Mauro Tognon, George A. Calin, Luis Del Valle

School of Medicine Faculty Publications

No abstract provided.

Should Health Systems Share Genetic Findings With At-Risk Relatives When The Proband Is Deceased? Interviews With Individuals Diagnosed With Lynch Syndrome, Jessica Ezzell Hunter, Jennifer L. Schneider, Alison J. Firemark, James V. Davis, Sara Gille, Pamala A. Pawloski, Su-Ying Liang, Victoria Schlieder, Alanna Kulchak Rahm

Journal of Patient-Centered Research and Reviews

Purpose: Genetic information has health implications for patients and their biological relatives. Death of a patient before sharing a genetic diagnosis with at-risk relatives is a missed opportunity to provide important information that could guide interventions to minimize cancer-related morbidity and mortality in relatives.

Methods: We performed semi-structured interviews with individuals diagnosed with Lynch syndrome at 1 of 4 health systems to explore their perspectives on whether health systems should share genetic risk information with relatives following a patient’s death. An inductive, open-coding approach was used to analyze audio-recorded content, with software-generated code reports undergoing iterative comparative analysis by a …

In-Depth Analysis Of Next-Generation Sequencing (Ngs) And Bioinformatics Results In Pediatric Adgrv1 Compound Heterozygotes, Sloane Clay, Adele Evans, Chindo Hicks, David Otohinoyi

Medical Student Research Poster Symposium

Genetic diagnosis of sensorineural hearing loss (SNHL) using NGS proves challenging when encountering multigenic, multiallelic variants of uncertain significance (VUS). These VUS make it difficult to provide anticipatory guidance regarding progressive disorders such as Type II Usher syndrome (SNHL at birth and retinitis pigmentosa in the second decade of life). With genetic testing companies are identifying, reporting, and reclassifying VUS at a rapid pace; there is a need for in depth-analysis and interpretation. For example, VUS in ADGRV1, a gene implicated in Type II Usher Syndrome, may be inherited in a compound heterozygous manner and misinterpreted as benign, when in …

The Fecal Position: Tracking Progressive Dna Repeat Expansion Via Stool Dna Extraction, Margaret Conrad, Hayley Ulloa, Ed Grabczyk

Medical Student Research Poster Symposium

Friedreich Ataxia is a progressive DNA repeat expansion disease. Examining DNA repeat expansion in mouse models require sacrificing the mouse and taking samples of organs. The obvious non-lethal targets, such as ears, tails, and blood do not have levels of repeat expansion comparable to internal organs. However, recent publications suggest that stool may be a suitable non-lethal candidate for tracking repeat expansion over time. Stool DNA may allow researchers to monitor the effect of interventions aimed at slowing DNA repeat expansion over time without harming the mouse. A commercial kit was first used to extract DNA from feces without success. …

Development Of Genetic Strategies To Treat Vision Loss In Usher Syndrome Type 1c (Ush1c), Dongjoon (Jason) Kim, Inga Kristaponyte, Bhagwat Alapure, Katelyn Robillard, Wadih Zein, Robert Koenekoop, Maria Reinoso, Jennifer J. Lentz

Medical Student Research Poster Symposium

Background: Usher Syndrome (Usher) is the most common genetic cause of deaf-blindness, characterized by the loss of hearing, vestibular function, and vision. Three clinical types (USH1- 3) and 10 genes are associated with the disease. USH1 is the most severe with congenital severeprofound sensorineural hearing loss and vestibular areflexia, and childhood onset of retinitis pigmentosa. Mutations in the USH1C gene account for 6-15% USH1, however USH1C c.216G>A (216A) accounts for nearly all USH1 cases in the Acadian populations in U.S. and Canada. The 216A splicing mutation results in a truncated harmonin protein, and photoreceptor and cochlear hair cell dysfunction. …

Mismatch In Mice And Men, Ryan Schroeder, Hayley Ulloa, Alan Williams, Ed Grabczyk

Medical Student Research Poster Symposium

Friedreich ataxia is a progressive degenerative neuromuscular disease that is caused by the expansion of a repetitive region of DNA, composed of three nucleotide repeats (GAA•TTC). Expansion of the DNA occurs throughout the lifespan of the patient and has been linked to the activity of specific DNA mismatch repair proteins. Disease onset occurs when the expansion increases in size beyond a certain threshold, silencing the gene and causing progressive ataxia, diabetes mellitus, and cardiomyopathy. These symptoms are linked to an increased repeat number observed within the heart, pancreas, and brain relative to other tissues within an individual. Friedreich ataxia is …

Risk Factors For Thoracic Aortic Dissection, Zhen Zhou, Alana C Cecchi, Siddharth K Prakash, Dianna M Milewicz

Journal Articles

Thoracic aortic aneurysms involving the root and/or the ascending aorta enlarge over time until an acute tear in the intimal layer leads to a highly fatal condition, an acute aortic dissection (AAD). These Stanford type A AADs, in which the tear occurs above the sinotubular junction, leading to the formation of a false lumen in the aortic wall that may extend to the arch and thoracoabdominal aorta. Type B AADs originate in the descending thoracic aorta just distal to the left subclavian artery. Genetic variants and various environmental conditions that disrupt the aortic wall integrity have been identified that increase …

Shared Brain And Genetic Architectures Between Mental Health And Physical Activity, Wei Zhang, Sarah E. Paul, Anderson M. Winkler, Ryan Bogdan, Janine D. Bijsterbosch

School of Medicine Publications and Presentations

Physical activity is correlated with, and effectively treats various forms of psychopathology. However, whether biological correlates of physical activity and psychopathology are shared remains unclear. Here, we examined the extent to which the neural and genetic architecture of physical activity and mental health are shared. Using data from the UK Biobank (N = 6389), we applied canonical correlation analysis to estimate associations between the amplitude and connectivity strength of subnetworks of three major neurocognitive networks (default mode, DMN; salience, SN; central executive networks, CEN) with accelerometer-derived measures of physical activity and self-reported mental health measures (primarily of depression, anxiety …

Interplay: The Essential Role Between Insm1 And N-Myc In Aggressive Neuroblastoma, Chiachen Chen, Michael S. Lan

School of Medicine Faculty Publications

An aggressive form of neuroblastoma (NB), a malignant childhood cancer derived from granule neuron precursors and sympathoadrenal lineage, frequently comprises MYCN amplification/elevated N-Myc expression, which contributes to the development of neural crest-derived embryonal malignancy. N-Myc is an oncogenic driver in NB. Persistent N-Myc expression during the maturation of SA precursor cells can cause blockage of the apoptosis and induce abnormal proliferation, resulting in NB development. An insulinoma-associated-1 (INSM1) zinc-finger transcription factor has emerged as an NB biomarker that plays a critical role in facilitating tumor cell growth and transformation. INSM1 plays an essential role in sympathoadrenal cell differentiation. N-Myc activates …

Association Of Methylenetetrahydrofolate Reductase Rs1801133 Genetic Variants With Type 2 Diabetes Mellitus And Diabetic Nephropathy, Aysegul Bayramoglu, Gokhan Bayramoglu, Halil Ibrahım Guler, Nezaket Coban, Mustafa Çagatay Korkmaz

Makara Journal of Health Research

Background: Type 2 diabetes mellitus (T2DM) is a complex metabolic disease with a genetic predisposition. Methylenetetrahydrofolatereductase (MTHFR) gene is one of the candidate genes associated with T2DM and diabetic nephropathy (DN). This research was carried out to determine the frequency of the C677T polymorphism (rs1801133) of the MTHFR gene and examine the role of rs1801133 polymorphism in T2DM and DN development.

Methods: DNA was obtained from peripheral blood samples (273 samples) using a DNA isolation kit. MTHFR rs1801133 polymorphism was determined using polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), and electrophoresis. PCR products were cut by …

The Genetic Contribution To Solving The Cocktail-Party Problem, Samuel R. Mathias, Emma Knowles, Josephine Mollon, Amanda Rodrigue, Mary K. Woolsey, Rene L. Olvera, Juan M. Peralta, Satish Kumar, Harald H. H. Goring, Ravi Duggirala, Joanne E. Curran, John Blangero, David C. Glahn

School of Medicine Publications and Presentations

Communicating in everyday situations requires solving the cocktail-party problem, or segregating the acoustic mixture into its constituent sounds and attending to those of most interest. Humans show dramatic variation in this ability, leading some to experience real-world problems irrespective of whether they meet criteria for clinical hearing loss. Here, we estimated the genetic contribution to cocktail-party listening by measuring speech-reception thresholds (SRTs) in 425 people from large families and ranging in age from 18 to 91 years. Roughly half the variance of SRTs was explained by genes (h 2 = 0.567). The genetic correlation between SRTs and hearing thresholds …

The Molecular Landscape Of Early-Stage Breast Cancer With Lymph Node Metastasis, Farhad Ghasemi

Electronic Thesis and Dissertation Repository

Axillary lymph nodes (ALNs) are the primary site of metastasis in breast cancer, and their involvement has implications in disease staging, prognostication, and treatment decisions. A non-invasive modality of assessing the risk of ALN metastasis can improve care in patients with early-stage breast cancer by omitting the morbidity and costs associated with axillary surgery.

This thesis explores the molecular landscape of early-stage breast cancers with ALN metastasis and shows the potential of tumour molecular signatures in predicting ALN involvement. After a systematic review of the literature, we use data from The Cancer Genome Atlas (TCGA) to develop molecular signatures correlated …

Metabolomics In Pulmonary Medicine: Extracting The Most From Your Data, Stacey N. Reinke, Romanas Chaleckis, Craig E. Wheelock

Research outputs 2022 to 2026

The metabolome enables unprecedented insight into biochemistry, providing an integrated signature of the genome, transcriptome, proteome and exposome. Measurement requires rigorous protocols combined with specialised data analysis to achieve its promise.

Mistranslating Trnas Alter The Heat Shock Activation By Hsf1, Rebecca Dib

Undergraduate Student Research Internships Conference

Translation, or the production of protein from an mRNA blueprint, is among the most fundamental processes to life as we know it. tRNAs are essential to accurate translation, as they decode the codons of mRNA and recruit corresponding amino acids. Variant tRNAs with anticodon mutations can decrease translational fidelity by recruiting the incorrect amino acid, an aberrant process known as mistranslation. When proteins are produced with incorrect amino acid sequences, they may misfold. The heat shock response functions to alleviate cellular stress caused by misfolded proteins, either by refolding or targeting misfolded proteins for degradation. Hsf1 acts as a transcriptional …

A Genome-Wide Screen Identifies Pdpk1 As A Target To Enhance The Efficacy Of Mek1/2 Inhibitors, Weijia Cai, Nicole A. Wilski, Timothy J. Purwin, Megane Vernon, Manoela Tiago, Andrew E. Aplin

Department of Cancer Biology Faculty Papers

Melanomas frequently harbor activating NRAS mutations. However, limited advance has been made in developing targeted therapy options for NRAS mutant melanoma patients. MEK inhibitors (MEKi) show modest efficacy in the clinic and their actions need to be optimized. In this study, we performed a genome-wide CRISPR-Cas9-based screen and demonstrated that loss of Phosphoinositide-dependent kinase-1 (PDPK1) enhances the efficacy of MEKi. The synergistic effects of PDPK1 loss and MEKi was validated in NRAS mutant melanoma cell lines using pharmacological and molecular approaches. Combined PDPK1 inhibitors (PDPK1i) with MEKi suppressed NRAS mutant xenograft growth and induced gasdermin E-associated pyroptosis. In an immune-competent …

Prenatal Care Providers’ Experience With Pre-Test Counselling For Nipt In Ontario: Counselling Challenges And Support Required, Leichelle A. Little

Electronic Thesis and Dissertation Repository

Non-invasive prenatal testing (NIPT) is a prenatal test that has experienced unprecedented commercial development and transformed prenatal care. The Ontario Ministry of Health presently funds NIPT as a first-tier prenatal screening option for high-risk singleton pregnancies and all twin pregnancies. Individuals who do not qualify for public funding or would like to screen for additional conditions can pay for NIPT privately, starting at approximately $495-$550 (CA) for baseline panels. Prenatal care providers such as family physicians, maternal-fetal-medicine specialists, obstetrician-gynaecologists, residents, midwives and registered nurses have an increasingly important role in offering NIPT in Ontario. Although these healthcare professionals do not …

Unlocking The Pediatric Transcriptome: A Combinatorial Approach For Total Rna Analysis, William Schleif

All Dissertations

The transcriptome is an oft-studied target in the pursuit to better understand the functional elements of the human genome as part of genomic research. The transcriptome possesses its own unique set of challenges that hamper utilization of RNA-based discoveries and translation into actionable findings. Scientific progress thus far has expanded annotated reference genes for protein-coding and non-coding (nc) regulatory transcripts, yet much of the variation from splicing events or retention of other regions remain an open challenge, especially in children. This dissertation explores the current state of diagnostic and methodological barriers in front of the full unlocking of the transcriptome, …

Weight Maintenance, A Prognostic Factor That Mediates The Incidence Of Dementia: From Genetics To Etiologies, Sunny Chen

All Dissertations

Objectives: Alzheimer’s disease-related dementia is a devastating neurodegenerative disease that affects millions of people. The goal of this work is to investigate biological mechanisms such as weight loss and mitochondrial function that can serve as prognostic factors for dementia, healthy aging, and longevity.

Methodologies: This work consists of two separate systematic literature reviews, and an investigational study. The first review examined existing studies on weight trends in dementia. The second review investigated the role of mitochondria and its associated gene TOMM40 in aging. The third paper included a nested case control analysis of weight change patterns before and …

Genetics And Genomics Education Among Physician Assistants, Wesley Patterson

All Dissertations

This dissertation comprises five chapters to describe genetics and genomics education among physician assistant/associate (PA) students and practicing PAs. Chapter I introduces the gap in supply and demand of genetic services, the need for non-genetics healthcare providers to fill the gap, and the PA profession as a solution.

Chapter II is a rapid literature review that summarizes the available literature regarding genetics and genomics education for PAs. A paucity of literature exists to describe the current state of PA genetics-genomics education. The few studies retrieved describe content being taught in PA programs, the number of genetics-genomics contact hours PA students …

Lower Sars-Cov-2 Seroprevalence Among Cancer Patients In Sub-Saharan Africa, For Yue Tso, Salum J. Lidenge, John R. Ngowi, Phoebe B. Peña, Ashley A. Clegg, Owen Ngalamika, Chacha J. Mwita, Julius Mwaiselage, Charles Wood

School of Medicine Faculty Publications

Background: Despite the high COVID-19 morbidity and mortality rates across the world, the reported rates in sub-Saharan Africa (SSA), which has a higher burden of other infectious diseases and overwhelmed healthcare systems, remain relatively low. This study aims to better understand the potential factors that contribute to this phenomenon, especially among cancer patients who are considered as a high-risk group for developing severe COVID-19. Methods: Plasma samples collected during the COVID-19 pandemic from SARS-CoV-2 unvaccinated cancer and potential blood donor populations were analyzed for SARS-CoV-2 (spike and nucleocapsid proteins) antibodies by an immunofluorescence assay. The relationships between SARS-CoV-2 seroprevalences and …

Structural Basis For The Simultaneous Recognition Of Nemo And Acceptor Ubiquitin By The Hoip Nzf1 Domain, Simin Rahighi, Mamta Iyer, Hamid Oveisi, Sammy Nasser, Vincent Duong

Pharmacy Faculty Articles and Research

Ubiquitination of NEMO by the linear ubiquitin chain assembly complex (LUBAC) is essential for activating the canonical NF-κB signaling pathway. While the NZF1 domain of the HOIP subunit of LUBAC recognizes the NEMO substrate, it is unclear how it cooperates with the catalytic domains in the ubiquitination process. Here, we report a crystal structure of NEMO in complex with HOIP NZF1 and linear diubiquitin chains, in which the two proteins bind to distinct sites on NEMO. Moreover, the NZF1 domain simultaneously interacts with NEMO and Ile44 surface of a proximal ubiquitin from a linear diubiquitin chain, where the C-term tail …

Identification Of Healthspan-Promoting Genes In Caenorhabditis Elegans Based On A Human Gwas Study, Nadine Saul, Ineke Dhondt, Mikko Kuokkanen, Markus Perola, Clara Verschuuren, Brecht Wouters, Henrik Von Chrzanowski, Winnok H. De Vos, Liesbet Temmerman, Walter Luyten

School of Medicine Publications and Presentations

To find drivers of healthy ageing, a genome-wide association study (GWAS) was performed in healthy and unhealthy older individuals. Healthy individuals were defined as free from cardiovascular disease, stroke, heart failure, major adverse cardiovascular event, diabetes, dementia, cancer, chronic obstructive pulmonary disease (COPD), asthma, rheumatism, Crohn’s disease, malabsorption or kidney disease. Six single nucleotide polymorphisms (SNPs) with unknown function associated with ten human genes were identified as candidate healthspan markers. Thirteen homologous or closely related genes were selected in the model organism C. elegans for evaluating healthspan after targeted RNAi-mediated knockdown using pathogen resistance, muscle integrity, chemotaxis index and the …

Channelopathy Of Small- And Intermediate-Conductance Ca2+-Activated K+ Channels, Young-Woo Nam, Myles Downey, Mohammad Asikur Rahman, Meng Cui, Miao Zhang

Pharmacy Faculty Articles and Research

Small- and intermediate-conductance Ca²⁺-activated K⁺ (K_Ca2.x/K_Ca3.1 also called SK/IK) channels are gated exclusively by intracellular Ca²⁺. The Ca²⁺ binding protein calmodulin confers sub-micromolar Ca²⁺ sensitivity to the channel-calmodulin complex. The calmodulin C-lobe is constitutively associated with the proximal C-terminus of the channel. Interactions between calmodulin N-lobe and the channel S4-S5 linker are Ca²⁺-dependent, which subsequently trigger conformational changes in the channel pore and open the gate. KCNN genes encode four subtypes, including KCNN1 for K_Ca2.1 (SK1), KCNN2 for K_Ca2.2 (SK2), KCNN3 for K …

Genomic Features Underlie The Co-Option Of Sva Transposons As Cis-Regulatory Elements In Human Pluripotent Stem Cells, Samantha M Barnada, Andrew Isopi, Daniela Tejada-Martinez, Clément Goubert, Sruti Patoori, Luca Pagliaroli, Mason Tracewell, Marco Trizzino

Department of Biochemistry and Molecular Biology Faculty Papers

Domestication of transposable elements (TEs) into functional cis-regulatory elements is a widespread phenomenon. However, the mechanisms behind why some TEs are co-opted as functional enhancers while others are not are underappreciated. SINE-VNTR-Alus (SVAs) are the youngest group of transposons in the human genome, where ~3,700 copies are annotated, nearly half of which are human-specific. Many studies indicate that SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such processes have not yet been thoroughly investigated. Here, we leveraged CRISPR-interference (CRISPRi), computational and functional genomics to elucidate the genomic features that underlie SVA domestication …

Epigenetic Mechanisms Influencing Therapeutic Response In Breast Cancer., Amaia Arruabarrena-Aristorena, Eneda Toska

Kimmel Cancer Center Faculty Papers

The majority of breast cancers are estrogen receptor (ER)+ and agents targeting the ER signaling pathway have markedly increased survival for women with breast cancer for decades. However, therapeutic resistance eventually emerges, especially in the metastatic setting. In the past decade disrupted epigenetic regulatory processes have emerged as major contributors to carcinogenesis in many cancer types. Aberrations in chromatin modifiers and transcription factors have also been recognized as mediators of breast cancer development and therapeutic outcome, and new epigenetic-based therapies in combination with targeted therapies have been proposed. Here we will discuss recent progress in our understanding of the chromatin-based …