Robust Meta-Analysis For Large-Scale Genomic Experiments Based On An Empirical Approach, 2022 Old Dominion University
Robust Meta-Analysis For Large-Scale Genomic Experiments Based On An Empirical Approach, Sinjini Sikdar
Mathematics & Statistics Faculty Publications
BACKGROUND: Recent high-throughput technologies have opened avenues for simultaneous analyses of thousands of genes. With the availability of a multitude of public databases, one can easily access multiple genomic study results where each study comprises of significance testing results of thousands of genes. Researchers currently tend to combine this genomic information from these multiple studies in the form of a meta-analysis. As the number of genes involved is very large, the classical meta-analysis approaches need to be updated to acknowledge this large-scale aspect of the data.
METHODS: In this article, we discuss how application of standard theoretical null distributional assumptions …
Plasmonic-Based Biosensor For The Early Diagnosis Of Prostate Cancer, 2022 Old Dominion University
Plasmonic-Based Biosensor For The Early Diagnosis Of Prostate Cancer, Thakshila Liyanage, Bayan Alharbi, Linh Quan, Aurora Esquela-Kerscher, Gymama Slaughter
A tapered optical fiber (TOF) plasmonic biosensor was fabricated and used for the sensitive detection of a panel of microRNAs (miRNAs) in human serum obtained from noncancer and prostate cancer (PCa) patients. Oncogenic and tumor suppressor miRNAs let7a, let-7c, miR-200b, miR-141, and miR-21 were tested as predictive cancer biomarkers since multianalyte detection minimizes false-positive and false-negative rates and establishes a strong foundation for early PCa diagnosis. The biosensing platform integrates metallic gold triangular nanoprisms (AuTNPs) laminated on the TOF to excite surface plasmon waves in the supporting metallic layer and enhance the evanescent mode of the fiber surface. …
Extracellular Mechanotransduction, 2022 University of Nebraska Medical Center
Extracellular Mechanotransduction, Stephen J. Haller, Andrew T. Dudley
Journal Articles: Genetics, Cell Biology & Anatomy
We highlight the force-sensing function of extracellular matrix and present a complementary mechanotransduction paradigm.
Reduction Of Plasmid Vector Backbone Length Enhances Reporter Gene Expression, 2022 Old Dominion University
Reduction Of Plasmid Vector Backbone Length Enhances Reporter Gene Expression, Carly Boye, Sezgi Arpag, Michael Francis, Scott Declemente, Aislin West, Richard Heller, Anna Bulysheva
Electrical & Computer Engineering Faculty Publications
Gene therapy has a wide range of applications for various types of pathologies. Viral methods of gene delivery provide high levels of gene expression but have various safety concerns. Non-viral methods are largely known to provide lower levels of expression. We aim to address this issue by using plasmid DNA with smaller backbones to increase gene expression levels when delivered using non-viral methods. In this study we compare gene expression levels between two vectors with firefly luciferase encoding gene insert using liposome complexes and gene electrotransfer as delivery methods. A 2-fold reduction in plasmid vector backbone size, disproportionately enhanced gene …
Applications Of Genetic Testing For Endocrine And Metabolic Disorders, 2021 The University of Western Ontario
Applications Of Genetic Testing For Endocrine And Metabolic Disorders, Amanda Berberich
Electronic Thesis and Dissertation Repository
Knowledge of inherited diseases and the ability to rapidly, efficiently and comprehensively perform genetic testing are advancing steadily. However, the ideal approach to translate this ability into clinical applications for endocrine disorders has yet to be determined. This work focuses on aspects of clinically translating knowledge of select heritable endocrine and metabolic conditions.
For maturity onset diabetes of the young (MODY), a monogenic disorder with no current consensus guidelines governing testing procedures, this work addresses methods to improve detection by validating the use of next generation sequencing-based techniques to identify MODY cases and to detect copy number variations.
For very …
Identifying The Molecular Cause Of Extreme Endoplasmic Reticulum Dilation In Pediatric Osteosarcoma And Its Relationship To The Disease, 2021 University of Tennessee Health Science Center
Identifying The Molecular Cause Of Extreme Endoplasmic Reticulum Dilation In Pediatric Osteosarcoma And Its Relationship To The Disease, Rachael Wood
Theses and Dissertations (ETD)
Pediatric osteosarcoma tumors are characterized by an unusual abundance of grossly dilated endoplasmic reticulum and an immense genomic instability that has complicated identifying new effective molecular therapeutic targets. Here we report a novel molecular signature that encompasses the majority of 108 patient tumor samples, PDXs and osteosarcoma cell lines. These tumors exhibit reduced expression of four critical COPII vesicle proteins that has resulted in the accumulation of procollagen-I protein within ‘hallmark’ dilated ER. Using CRISPR activation technology, increased expression of only SAR1A and SEC24D to physiologically normal levels was sufficient to restore both collagen-I secretion and resolve dilated ER morphology …
Nitrous Oxide Adaptation On Gene Expression In Breast Cancer Cells, 2021 Nova Southeastern University
Nitrous Oxide Adaptation On Gene Expression In Breast Cancer Cells, Harsh Chheda, Estevan Ruiz Limón López, Zainab Mahmood, Ankit Sharma, Tina Tran, Uzma Abdulbaseer, Farouk Alshatti, James A. Radosevich
Chemistry and Physics Faculty Proceedings, Presentations, Speeches, Lectures
Hypothesis and Objective: Genes participating in the notch signaling pathway are influenced by exposure to high nitrous oxide (HNO) levels. Notch signaling pathway genes are responsible for regulating cell fate, differentiation, and apoptosis. Dysregulation of these genes can contribute to tumorigenesis. Alterations in the expression of these genes in MCF7 breast cancer cells could help determine the effects of the notch signaling pathway on tumorigenesis as a result of exposure to nitrous oxide.
Methods: Samples of cDNA from MCF7 and MCF7-HNO cells were used in DNA microarray analysis. Qualifying genes of interest provided a p value < .05. Differentially expressed genes (DEGs) were defined and categorized using the Gene Oncology Uniprot (GO) Molecular Function database. These cells were further analyzed using a proprietary bioinformatics analysis created by our laboratory.
Results: Exposure to HNO …
Role Of Smad2 And Smad3 On Adipose Tissue Development And Function, 2021 University of Tennessee Health Science Center
Role Of Smad2 And Smad3 On Adipose Tissue Development And Function, Roshan Kumari
Theses and Dissertations (ETD)
Introduction: Obesity and its associated metabolic syndrome are major medical problems worldwide including United States. Adipose tissue is the primary site of energy storage, playing important roles in health. Adipose tissue also has other critical functions, producing adipocytokines and contributing to normal nutrient metabolism, which in turn play important roles in satiety, inflammation, and total energy homeostasis. Activin A and activin B play important roles in maintaining body composition and energy homeostasis. This dissertation highlights the role of activin/SMADs signaling in adipose tissue development, function, and maintenance.
SMAD2/3 proteins are downstream mediators of transforming growth factor-β (TGFβ) family signaling, including …
Comparing Empirical Kinship Derived Heritability For Imaging Genetics Traits In The Uk Biobank And Human Connectome Project, 2021 The University of Texas Rio Grande Valley
Comparing Empirical Kinship Derived Heritability For Imaging Genetics Traits In The Uk Biobank And Human Connectome Project, Si Gao, Brian Donohue, Kathryn S. Hatch, Shuo Chen, Tianzhou Ma, Yizhou Ma, Mark D. Kvarta, Bhim M. Adhikari, Neda Jahanshad, John Blangero
School of Medicine Publications and Presentations
Imaging genetics analyses use neuroimaging traits as intermediate phenotypes to infer the degree of genetic contribution to brain structure and function in health and/or illness. Coefficients of relatedness (CR) summarize the degree of genetic similarity among subjects and are used to estimate the heritability – the proportion of phenotypic variance explained by genetic factors. The CR can be inferred directly from genome-wide genotype data to explain the degree of shared variation in common genetic polymorphisms (SNP-heritability) among related or unrelated subjects. We developed a central processing and graphics processing unit (CPU and GPU) accelerated Fast and Powerful Heritability Inference …
The Ratio Method: Addressing Complex Tort Liability In The Fourth Industrial Revolution, 2021 UCLA School of Law
The Ratio Method: Addressing Complex Tort Liability In The Fourth Industrial Revolution, Harrison C. Margolin, Grant H. Frazier
St. Mary's Law Journal
Emerging technologies of the Fourth Industrial Revolution show fundamental promise for improving productivity and quality of life, though their misuse may also cause significant social disruption. For example, while artificial intelligence will be used to accelerate society’s processes, it may also displace millions of workers and arm cybercriminals with increasingly powerful hacking capabilities. Similarly, human gene editing shows promise for curing numerous diseases, but also raises significant concerns about adverse health consequences related to the corruption of human and pathogenic genomes.
In most instances, only specialists understand the growing intricacies of these novel technologies. As the complexity and speed of …
Asymptomatic Covid-19 On Lsuhsc’S Campus: Antibodies, Pcr Tests, And Variants, 2021 LSU Health Sciences Center- New Orleans
Asymptomatic Covid-19 On Lsuhsc’S Campus: Antibodies, Pcr Tests, And Variants, Mallory K. Varnado, San Chu, Caroline Duncan, Ron Horswell, Lucio Miele, Judy Crabtree
Medical Research Day
Background: Rapid spreading of the highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic of coronavirus disease 2019 (COVID- 19) which has infected 188,128,952 people and resulted in 4,059,339 deaths worldwide (WHO COVID-19 Dashboard). Despite profound disease prevention measures and recent attempts at widespread vaccination, the virus continues to mutate and infect new people each day. Objective: The goal of this study is to analyze the data collected from the COVID-19 screening and testing program at LSUHSC-New Orleans. This includes antibody testing data, exposure and symptom questionnaires, PCR viral testing, and viral RNA sequencing data from deidentified, …
The Heart Of The Matter: Cardiac Specific Discrepancies Between Human And Mouse Models Of Friedreich Ataxia, 2021 LSU Health Sciences Center- New Orleans
The Heart Of The Matter: Cardiac Specific Discrepancies Between Human And Mouse Models Of Friedreich Ataxia, Katherine Copenhaver, Ed Grabczyk
Medical Research Day
Friedreich Ataxia (FRDA) is a relentlessly progressive neurodegenerative disease that manifests with multiple symptoms, which may include progressive gait and limb ataxia, loss of vibratory and position sense, progressive motor weakness, diabetes mellitus, and scoliosis. This condition also affects the heart, and hypertrophic cardiomyopathy is the cause of death in approximately 60% of patients. FRDA is a DNA repeat disorder, caused by the somatic expansion of GAA•TTC repeats within the first intron of the frataxin (FXN) gene. This leads to decreased FXN mRNA expression. The length of the repeat tract correlates with the severity of FRDA symptoms and inversely with …
Integrating Patient-Reported Outcomes Into Clinical Genetic Testing For Familial Hypercholesterolemia, 2021 Harvard Pilgrim Health Care Institute and Harvard Medical School
Integrating Patient-Reported Outcomes Into Clinical Genetic Testing For Familial Hypercholesterolemia, Rachele M. Hendricks-Sturrup, Robert Block, Christine Y. Lu
Journal of Patient-Centered Research and Reviews
Patient-reported outcomes (PROs) and PRO measures (PROMs) are often used to help clinicians and researchers understand patients’ personal concerns, feelings, experiences, and perspectives following the implementation of an intervention. Notably, PROs and PROMs can inform health systems, health policy, and payers on the utility of clinical genetic testing based on each patient’s personal values, perspectives, and potential health behaviors subsequent to testing. In this topic synopsis, we discuss the underexplored role of and implications for PROs and PROMs following genetic testing for familial hypercholesterolemia (FH), an autosomal dominant genetic disorder of cholesterol metabolism that can lead to highly premature fatal …
Collagen-Based Biomaterials With Possible Therapeutic Effects, 2021 CRAIOVA UNIVERSITY OF MEDICINE AND PHARMACY, DEPARTMENT OF PEDIATRICS, CRAIOVA, ROMANIA
Collagen-Based Biomaterials With Possible Therapeutic Effects, Ramona Mihaela Nedelcuţă, Gigi Călin, Mihai Cristian Nedelcuţă, Vlad Dumitru Baleanu, Dragos Virgil Davitoiu, Bogdan Socea, Bogdan-Petre Stănoiu
Journal of Mind and Medical Sciences
Epidermolysis bullosa (EB) is a rare, serious genetic disease, incurable through the current means. Apart from this initial definition, there was later some ease in the definition of the disease, including the manifestations of toxic epidermal necrolysis and Stevens Johnson syndrome in this entity. In medical practice, there are cases that do not overlap with the description in the literature, thus the treatment must be adapted and personalized to the particularities. We present the case of a female new-born, with "de novo" mutation for the early-onset antenatal epidermolysis and our personalized therapeutic management, based on collagen from bovine corneas by …
How Opportune Is Multigene Testing In Metastatic Colorectal Cancer? A Review, 2021 CAROL DAVILA UNIVERSITY OF MEDICINE AND PHARMACY, FACULTY OF GENERAL MEDICINE, DEPARTMENT OF ONCOLOGY, BUCHAREST, ROMANIA
How Opportune Is Multigene Testing In Metastatic Colorectal Cancer? A Review, Cristina Orlov-Slavu, Andreea Parosanu, Mihaela Olaru, Dragos Serban, Ioana Paunica, Cornelia Nitipir
Journal of Mind and Medical Sciences
Personalized treatment in oncology is the most innovative method of care. The best method to establish personalized treatment is by genetic characterization of the malignant cell.
Theoretically, the more detailed the characterization, the more effective the choice of treatment becomes. Currently, there are fast and relatively low-cost options that allow such genetic characterization. However, test results sometimes do not detect targetable alterations and, even if they do detect, the use of the treatment-alteration combination does not always generate a satisfactory oncological response.
The present paper aims to answer two questions. First, how targetable can the most common gene alterations in …
Rare Variants In Kdr, Encoding Vegf Receptor 2, Are Associated With Tetralogy Of Fallot., 2021 Children's Mercy Hospital
Rare Variants In Kdr, Encoding Vegf Receptor 2, Are Associated With Tetralogy Of Fallot., Doris Škorić-Milosavljević, Najim Lahrouchi, Fernanda M. Bosada, Gregor Dombrowsky, Simon G. Williams, Robert Lesurf, Fleur V Y Tjong, Roddy Walsh, Ihssane El Bouchikhi, Jeroen Breckpot, Enrique Audain, Aho Ilgun, Leander Beekman, Ilham Ratbi, Alanna Strong, Maximilian Muenke, Solveig Heide, Alison M. Muir, Mariam Hababa, Laura A. Cross, Dihong Zhou, T Pastinen, German Competence Network For Congenital Heart Defects, Elaine Zackai, Samir Atmani, Karim Ouldim, Najlae Adadi, Katharina Steindl, Anita Rauch, David Brook, Anna Wilsdon, Irene Kuipers, Nico A. Blom, Barbara J. Mulder, Heather C. Mefford, Boris Keren, Pascal Joset, Paul Kruszka, Isabelle Thiffault, Sarah E. Sheppard, Amy Roberts, Elisabeth M. Lodder, Bernard D. Keavney, Sally-Ann B. Clur, Seema Mital, Marc-Philip Hitz, Vincent M. Christoffels, Alex V. Postma, Connie R. Bezzina
Manuscripts, Articles, Book Chapters and Other Papers
Purpose: Rare genetic variants in KDR, encoding the vascular endothelial growth factor receptor 2 (VEGFR2), have been reported in patients with tetralogy of Fallot (TOF). However, their role in disease causality and pathogenesis remains unclear.
Methods: We conducted exome sequencing in a familial case of TOF and large-scale genetic studies, including burden testing, in >1,500 patients with TOF. We studied gene-targeted mice and conducted cell-based assays to explore the role of KDR genetic variation in the etiology of TOF.
Results: Exome sequencing in a family with two siblings affected by TOF revealed biallelic missense variants in KDR. Studies in knock-in …
Effects Of Hormone Replacement Therapy (Hrt) On Gene Expression In The Amyloid Processing Pathway Of Ovariectomized Rhesus Macaque Females Under An Obesogenic Diet, 2021 Portland State University
Effects Of Hormone Replacement Therapy (Hrt) On Gene Expression In The Amyloid Processing Pathway Of Ovariectomized Rhesus Macaque Females Under An Obesogenic Diet, Megan Ball
University Honors Theses
Estrogens rapidly decline at the onset of menopause, putting women at higher risk of osteoporosis, obesity, and neurodegenerative diseases, including Alzheimer’s disease (AD). Estradiol hormone therapies (HT) have been suggested to limit these negative effects on women, with controversial findings as to their effectiveness. A study at OHSU recently found differentially expressed genes (DEGs) using RNAseq between ovariectomized/hysterectomized (OvH) old (range = 19.4–23.2 years) female rhesus macaques on HT and those on a placebo on chronic western style diet (WSD). The DEGs identified in the amyloid processing pathway of the amygdala were selected for validation using RT-qPCR because β-amyloid peptide …
Multi-Phenotype Genome-Wide Association Studies Of The Norfolk Island Isolate Implicate Pleiotropic Loci Involved In Chronic Kidney Disease, 2021 The University of Texas Rio Grande Valley
Multi-Phenotype Genome-Wide Association Studies Of The Norfolk Island Isolate Implicate Pleiotropic Loci Involved In Chronic Kidney Disease, Ngan K. Tran, Rodney A. Lea, Samuel Holland, Quan Nguyen, Arti M. Raghubar, Heidi G. Sutherland, Miles C. Benton, Nicholas B. Blackburn, Joanne E. Curran, John Blangero
School of Medicine Publications and Presentations
Chronic kidney disease (CKD) is a persistent impairment of kidney function. Genome-wide association studies (GWAS) have revealed multiple genetic loci associated with CKD susceptibility but the complete genetic basis is not yet clear. Since CKD shares risk factors with cardiovascular diseases and diabetes, there may be pleiotropic loci at play but may go undetected when using single phenotype GWAS. Here, we used multi-phenotype GWAS in the Norfolk Island isolate (n = 380) to identify new loci associated with CKD. We performed a principal components analysis on different combinations of 29 quantitative traits to extract principal components (PCs) representative of multiple …
Clinical Implications Of Combinatorial Pharmacogenomic Tests Based On Cytochrome P450 Variant Selection, 2021 Chapman University
Clinical Implications Of Combinatorial Pharmacogenomic Tests Based On Cytochrome P450 Variant Selection, Michael R. Sayer, Ashley Duche, Trang Jenny Tran Nguyen, Michelle Le, Kunj Patel, Jacqueline Vu, Danny Pham, Brianne Vernick, Richard Beuttler, Don Roosan, Moom R. Roosan
Pharmacy Faculty Articles and Research
Despite the potential to improve patient outcomes, the application of pharmacogenomics (PGx) is yet to be routine. A growing number of PGx implementers are leaning toward using combinatorial PGx (CPGx) tests (i.e., multigene tests) that are reusable over patients’ lifetimes. However, selecting a single best available CPGx test is challenging owing to many patient- and population-specific factors, including variant frequency differences across ethnic groups. The primary objective of this study was to evaluate the detection rate of currently available CPGx tests based on the cytochrome P450 (CYP) gene variants they target. The detection rate was defined as the percentage of …
Genetic Testing Reveals Germline Mutations Among Patients Undergoing Surgery For Colorectal Carcinoma In A Community Hospital Setting, 2021 Tufts University School of Medicine
Genetic Testing Reveals Germline Mutations Among Patients Undergoing Surgery For Colorectal Carcinoma In A Community Hospital Setting, Alex R. Jones, Dana Greer Rn, Bsn, Ocn, Karin L. Cole Md
Journal of Maine Medical Center
Introduction: Defined germline mutations contribute to 5% to 10% of cases of colorectal carcinoma (CRC). While protocols for universal tumor screening have been adopted to detect mismatch repair (MMR) protein deficiency, widespread multigene panel testing has not been achieved. Barriers to implementing testing protocols may occur in community settings.
Methods: A total of 160 patients presenting for surgical management of CRC between 2011 and 2020 were considered for retrospective analysis in a single-surgeon, single-institution, community-based cohort. The rate of multigene panel testing and prevalence of germline mutations were calculated, and patient characteristics were assessed.
Results: A total of 32/160 (20%) …