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Full-Text Articles in Physical Sciences and Mathematics
Genomic Regions Associated With Pseudorabies Virus Infection Status In Naturally Infected Feral Swine (Sus Scrofa), Courtney F. Bowden, Jennifer N. Kiser, Ryan S. Miller, Alexandra C. Buckley, Paola M. Boggiatto, Rachael M. Giglio, Vienna R. Brown, Dorian Garrick, Holly L. Neibergs, Antoinette J. Piaggio, Scott E. Speidel, Timothy J. Smyser
Genomic Regions Associated With Pseudorabies Virus Infection Status In Naturally Infected Feral Swine (Sus Scrofa), Courtney F. Bowden, Jennifer N. Kiser, Ryan S. Miller, Alexandra C. Buckley, Paola M. Boggiatto, Rachael M. Giglio, Vienna R. Brown, Dorian Garrick, Holly L. Neibergs, Antoinette J. Piaggio, Scott E. Speidel, Timothy J. Smyser
USDA Wildlife Services: Staff Publications
Pseudorabies virus (PRV)—the causative agent of Aujeszky’s disease—was eliminated from commercial pig production herds in the United States (US) in 2004; however, PRV remains endemic among invasive feral swine (Sus scrofa). The circulation of PRV among abundant, widespread feral swine populations poses a sustained risk for disease spillover to production herds. Risk–based surveillance has been successfully implemented for PRV in feral swine populations in the US. However, understanding the role of host genetics in infection status may offer new insights into the epidemiology and disease dynamics of PRV that can be applied to management strategies. Genetic mechanisms underlying …
Analysis Of Genetic Variants Associated With Levels Of Immune Modulating Proteins For Impact On Alzheimer’S Disease Risk Reveal A Potential Role For Siglec14, Benjamin C. Shaw, Yuriko Katsumata, James F. Simpson, David W. Fardo, Steven Estus
Analysis Of Genetic Variants Associated With Levels Of Immune Modulating Proteins For Impact On Alzheimer’S Disease Risk Reveal A Potential Role For Siglec14, Benjamin C. Shaw, Yuriko Katsumata, James F. Simpson, David W. Fardo, Steven Estus
Biostatistics Faculty Publications
Genome-wide association studies (GWAS) have identified immune-related genes as risk factors for Alzheimer’s disease (AD), including TREM2 and CD33, frequently passing a stringent false-discovery rate. These genes either encode or signal through immunomodulatory tyrosine-phosphorylated inhibitory motifs (ITIMs) or activation motifs (ITAMs) and govern processes critical to AD pathology, such as inflammation and amyloid phagocytosis. To investigate whether additional ITIM and ITAM-containing family members may contribute to AD risk and be overlooked due to the stringent multiple testing in GWAS, we combined protein quantitative trait loci (pQTL) data from a recent plasma proteomics study with AD associations in a recent …
Multi-Ancestry Genome-Wide Association Study Accounting For Gene-Psychosocial Factor Interactions Identifies Novel Loci For Blood Pressure Traits, Daokun Sun, Melissa A. Richard, Soloman K. Musani, Yun Ju Sung, Thomas W. Winkler, Karen Schwander, Jin Fang Chai, Xiuqing Guo, Tuomas O. Kilpeläinen, Dina Vojinovic, Hugues Aschard, Traci M. Bartz, Lawrence F. Bielak, Michael R. Brown, Kumaraswamy Chitrala, Fernando P. Hartwig, Andrea R. V. R. Horimoto, Yongmei Liu, Alisa K. Manning, Raymond Noordam, Donna K. Arnett
Multi-Ancestry Genome-Wide Association Study Accounting For Gene-Psychosocial Factor Interactions Identifies Novel Loci For Blood Pressure Traits, Daokun Sun, Melissa A. Richard, Soloman K. Musani, Yun Ju Sung, Thomas W. Winkler, Karen Schwander, Jin Fang Chai, Xiuqing Guo, Tuomas O. Kilpeläinen, Dina Vojinovic, Hugues Aschard, Traci M. Bartz, Lawrence F. Bielak, Michael R. Brown, Kumaraswamy Chitrala, Fernando P. Hartwig, Andrea R. V. R. Horimoto, Yongmei Liu, Alisa K. Manning, Raymond Noordam, Donna K. Arnett
Epidemiology and Environmental Health Faculty Publications
Psychological and social factors are known to influence blood pressure (BP) and risk of hypertension and associated cardiovascular diseases. To identify novel BP loci, we carried out genome-wide association meta-analyses of systolic, diastolic, pulse, and mean arterial BP, taking into account the interaction effects of genetic variants with three psychosocial factors: depressive symptoms, anxiety symptoms, and social support. Analyses were performed using a two-stage design in a sample of up to 128,894 adults from five ancestry groups. In the combined meta-analyses of stages 1 and 2, we identified 59 loci (p value < 5e−8), including nine novel BP loci. The novel associations were observed mostly with pulse pressure, with fewer observed with mean arterial pressure. Five novel loci were identified in African ancestry, and all but one showed patterns of interaction with at least one psychosocial factor. Functional annotation of the novel loci supports a major role for genes implicated in the immune response (PLCL2), synaptic function and neurotransmission (LIN7A …
A New Efficient Method To Detect Genetic Interactions For Lung Cancer Gwas, Jennifer Luyapan, Xuemei Ji, Siting Li, Xiangjun Xiao, Dakai Zhu, Eric J. Duell, David C. Christiani, Matthew B. Schabath, Susanne M. Arnold, Shanbeh Zienolddiny, Hans Brunnström, Olle Melander, Mark D. Thornquist, Todd A. Mackenzie, Christopher I. Amos, Jiang Gui
A New Efficient Method To Detect Genetic Interactions For Lung Cancer Gwas, Jennifer Luyapan, Xuemei Ji, Siting Li, Xiangjun Xiao, Dakai Zhu, Eric J. Duell, David C. Christiani, Matthew B. Schabath, Susanne M. Arnold, Shanbeh Zienolddiny, Hans Brunnström, Olle Melander, Mark D. Thornquist, Todd A. Mackenzie, Christopher I. Amos, Jiang Gui
Markey Cancer Center Faculty Publications
BACKGROUND: Genome-wide association studies (GWAS) have proven successful in predicting genetic risk of disease using single-locus models; however, identifying single nucleotide polymorphism (SNP) interactions at the genome-wide scale is limited due to computational and statistical challenges. We addressed the computational burden encountered when detecting SNP interactions for survival analysis, such as age of disease-onset. To confront this problem, we developed a novel algorithm, called the Efficient Survival Multifactor Dimensionality Reduction (ES-MDR) method, which used Martingale Residuals as the outcome parameter to estimate survival outcomes, and implemented the Quantitative Multifactor Dimensionality Reduction method to identify significant interactions associated with age of …
Loci Associated With Antibody Response In Feral Swine (Sus Scrofa) Infected With Brucella Suis, Courtney F. Pierce, Vienna R. Brown, Steven C. Olsen, Paola Boggiatto, Kerri Pedersen, Ryan S. Miller, Scott E. Speidel, Timothy J. Smyser
Loci Associated With Antibody Response In Feral Swine (Sus Scrofa) Infected With Brucella Suis, Courtney F. Pierce, Vienna R. Brown, Steven C. Olsen, Paola Boggiatto, Kerri Pedersen, Ryan S. Miller, Scott E. Speidel, Timothy J. Smyser
USDA Wildlife Services: Staff Publications
Feral swine (Sus scrofa) are a destructive invasive species widespread throughout the United States that disrupt ecosystems, damage crops, and carry pathogens of concern for the health of domestic stock and humans including Brucella suis—the causative organism for swine brucellosis. In domestic swine, brucellosis results in reproductive failure due to abortions and infertility. Contact with infected feral swine poses spillover risks to domestic pigs as well as humans, companion animals, wildlife, and other livestock. Genetic factors influence the outcome of infectious diseases; therefore, genome wide association studies (GWAS) of differential immune responses among feral swine can provide …
Genome-Wide Association Study In Accessions Of The Mini-Core Collection Of Mungbean (Vigna Radiata) From The World Vegetable Gene Bank (Taiwan), Alena Sokolkova, Marina Burlyaeva, Tatjana Valiannikova, Margarita Vishnyakova, Roland Schafleitner, Cheng Ruei Lee, Chau Ti Ting, Ramakrishnan Madhavan Nair, Sergey Nuzhdin, Maria Samsonova, Eric Von Wettberg
Genome-Wide Association Study In Accessions Of The Mini-Core Collection Of Mungbean (Vigna Radiata) From The World Vegetable Gene Bank (Taiwan), Alena Sokolkova, Marina Burlyaeva, Tatjana Valiannikova, Margarita Vishnyakova, Roland Schafleitner, Cheng Ruei Lee, Chau Ti Ting, Ramakrishnan Madhavan Nair, Sergey Nuzhdin, Maria Samsonova, Eric Von Wettberg
College of Agriculture and Life Sciences Faculty Publications
Background: Mungbean (Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the mini-core collection established by the World Vegetable Center, which includes 296 accessions that represent the major market classes. This collection has been grown in a common field plot in southern European part of Russia in 2018. Results: We used 5041 SNPs in 293 accessions that passed strict filtering for genetic diversity, linkage disequilibrium, population …
Dynamical Climatic Model For Time To Flowering In Vigna Radiata, Konstantin Kozlov, Alena Sokolkova, Cheng Ruei Lee, Chau Ti Ting, Roland Schafleitner, Eric Bishop-Von Wettberg, Sergey Nuzhdin, Maria Samsonova
Dynamical Climatic Model For Time To Flowering In Vigna Radiata, Konstantin Kozlov, Alena Sokolkova, Cheng Ruei Lee, Chau Ti Ting, Roland Schafleitner, Eric Bishop-Von Wettberg, Sergey Nuzhdin, Maria Samsonova
College of Agriculture and Life Sciences Faculty Publications
Background: Phenology data collected recently for about 300 accessions of Vigna radiata (mungbean) is an invaluable resource for investigation of impacts of climatic factors on plant development. Results: We developed a new mathematical model that describes the dynamic control of time to flowering by daily values of maximal and minimal temperature, precipitation, day length and solar radiation. We obtained model parameters by adaptation to the available experimental data. The models were validated by cross-validation and used to demonstrate that the phenology of adaptive traits, like flowering time, is strongly predicted not only by local environmental factors but also by plant …
Association Of Copy Number Variations With Chronic Hepatitis B In Chinese Population, Fang Niu
Association Of Copy Number Variations With Chronic Hepatitis B In Chinese Population, Fang Niu
Capstone Experience
With one third of the Hepatitis B virus (HBV) infection population of the world, chronic Hepatitis B (CHB) has become a top burden in China. CHB is a lifelong infection with HBV which can cause serious health problems, like cirrhosis, liver cancer or even death. HBV infection is known to result in various clinical conditions, including asymptomatic HBV carriers to chronic hepatitis and primary hepatocellular carcinoma. Several studies have shown that host genetic susceptibility could be an important factor that determines these various outcomes of HBV infection. Many Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) have been associated …
Non-Linear Regression Models For Time To Flowering In Wild Chickpea Combine Genetic And Climatic Factors, Konstantin Kozlov, Anupam Singh, Jens Berger, Eric Bishop-Von Wettberg, Abdullah Kahraman, Abdulkadir Aydogan, Douglas Cook, Sergey Nuzhdin, Maria Samsonova
Non-Linear Regression Models For Time To Flowering In Wild Chickpea Combine Genetic And Climatic Factors, Konstantin Kozlov, Anupam Singh, Jens Berger, Eric Bishop-Von Wettberg, Abdullah Kahraman, Abdulkadir Aydogan, Douglas Cook, Sergey Nuzhdin, Maria Samsonova
College of Agriculture and Life Sciences Faculty Publications
Background: Accurate prediction of crop flowering time is required for reaching maximal farm efficiency. Several models developed to accomplish this goal are based on deep knowledge of plant phenology, requiring large investment for every individual crop or new variety. Mathematical modeling can be used to make better use of more shallow data and to extract information from it with higher efficiency. Cultivars of chickpea, Cicer arietanum, are currently being improved by introgressing wild C. reticulatum biodiversity with very different flowering time requirements. More understanding is required for how flowering time will depend on environmental conditions in these cultivars developed by …
Penalized Mixed-Effects Ordinal Response Models For High-Dimensional Genomic Data In Twins And Families, Amanda E. Gentry
Penalized Mixed-Effects Ordinal Response Models For High-Dimensional Genomic Data In Twins And Families, Amanda E. Gentry
Theses and Dissertations
The Brisbane Longitudinal Twin Study (BLTS) was being conducted in Australia and was funded by the US National Institute on Drug Abuse (NIDA). Adolescent twins were sampled as a part of this study and surveyed about their substance use as part of the Pathways to Cannabis Use, Abuse and Dependence project. The methods developed in this dissertation were designed for the purpose of analyzing a subset of the Pathways data that includes demographics, cannabis use metrics, personality measures, and imputed genotypes (SNPs) for 493 complete twin pairs (986 subjects.) The primary goal was to determine what combination of SNPs and …
Abcc9/Sur2 In The Brain: Implications For Hippocampal Sclerosis Of Aging And A Potential Therapeutic Target, Peter T. Nelson, Gregory A. Jicha, Wang-Xia Wang, Eseosa T. Ighodaro, Sergey C. Artiushin, Colin G. Nichols, David W. Fardo
Abcc9/Sur2 In The Brain: Implications For Hippocampal Sclerosis Of Aging And A Potential Therapeutic Target, Peter T. Nelson, Gregory A. Jicha, Wang-Xia Wang, Eseosa T. Ighodaro, Sergey C. Artiushin, Colin G. Nichols, David W. Fardo
Sanders-Brown Center on Aging Faculty Publications
The ABCC9 gene and its polypeptide product, SUR2, are increasingly implicated in human neurologic disease, including prevalent diseases of the aged brain. SUR2 proteins are a component of the ATP-sensitive potassium (“K ATP ”) channel, a metabolic sensor for stress and/or hypoxia that has been shown to change in aging. The K ATP channel also helps regulate the neurovascular unit. Most brain cell types express SUR2, including neurons, astrocytes, oligodendrocytes, microglia, vascular smooth muscle, pericytes, and endothelial cells. Thus it is not surprising that ABCC9 gene variants are associated with risk for human brain diseases. For example, Cantu syndrome is …
Reassessment Of Risk Genotypes (Grn, Tmem106b, And Abcc9 Variants) Associated With Hippocampal Sclerosis Of Aging Pathology, Peter T. Nelson, Wang-Xia Wang, Amanda B. Partch, Sarah E. Monsell, Otto Valladares, Sally R. Ellingson, Bernard R. Wilfred, Adam C. Naj, Li-San Wang, Walter A. Kukull, David W. Fardo
Reassessment Of Risk Genotypes (Grn, Tmem106b, And Abcc9 Variants) Associated With Hippocampal Sclerosis Of Aging Pathology, Peter T. Nelson, Wang-Xia Wang, Amanda B. Partch, Sarah E. Monsell, Otto Valladares, Sally R. Ellingson, Bernard R. Wilfred, Adam C. Naj, Li-San Wang, Walter A. Kukull, David W. Fardo
Pathology and Laboratory Medicine Faculty Publications
Hippocampal sclerosis of aging (HS-Aging) is a common high-morbidity neurodegenerative condition in elderly persons. To understand the risk factors for HS-Aging, we analyzed data from the Alzheimer’s Disease Genetics Consortium and correlated the data with clinical and pathologic information from the National Alzheimer’s Coordinating Center database. Overall, 268 research volunteers with HS-Aging and 2,957 controls were included; detailed neuropathologic data were available for all. The study focused on single-nucleotide polymorphisms previously associated with HS-Aging risk: rs5848 ( GRN ), rs1990622 ( TMEM106B ), and rs704180 ( ABCC9 ). Analyses of a subsample that was not previously evaluated (51 HS-Aging cases …
Genetic Predictors Of Metabolic Side Effects Of Diuretic Therapy, Jorge L. Del Aguila
Genetic Predictors Of Metabolic Side Effects Of Diuretic Therapy, Jorge L. Del Aguila
Dissertations & Theses (Open Access)
Thiazide diuretics are a recommended first-line monotherapy for hypertension (i.e.SBP>140 mmHg or DBP>90 mmHg). Even so, diuretics are associated with adverse metabolic side effects, such as hyperlipidemia, hyperglycemia and hypokalemia which increase the risk of developing type II diabetes. This thesis used three analytical strategies to identify and quantify genetic factors that contribute to the development of adverse metabolic effects due to thiazide diuretic treatment. I performed a genome-wide association study (GWAS) and meta-analysis of the change in fasting plasma glucose and triglycerides in response to HCTZ from two different clinical trials: the Pharmacogenomic Evaluation of Antihypertensive Responses …
Sberia: Set Based Gene Environment Interaction Test For Rare And Common Variants In Complex Diseases, Shuo Jiao, Li Hsu, Stéphane Bézieau, Hermann Brenner, Andrew T. Chan, Jenny Chang-Claude, Loic Le Marchand, Mathieu Lemire, Polly A. Newcomb, Martha L. Slattery, Ulrike Peters
Sberia: Set Based Gene Environment Interaction Test For Rare And Common Variants In Complex Diseases, Shuo Jiao, Li Hsu, Stéphane Bézieau, Hermann Brenner, Andrew T. Chan, Jenny Chang-Claude, Loic Le Marchand, Mathieu Lemire, Polly A. Newcomb, Martha L. Slattery, Ulrike Peters
Shuo Jiao
Identification of gene-environment interaction (GxE) is important in understanding the etiology of complex diseases. However, partially due to the lack of power, there have been very few replicated GxE findings compared to the success in marginal association studies. The existing GxE testing methods mainly focus on improving the power for individual markers. In this paper, we took a different strategy and proposed a Set Based gene EnviRonment InterAction test (SBERIA), which can improve the power by reducing the multiple testing burdens and aggregating signals within a set. The major challenge of the signal aggregation within a set is how to …
Gene By Bmi Interactions Influencing C-Reactive Protein Levels In European-Americans, Sarah Tudor
Gene By Bmi Interactions Influencing C-Reactive Protein Levels In European-Americans, Sarah Tudor
Dissertations & Theses (Open Access)
C-Reactive Protein (CRP) is a biomarker indicating tissue damage, inflammation, and infection. High-sensitivity CRP (hsCRP) is an emerging biomarker often used to estimate an individual’s risk for future coronary heart disease (CHD). hsCRP levels falling below 1.00 mg/l indicate a low risk for developing CHD, levels ranging between 1.00 mg/l and 3.00 mg/l indicate an elevated risk, and levels exceeding 3.00 mg/l indicate high risk. Multiple Genome-Wide Association Studies (GWAS) have identified a number of genetic polymorphisms which influence CRP levels. SNPs implicated in such studies have been found in or near genes of interest including: CRP, APOE, APOC, IL-6, …