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GRIK5 Genetically Regulated Expression Associated with Eye and Vascular Phenomes: Discovery through Iteration among Biobanks, Electronic Health Records, and Zebrafish.
Unlu G, Gamazon ER, Qi X, Levic DS, Bastarache L, Denny JC, Roden DM, Mayzus I, Breyer M, Zhong X, Konkashbaev AI, Rzhetsky A, Knapik EW, Cox NJ
(2019) Am J Hum Genet 104: 503-519
MeSH Terms: Animals, Biological Specimen Banks, Electronic Health Records, Embryo, Nonmammalian, Eye Diseases, Gene Expression Regulation, Genotype, Humans, Phenomics, Phenotype, Receptors, Kainic Acid, Vascular Diseases, Zebrafish
Show Abstract · Added March 23, 2019
Although the use of model systems for studying the mechanism of mutations that have a large effect is common, we highlight here the ways that zebrafish-model-system studies of a gene, GRIK5, that contributes to the polygenic liability to develop eye diseases have helped to illuminate a mechanism that implicates vascular biology in eye disease. A gene-expression prediction derived from a reference transcriptome panel applied to BioVU, a large electronic health record (EHR)-linked biobank at Vanderbilt University Medical Center, implicated reduced GRIK5 expression in diverse eye diseases. We tested the function of GRIK5 by depletion of its ortholog in zebrafish, and we observed reduced blood vessel numbers and integrity in the eye and increased vascular permeability. Analyses of EHRs in >2.6 million Vanderbilt subjects revealed significant comorbidity of eye and vascular diseases (relative risks 2-15); this comorbidity was confirmed in 150 million individuals from a large insurance claims dataset. Subsequent studies in >60,000 genotyped BioVU participants confirmed the association of reduced genetically predicted expression of GRIK5 with comorbid vascular and eye diseases. Our studies pioneer an approach that allows a rapid iteration of the discovery of gene-phenotype relationships to the primary genetic mechanism contributing to the pathophysiology of human disease. Our findings also add dimension to the understanding of the biology driven by glutamate receptors such as GRIK5 (also referred to as GLUK5 in protein form) and to mechanisms contributing to human eye diseases.
Copyright © 2019 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
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13 MeSH Terms
MR-PheWAS: exploring the causal effect of SUA level on multiple disease outcomes by using genetic instruments in UK Biobank.
Li X, Meng X, Spiliopoulou A, Timofeeva M, Wei WQ, Gifford A, Shen X, He Y, Varley T, McKeigue P, Tzoulaki I, Wright AF, Joshi P, Denny JC, Campbell H, Theodoratou E
(2018) Ann Rheum Dis 77: 1039-1047
MeSH Terms: Adult, Arthritis, Autoimmune Diseases, Biological Specimen Banks, Celiac Disease, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Gout, Humans, Hypertension, Male, Mendelian Randomization Analysis, Middle Aged, Multimorbidity, Myocardial Infarction, Prognosis, Risk Assessment, United Kingdom, Uric Acid
Show Abstract · Added March 14, 2018
OBJECTIVES - We aimed to investigate the role of serum uric acid (SUA) level in a broad spectrum of disease outcomes using data for 120 091 individuals from UK Biobank.
METHODS - We performed a phenome-wide association study (PheWAS) to identify disease outcomes associated with SUA genetic risk loci. We then implemented conventional Mendelianrandomisation (MR) analysis to investigate the causal relevance between SUA level and disease outcomes identified from PheWAS. We next applied MR Egger analysis to detect and account for potential pleiotropy, which conventional MR analysis might mistake for causality, and used the HEIDI (heterogeneity in dependent instruments) test to remove cross-phenotype associations that were likely due to genetic linkage.
RESULTS - Our PheWAS identified 25 disease groups/outcomes associated with SUA genetic risk loci after multiple testing correction (P<8.57e-05). Our conventional MR analysis implicated a causal role of SUA level in three disease groups: inflammatory polyarthropathies (OR=1.22, 95% CI 1.11 to 1.34), hypertensive disease (OR=1.08, 95% CI 1.03 to 1.14) and disorders of metabolism (OR=1.07, 95% CI 1.01 to 1.14); and four disease outcomes: gout (OR=4.88, 95% CI 3.91 to 6.09), essential hypertension (OR=1.08, 95% CI 1.03 to 1.14), myocardial infarction (OR=1.16, 95% CI 1.03 to 1.30) and coeliac disease (OR=1.41, 95% CI 1.05 to 1.89). After balancing pleiotropic effects in MR Egger analysis, only gout and its encompassing disease group of inflammatory polyarthropathies were considered to be causally associated with SUA level. Our analysis highlighted a locus () that may influence SUA level and multiple cardiovascular and autoimmune diseases via pleiotropy.
CONCLUSIONS - Elevated SUA level is convincing to cause gout and inflammatory polyarthropathies, and might act as a marker for the wider range of diseases with which it associates. Our findings support further investigation on the clinical relevance of SUA level with cardiovascular, metabolic, autoimmune and respiratory diseases.
© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.
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20 MeSH Terms
Admixture mapping of uterine fibroid size and number in African American women.
Bray MJ, Edwards TL, Wellons MF, Jones SH, Hartmann KE, Velez Edwards DR
(2017) Fertil Steril 108: 1034-1042.e26
MeSH Terms: Adult, African Americans, Biological Specimen Banks, Biomarkers, Tumor, Cross-Sectional Studies, Databases, Factual, Electronic Health Records, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Heredity, Humans, Leiomyoma, Leiomyomatosis, Linear Models, Logistic Models, Middle Aged, Odds Ratio, Phenotype, Polymorphism, Single Nucleotide, Risk Factors, Tumor Burden, United States, Uterine Neoplasms
Show Abstract · Added February 21, 2019
OBJECTIVE - To evaluate the relationship between genetic ancestry and uterine fibroid characteristics.
DESIGN - Cross-sectional study.
SETTING - Not applicable.
PATIENT(S) - A total of 609 African American participants with image- or surgery-confirmed fibroids in a biorepository at Vanderbilt University electronic health record biorepository and the Coronary Artery Risk Development in Young Adults studies were included.
INTERVENTION(S) - None.
MAIN OUTCOME MEASURE(S) - Outcome measures include fibroid number (single vs. multiple), volume of largest fibroid, and largest fibroid dimension of all fibroid measurements.
RESULT(S) - Global ancestry meta-analyses revealed a significant inverse association between percentage of European ancestry and risk of multiple fibroids (odds ratio: 0.78; 95% confidence interval 0.66, 0.93; P=6.05 × 10). Local ancestry meta-analyses revealed five suggestive (P<4.80 × 10) admixture mapping peaks in 2q14.3-2q21.1, 3p14.2-3p14.1, 7q32.2-7q33, 10q21.1, 14q24.2-14q24.3, for number of fibroids and one suggestive admixture mapping peak (P<1.97 × 10) in 10q24.1-10q24.32 for volume of largest fibroid. Single variant association meta-analyses of the strongest associated region from admixture mapping of fibroid number (10q21.1) revealed a strong association at single nucleotide polymorphism variant rs12219990 (odds ratio: 0.41; 95% confidence interval 0.28, 0.60; P=3.82 × 10) that was significant after correction for multiple testing.
CONCLUSION(S) - Increasing African ancestry is associated with multiple fibroids but not with fibroid size. Local ancestry analyses identified several novel genomic regions not previously associated with fibroid number and increasing volume. Future studies are needed to explore the genetic impact that ancestry plays into the development of fibroid characteristics.
Copyright © 2017 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.
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MeSH Terms
Identification of unique venous thromboembolism-susceptibility variants in African-Americans.
Heit JA, Armasu SM, McCauley BM, Kullo IJ, Sicotte H, Pathak J, Chute CG, Gottesman O, Bottinger EP, Denny JC, Roden DM, Li R, Ritchie MD, de Andrade M
(2017) Thromb Haemost 117: 758-768
MeSH Terms: Adult, African Americans, Aged, Biological Specimen Banks, Case-Control Studies, Databases, Genetic, Electronic Health Records, Female, Genetic Association Studies, Genetic Predisposition to Disease, Humans, Logistic Models, Male, Middle Aged, Odds Ratio, Phenotype, Polymorphism, Single Nucleotide, Risk Factors, Sex Factors, United States, Venous Thromboembolism
Show Abstract · Added March 14, 2018
To identify novel single nucleotide polymorphisms (SNPs) associated with venous thromboembolism (VTE) in African-Americans (AAs), we performed a genome-wide association study (GWAS) of VTE in AAs using the Electronic Medical Records and Genomics (eMERGE) Network, comprised of seven sites each with DNA biobanks (total ~39,200 unique DNA samples) with genome-wide SNP data (imputed to 1000 Genomes Project cosmopolitan reference panel) and linked to electronic health records (EHRs). Using a validated EHR-driven phenotype extraction algorithm, we identified VTE cases and controls and tested for an association between each SNP and VTE using unconditional logistic regression, adjusted for age, sex, stroke, site-platform combination and sickle cell risk genotype. Among 393 AA VTE cases and 4,941 AA controls, three intragenic SNPs reached genome-wide significance: LEMD3 rs138916004 (OR=3.2; p=1.3E-08), LY86 rs3804476 (OR=1.8; p=2E-08) and LOC100130298 rs142143628 (OR=4.5; p=4.4E-08); all three SNPs validated using internal cross-validation, parametric bootstrap and meta-analysis methods. LEMD3 rs138916004 and LOC100130298 rs142143628 are only present in Africans (1000G data). LEMD3 showed a significant differential expression in both NCBI Gene Expression Omnibus (GEO) and the Mayo Clinic gene expression data, LOC100130298 showed a significant differential expression only in the GEO expression data, and LY86 showed a significant differential expression only in the Mayo expression data. LEMD3 encodes for an antagonist of TGF-β-induced cell proliferation arrest. LY86 encodes for MD-1 which down-regulates the pro-inflammatory response to lipopolysaccharide; LY86 variation was previously associated with VTE in white women; LOC100130298 is a non-coding RNA gene with unknown regulatory activity in gene expression and epigenetics.
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21 MeSH Terms
A Community-Driven Intervention for Improving Biospecimen Donation in African American Communities.
Patel K, Inman W, Gishe J, Johnson O, Brown E, Kanu M, Theriot R, Sanderson M, Hull P, Hargreaves M
(2018) J Racial Ethn Health Disparities 5: 15-23
MeSH Terms: Adult, African Americans, Biological Specimen Banks, Community-Based Participatory Research, Female, Health Education, Health Knowledge, Attitudes, Practice, Humans, Male, Middle Aged
Show Abstract · Added August 22, 2017
INTRODUCTION - Human biospecimens are an invaluable resource for addressing cancers and other chronic diseases. The purpose of this study was to assess the impact of an educational intervention on biospecimen knowledge and attitudes.
METHODS - The participants consisted of 112 African Americans, 18 years and older, and who had not provided biospecimens for any health-related research in the past. A total of 55 participants received the educational brochure, and 57 received the educational video. The main outcomes of the study were knowledge and attitudes for biospecimen donation. This information was collected pre- and post-intervention.
RESULTS - The average knowledge scores increased (p < 0.0001) and the average attitude scores for biospecimen donation improved (p < 0.0001) post-intervention for both the video and brochure conditions. There was an interaction between the intervention condition and knowledge where the participants who received the educational video showed a greater increase in knowledge pre-to-post compared to those who received the educational brochure (p = 0.0061). There were no significant interactions between the two intervention conditions for attitudes toward biospecimen donation.
DISCUSSION - The results of this study demonstrated the feasibility and efficacy of an academic institution collaborating with the African American community in developing educational tools for biospecimen donation.
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10 MeSH Terms
Lung cancer risk test trial: study design, participant baseline characteristics, bronchoscopy safety, and establishment of a biospecimen repository.
Crawford EL, Levin A, Safi F, Lu M, Baugh A, Zhang X, Yeo J, Khuder SA, Boulos AM, Nana-Sinkam P, Massion PP, Arenberg DA, Midthun D, Mazzone PJ, Nathan SD, Wainz R, Silvestri G, Tita J, Willey JC
(2016) BMC Pulm Med 16: 16
MeSH Terms: Aged, Aged, 80 and over, Agriculture, Asbestos, Biological Specimen Banks, Bronchi, Bronchoscopy, Cohort Studies, Early Detection of Cancer, Epithelial Cells, Female, Forced Expiratory Volume, Genetic Predisposition to Disease, Humans, Incidence, Lung Diseases, Obstructive, Lung Neoplasms, Male, Middle Aged, Occupational Exposure, Prospective Studies, Respiratory Mucosa, Risk Assessment, Smoking, Tomography, Spiral Computed, Vital Capacity
Show Abstract · Added February 16, 2016
BACKGROUND - The Lung Cancer Risk Test (LCRT) trial is a prospective cohort study comparing lung cancer incidence among persons with a positive or negative value for the LCRT, a 15 gene test measured in normal bronchial epithelial cells (NBEC). The purpose of this article is to describe the study design, primary endpoint, and safety; baseline characteristics of enrolled individuals; and establishment of a bio-specimen repository.
METHODS/DESIGN - Eligible participants were aged 50-90 years, current or former smokers with 20 pack-years or more cigarette smoking history, free of lung cancer, and willing to undergo bronchoscopic brush biopsy for NBEC sample collection. NBEC, peripheral blood samples, baseline CT, and medical and demographic data were collected from each subject.
DISCUSSION - Over a two-year span (2010-2012), 403 subjects were enrolled at 12 sites. At baseline 384 subjects remained in study and mean age and smoking history were 62.9 years and 50.4 pack-years respectively, with 34% current smokers. Obstructive lung disease (FEV1/FVC <0.7) was present in 157 (54%). No severe adverse events were associated with bronchoscopic brushing. An NBEC and matched peripheral blood bio-specimen repository was established. The demographic composition of the enrolled group is representative of the population for which the LCRT is intended. Specifically, based on baseline population characteristics we expect lung cancer incidence in this cohort to be representative of the population eligible for low-dose Computed Tomography (LDCT) lung cancer screening. Collection of NBEC by bronchial brush biopsy/bronchoscopy was safe and well-tolerated in this population. These findings support the feasibility of testing LCRT clinical utility in this prospective study. If validated, the LCRT has the potential to significantly narrow the population of individuals requiring annual low-dose helical CT screening for early detection of lung cancer and delay the onset of screening for individuals with results indicating low lung cancer risk. For these individuals, the small risk incurred by undergoing once in a lifetime bronchoscopic sample collection for LCRT may be offset by a reduction in their CT-related risks. The LCRT biospecimen repository will enable additional studies of genetic basis for COPD and/or lung cancer risk.
TRIAL REGISTRATION - The LCRT Study, NCT 01130285, was registered with Clinicaltrials.gov on May 24, 2010.
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26 MeSH Terms
RePORT International: Advancing Tuberculosis Biomarker Research Through Global Collaboration.
Hamilton CD, Swaminathan S, Christopher DJ, Ellner J, Gupta A, Sterling TR, Rolla V, Srinivasan S, Karyana M, Siddiqui S, Stoszek SK, Kim P
(2015) Clin Infect Dis 61Suppl 3: S155-9
MeSH Terms: Biological Specimen Banks, Biomarkers, Biomedical Research, Brazil, Humans, India, Indonesia, International Cooperation, Prospective Studies, Specimen Handling, Tuberculosis
Show Abstract · Added February 17, 2016
Progress in tuberculosis clinical research is hampered by a lack of reliable biomarkers that predict progression from latent to active tuberculosis, and subsequent cure, relapse, or failure. Regional Prospective Observational Research in Tuberculosis (RePORT) International represents a consortium of regional cohorts (RePORT India, RePORT Brazil, and RePORT Indonesia) that are linked through the implementation of a Common Protocol for data and specimen collection, and are poised to address this critical research need. Each RePORT network is designed to support local, in-country tuberculosis-specific data and specimen biorepositories, and associated research. Taken together, the expected results include greater global clinical research capacity in high-burden settings, and increased local access to quality data and specimens for members of each network and their domestic and international collaborators. Additional networks are expected to be added, helping to spur tuberculosis treatment and prevention research around the world.
© The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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11 MeSH Terms
Genotype and risk of major bleeding during warfarin treatment.
Kawai VK, Cunningham A, Vear SI, Van Driest SL, Oginni A, Xu H, Jiang M, Li C, Denny JC, Shaffer C, Bowton E, Gage BF, Ray WA, Roden DM, Stein CM
(2014) Pharmacogenomics 15: 1973-83
MeSH Terms: Adult, Aged, Biological Specimen Banks, Cytochrome P-450 CYP2C9, Cytochrome P-450 Enzyme System, Cytochrome P450 Family 4, Dose-Response Relationship, Drug, Ethnic Groups, Female, Gene Frequency, Genetic Association Studies, Genetic Variation, Genotype, Hemorrhage, Humans, Male, Middle Aged, Risk Factors, Vitamin K Epoxide Reductases, Warfarin
Show Abstract · Added January 23, 2015
AIM - To determine whether genetic variants associated with warfarin dose variability were associated with increased risk of major bleeding during warfarin therapy.
MATERIALS & METHODS - Using Vanderbilt's DNA biobank we compared the prevalence of CYP2C9, VKORC1 and CYP4F2 variants in 250 cases with major bleeding and 259 controls during warfarin therapy.
RESULTS - CYP2C9*3 was the only allele that differed significantly among cases (14.2%) and controls (7.8%; p = 0.022). In the 214 (85.6%) cases with a major bleed 30 or more days after warfarin initiation, CYP2C9*3 was the only variant associated with bleeding (adjusted odds ratio: 2.05; 95% CI: 1.04, 4.04).
CONCLUSION - The CYP2C9*3 allele may double the risk of major bleeding among patients taking warfarin for 30 or more days.
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20 MeSH Terms
A genome-wide association study of heparin-induced thrombocytopenia using an electronic medical record.
Karnes JH, Cronin RM, Rollin J, Teumer A, Pouplard C, Shaffer CM, Blanquicett C, Bowton EA, Cowan JD, Mosley JD, Van Driest SL, Weeke PE, Wells QS, Bakchoul T, Denny JC, Greinacher A, Gruel Y, Roden DM
(2015) Thromb Haemost 113: 772-81
MeSH Terms: Adult, Aged, Antibodies, Anticoagulants, Biological Specimen Banks, Chi-Square Distribution, Electronic Health Records, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, HLA-DR alpha-Chains, Heparin, Humans, Linear Models, Logistic Models, Male, Middle Aged, Odds Ratio, Phenotype, Platelet Factor 4, Polymorphism, Single Nucleotide, Receptors, G-Protein-Coupled, Retrospective Studies, Risk Factors, Thrombocytopenia
Show Abstract · Added January 23, 2015
Heparin-induced thrombocytopenia (HIT) is an unpredictable, potentially catastrophic adverse effect of heparin treatment resulting from an immune response to platelet factor 4 (PF4)/heparin complexes. No genome-wide evaluations have been performed to identify potential genetic influences on HIT. Here, we performed a genome-wide association study (GWAS) and candidate gene study using HIT cases and controls identified using electronic medical records (EMRs) coupled to a DNA biobank and attempted to replicate GWAS associations in an independent cohort. We subsequently investigated influences of GWAS-associated single nucleotide polymorphisms (SNPs) on PF4/heparin antibodies in non-heparin treated individuals. In a recessive model, we observed significant SNP associations (odds ratio [OR] 18.52; 95% confidence interval [CI] 6.33-54.23; p=3.18×10(-9)) with HIT near the T-Cell Death-Associated Gene 8 (TDAG8). These SNPs are in linkage disequilibrium with a missense TDAG8 SNP. TDAG8 SNPs trended toward an association with HIT in replication analysis (OR 5.71; 0.47-69.22; p=0.17), and the missense SNP was associated with PF4/heparin antibody levels and positive PF4/heparin antibodies in non-heparin treated patients (OR 3.09; 1.14-8.13; p=0.02). In the candidate gene study, SNPs at HLA-DRA were nominally associated with HIT (OR 0.25; 0.15-0.44; p=2.06×10(-6)). Further study of TDAG8 and HLA-DRA SNPs is warranted to assess their influence on the risk of developing HIT.
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25 MeSH Terms
Implementation of an error-reporting module within a biorepository IT application to enhance operations.
Wiles KR, Washington MK
(2014) Biopreserv Biobank 12: 365-73
MeSH Terms: Biological Specimen Banks, Preservation, Biological
Show Abstract · Added April 12, 2016
The Collaborative (formerly the Cooperative) Human Tissue Network (CHTN) is a federally funded service oriented grant that provides high-quality biospecimens and services to the research community. The CHTN consists of six institutions located throughout the United States to assist investigators in obtaining research specimens required for basic research. The CHTN divisions have similar operating goals: however, each division is responsible for maintaining operations at their local institutions. This requires the divisions to identify ways to maintain and sustain operations in a challenging federally funded environment, especially when the number of investigators requesting services drives the operation. Sustainability plans and goals are often times patched together out of necessity rather than taking a thoughtful approach by clearly defining and aligning activities with business strategy and priorities. The CHTN Western Division at Vanderbilt University Medical Center (CHTN-WD) has responded to this challenge of biospecimen resource sustainability in the face of diminished funding by continually identifying ways to innovate our processes through IT enhancements and requiring that the innovation produce measurable and relevant criteria for credibly reporting our operations progress and performance issues. With these overarching goals in mind, CHTN-WD underwent a Lean Six Sigma (LSS) series to identify operational inefficiencies that could be addressed with redesigning workflow and innovating the processes using IT solutions. The result of this internal collaborative innovation process was the implementation of an error-reporting module (ERM) hosted within our biorepository donor IT application, which allowed staff to report errors immediately; determine the operational area responsible; assess the severity of the error; determine course of action; determine if standard operating procedure (SOPs) revisions were required; and through automated e-mails, alert the area personnel responsible. The module provides a data-reporting feature by date range and area of operation for management and analysis.
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