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Defining a Contemporary Ischemic Heart Disease Genetic Risk Profile Using Historical Data.
Mosley JD, van Driest SL, Wells QS, Shaffer CM, Edwards TL, Bastarache L, McCarty CA, Thompson W, Chute CG, Jarvik GP, Crosslin DR, Larson EB, Kullo IJ, Pacheco JA, Peissig PL, Brilliant MH, Linneman JG, Denny JC, Roden DM
(2016) Circ Cardiovasc Genet 9: 521-530
MeSH Terms: Aged, Aged, 80 and over, Atherosclerosis, Blood Pressure, Case-Control Studies, Chi-Square Distribution, Cross-Sectional Studies, Diabetes Mellitus, Type 2, Electronic Health Records, Female, Genetic Markers, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Hypertension, Incidence, Linear Models, Lipids, Male, Middle Aged, Molecular Epidemiology, Myocardial Ischemia, Phenotype, Polymorphism, Single Nucleotide, Prevalence, Prognosis, Proportional Hazards Models, Risk Assessment, Risk Factors, Time Factors, United States
Show Abstract · Added April 6, 2017
BACKGROUND - Continued reductions in morbidity and mortality attributable to ischemic heart disease (IHD) require an understanding of the changing epidemiology of this disease. We hypothesized that we could use genetic correlations, which quantify the shared genetic architectures of phenotype pairs and extant risk factors from a historical prospective study to define the risk profile of a contemporary IHD phenotype.
METHODS AND RESULTS - We used 37 phenotypes measured in the ARIC study (Atherosclerosis Risk in Communities; n=7716, European ancestry subjects) and clinical diagnoses from an electronic health record (EHR) data set (n=19 093). All subjects had genome-wide single-nucleotide polymorphism genotyping. We measured pairwise genetic correlations (rG) between the ARIC and EHR phenotypes using linear mixed models. The genetic correlation estimates between the ARIC risk factors and the EHR IHD were modestly linearly correlated with hazards ratio estimates for incident IHD in ARIC (Pearson correlation [r]=0.62), indicating that the 2 IHD phenotypes had differing risk profiles. For comparison, this correlation was 0.80 when comparing EHR and ARIC type 2 diabetes mellitus phenotypes. The EHR IHD phenotype was most strongly correlated with ARIC metabolic phenotypes, including total:high-density lipoprotein cholesterol ratio (rG=-0.44, P=0.005), high-density lipoprotein (rG=-0.48, P=0.005), systolic blood pressure (rG=0.44, P=0.02), and triglycerides (rG=0.38, P=0.02). EHR phenotypes related to type 2 diabetes mellitus, atherosclerotic, and hypertensive diseases were also genetically correlated with these ARIC risk factors.
CONCLUSIONS - The EHR IHD risk profile differed from ARIC and indicates that treatment and prevention efforts in this population should target hypertensive and metabolic disease.
© 2016 American Heart Association, Inc.
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4 Members
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31 MeSH Terms
Genetic epidemiology of pelvic organ prolapse: a systematic review.
Ward RM, Velez Edwards DR, Edwards T, Giri A, Jerome RN, Wu JM
(2014) Am J Obstet Gynecol 211: 326-35
MeSH Terms: Collagen Type III, Female, Genetic Markers, Genetic Predisposition to Disease, Genome-Wide Association Study, Global Health, Humans, Models, Statistical, Molecular Epidemiology, Odds Ratio, Pelvic Organ Prolapse, Polymorphism, Single Nucleotide
Show Abstract · Added February 22, 2016
Given current evidence supporting a genetic predisposition for pelvic organ prolapse, we conducted a systematic review of published literature on the genetic epidemiology of pelvic organ prolapse. Inclusion criteria were linkage studies, candidate gene association and genome-wide association studies in adult women published in English and indexed in PubMed through Dec. 2012, with no limit on date of publication. Methodology adhered to the PRISMA guidelines. Data were systematically extracted by 2 reviewers and graded by the Venice criteria for studies of genetic associations. A metaanalysis was performed on all single nucleotide polymorphisms evaluated by 2 or more studies with similar methodology. The metaanalysis suggests that collagen type 3 alpha 1 (COL3A1) rs1800255 genotype AA is associated with pelvic organ prolapse (odds ratio, 4.79; 95% confidence interval, 1.91-11.98; P = .001) compared with the reference genotype GG in populations of Asian and Dutch women. There was little evidence of heterogeneity for rs1800255 (P value for heterogeneity = .94; proportion of variance because of heterogeneity, I(2) = 0.00%). There was insufficient evidence to determine whether other single nucleotide polymorphisms evaluated by 2 or more papers were associated with pelvic organ prolapse. An association with pelvic organ prolapse was seen in individual studies for estrogen receptor alpha (ER-α) rs2228480 GA, COL3A1 exon 31, chromosome 9q21 (heterogeneity logarithm of the odds score 3.41) as well as 6 single nucleotide polymorphisms identified by a genome-wide association study. Overall, individual studies were of small sample size and often of poor quality. Future studies would benefit from more rigorous study design as outlined in the Venice recommendations.
Copyright © 2014 Elsevier Inc. All rights reserved.
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2 Members
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12 MeSH Terms
Molecular epidemiology of contemporary G2P[4] human rotaviruses cocirculating in a single U.S. community: footprints of a globally transitioning genotype.
Dennis AF, McDonald SM, Payne DC, Mijatovic-Rustempasic S, Esona MD, Edwards KM, Chappell JD, Patton JT
(2014) J Virol 88: 3789-801
MeSH Terms: Academic Medical Centers, Child, Preschool, Cluster Analysis, Evolution, Molecular, Gastroenteritis, Genome, Viral, Genotype, Humans, Infant, Infant, Newborn, Molecular Epidemiology, Molecular Sequence Data, Phylogeny, Rotavirus, Rotavirus Infections, Sequence Analysis, DNA, Tennessee
Show Abstract · Added May 28, 2014
UNLABELLED - Group A rotaviruses (RVs) remain a leading cause of childhood gastroenteritis worldwide. Although the G/P types of locally circulating RVs can vary from year to year and differ depending upon geographical location, those with G1P[8], G2P[4], G3P[8], G4P[8], G9P[8], and G12P[8] specificities typically dominate. Little is known about the evolution and diversity of G2P[4] RVs and the possible role that widespread vaccine use has had on their increased frequency of detection. To address these issues, we analyzed the 12 G2P[4] RV isolates associated with a rise in RV gastroenteritis cases at Vanderbilt University Medical Center (VUMC) during the 2010-2011 winter season. Full-genome sequencing revealed that the isolates had genotype 2 constellations typical of DS-1-like viruses (G2P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2). Phylogenetic analyses showed that the genome segments of the isolates were comprised of two or three different subgenotype alleles; this enabled recognition of three distinct clades of G2P[4] viruses that caused disease at VUMC in the 2010-2011 season. Although the three clades cocirculated in the same community, there was no evidence of interclade reassortment. Bayesian analysis of 328 VP7 genes of G2 viruses isolated in the last 39 years indicate that existing G2 VP7 gene lineages continue to evolve and that novel lineages, as represented by the VUMC isolates, are constantly being formed. Moreover, G2 lineages are characteristically shaped by lineage turnover events that introduce new globally dominant strains every 7 years, on average. The ongoing evolution of G2 VP7 lineages may give rise to antigenic changes that undermine vaccine effectiveness in the long term.
IMPORTANCE - Little is known about the diversity of cocirculating G2 rotaviruses and how their evolution may undermine the effectiveness of rotavirus vaccines. To expand our understanding of the potential genetic range exhibited by rotaviruses circulating in postvaccine communities, we analyzed part of a collection of rotaviruses recovered from pediatric patients in the United States from 2010 to 2011. Examining the genetic makeup of these viruses revealed they represented three segregated groups that did not exchange genetic material. The distinction between these three groups may be explained by three separate introductions. By comparing a specific gene, namely, VP7, of the recent rotavirus isolates to those from a collection recovered from U.S. children between 1974 and 1991 and other globally circulating rotaviruses, we were able to reconstruct the timing of events that shaped their ancestry. This analysis indicates that G2 rotaviruses are continuously evolving, accumulating changes in their genetic material as they infect new patients.
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17 MeSH Terms
Distinct molecular features of colorectal cancer in Ghana.
Raskin L, Dakubo JC, Palaski N, Greenson JK, Gruber SB
(2013) Cancer Epidemiol 37: 556-61
MeSH Terms: African Americans, Colorectal Neoplasms, DNA Mismatch Repair, DNA, Neoplasm, Exons, Female, Genes, ras, Ghana, Humans, Immunohistochemistry, Male, Microsatellite Instability, Middle Aged, Molecular Epidemiology, Paraffin Embedding, Proto-Oncogene Proteins B-raf
Show Abstract · Added March 7, 2014
OBJECTIVES - While colorectal cancer (CRC) is common, its incidence significantly varies around the globe. The incidence of CRC in West Africa is relatively low, but it has a distinctive clinical pattern and its molecular characteristics have not been studied. This study is one of the first attempts to analyze molecular, genetic, and pathological characteristics of colorectal cancer in Ghana.
METHODS - DNA was extracted from microdissected tumor and adjacent normal tissue of 90 paraffin blocks of CRC cases (1997-2007) collected at the University of Ghana. Microsatellite instability (MSI) was determined using fragment analysis of ten microsatellite markers. We analyzed expression of mismatch repair (MMR) proteins by immunohistochemistry and sequenced exons 2 and 3 of KRAS and exon 15 of BRAF.
RESULTS - MSI analysis showed 41% (29/70) MSI-High, 20% (14/70) MSI-Low, and 39% (27/70) microsatellite-stable (MSS) tumors. Sequencing of KRAS exons 2 and 3 identified activating mutations in 32% (24/75) of tumors, and sequencing of BRAF exon 15, the location of the common activating mutation (V600), did not show mutations at codons 599 and 600 in 88 tumors.
CONCLUSIONS - Our study found a high frequency of MSI-High colorectal tumors (41%) in Ghana. While the frequency of KRAS mutations is comparable with other populations, absence of BRAF mutations is intriguing and would require further analysis of the molecular epidemiology of CRC in West Africa.
Copyright © 2013 Elsevier Ltd. All rights reserved.
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16 MeSH Terms
Serum vitamins A and E as modifiers of lipid trait genetics in the National Health and Nutrition Examination Surveys as part of the Population Architecture using Genomics and Epidemiology (PAGE) study.
Dumitrescu L, Goodloe R, Brown-Gentry K, Mayo P, Allen M, Jin H, Gillani NB, Schnetz-Boutaud N, Dilks HH, Crawford DC
(2012) Hum Genet 131: 1699-708
MeSH Terms: Adult, African Americans, Cholesterol, HDL, Cholesterol, LDL, Cohort Studies, European Continental Ancestry Group, Female, Fluorescent Antibody Technique, Gene-Environment Interaction, Genetic Association Studies, Genetic Markers, Genome-Wide Association Study, Humans, Mexican Americans, Molecular Epidemiology, Nutrition Surveys, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Risk Factors, Triglycerides, Vitamin A, Vitamin E
Show Abstract · Added December 10, 2013
Both environmental and genetic factors impact lipid traits. Environmental modifiers of known genotype-phenotype associations may account for some of the "missing heritability" of these traits. To identify such modifiers, we genotyped 23 lipid-associated variants identified previously through genome-wide association studies (GWAS) in 2,435 non-Hispanic white, 1,407 non-Hispanic black, and 1,734 Mexican-American samples collected for the National Health and Nutrition Examination Surveys (NHANES). Along with lipid levels, NHANES collected environmental variables, including fat-soluble macronutrient serum levels of vitamin A and E levels. As part of the Population Architecture using Genomics and Epidemiology (PAGE) study, we modeled gene-environment interactions between vitamin A or vitamin E and 23 variants previously associated with high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. We identified three SNP × vitamin A and six SNP × vitamin E interactions at a significance threshold of p < 2.2 × 10(-3). The most significant interaction was APOB rs693 × vitamin E (p = 8.9 × 10(-7)) for LDL-C levels among Mexican-Americans. The nine significant interaction models individually explained 0.35-1.61% of the variation in any one of the lipid traits. Our results suggest that vitamins A and E may modify known genotype-phenotype associations; however, these interactions account for only a fraction of the overall variability observed for HDL-C, LDL-C, and TG levels in the general population.
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1 Members
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22 MeSH Terms
The HIV Epidemic: High-Income Countries.
Vermund SH, Leigh-Brown AJ
(2012) Cold Spring Harb Perspect Med 2: a007195
MeSH Terms: Alcohol Drinking, Developed Countries, Drug Resistance, Viral, Epidemics, Female, HIV Infections, Heterosexuality, Homosexuality, Male, Humans, Income, Infectious Disease Transmission, Vertical, Male, Molecular Epidemiology, Needle Sharing, Risk Factors, Substance Abuse, Intravenous, Transfusion Reaction, Unsafe Sex
Show Abstract · Added March 5, 2014
The HIV epidemic in higher-income nations is driven by receptive anal intercourse, injection drug use through needle/syringe sharing, and, less efficiently, vaginal intercourse. Alcohol and noninjecting drug use increase sexual HIV vulnerability. Appropriate diagnostic screening has nearly eliminated blood/blood product-related transmissions and, with antiretroviral therapy, has reduced mother-to-child transmission radically. Affected subgroups have changed over time (e.g., increasing numbers of Black and minority ethnic men who have sex with men). Molecular phylogenetic approaches have established historical links between HIV strains from central Africa to those in the United States and thence to Europe. However, Europe did not just receive virus from the United States, as it was also imported from Africa directly. Initial introductions led to epidemics in different risk groups in Western Europe distinguished by viral clades/sequences, and likewise, more recent explosive epidemics linked to injection drug use in Eastern Europe are associated with specific strains. Recent developments in phylodynamic approaches have made it possible to obtain estimates of sequence evolution rates and network parameters for epidemics.
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1 Members
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18 MeSH Terms
J-Western forms of Helicobacter pylori cagA constitute a distinct phylogenetic group with a widespread geographic distribution.
Duncan SS, Valk PL, Shaffer CL, Bordenstein SR, Cover TL
(2012) J Bacteriol 194: 1593-604
MeSH Terms: Antigens, Bacterial, Bacterial Proteins, Cluster Analysis, DNA, Bacterial, Evolution, Molecular, Genetic Variation, Genotype, Helicobacter Infections, Helicobacter pylori, Humans, Japan, Molecular Epidemiology, Multilocus Sequence Typing, Phylogeography
Show Abstract · Added August 16, 2012
Chronic infection with Helicobacter pylori strains expressing the bacterial oncoprotein CagA confers an increased risk of gastric cancer. While much is known about the ancestry and molecular evolution of Western, East Asian, and Amerindian cagA sequences, relatively little is understood about a fourth group, known as "J-Western," which has been detected mainly in strains from Okinawa, Japan. We show here that J-Western cagA sequences have a more widespread global distribution than previously recognized, occur in strains with multiple different ancestral origins (based on multilocus sequence typing [MLST] analysis), and did not arise recently. As shown by comparisons of Western and J-Western forms of CagA, there are 45 fixed or nearly fixed amino acid differences, and J-Western forms contain a unique 4-amino-acid insertion. The mean nucleotide diversity of synonymous sites (π(s)) is slightly lower in the J-Western group than in the Western and East Asian groups (0.066, 0.086, and 0.083, respectively), which suggests that the three groups have comparable, but not equivalent, effective population sizes. The reduced π(s) of the J-Western group is attributable to ancestral recombination events within the 5' region of cagA. Population genetic analyses suggest that within the cagA region encoding EPIYA motifs, the East Asian group underwent a marked reduction in effective population size compared to the Western and J-Western groups, in association with positive selection. Finally, we show that J-Western cagA sequences are found mainly in strains producing m2 forms of the secreted VacA toxin and propose that these functionally interacting proteins coevolved to optimize the gastric colonization capacity of H. pylori.
1 Communities
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14 MeSH Terms
Next generation analytic tools for large scale genetic epidemiology studies of complex diseases.
Mechanic LE, Chen HS, Amos CI, Chatterjee N, Cox NJ, Divi RL, Fan R, Harris EL, Jacobs K, Kraft P, Leal SM, McAllister K, Moore JH, Paltoo DN, Province MA, Ramos EM, Ritchie MD, Roeder K, Schaid DJ, Stephens M, Thomas DC, Weinberg CR, Witte JS, Zhang S, Zöllner S, Feuer EJ, Gillanders EM
(2012) Genet Epidemiol 36: 22-35
MeSH Terms: Data Mining, Gene-Environment Interaction, Genetic Variation, Genome-Wide Association Study, Humans, Molecular Epidemiology, National Institutes of Health (U.S.), Neoplasms, Phenotype, United States
Show Abstract · Added February 22, 2016
Over the past several years, genome-wide association studies (GWAS) have succeeded in identifying hundreds of genetic markers associated with common diseases. However, most of these markers confer relatively small increments of risk and explain only a small proportion of familial clustering. To identify obstacles to future progress in genetic epidemiology research and provide recommendations to NIH for overcoming these barriers, the National Cancer Institute sponsored a workshop entitled "Next Generation Analytic Tools for Large-Scale Genetic Epidemiology Studies of Complex Diseases" on September 15-16, 2010. The goal of the workshop was to facilitate discussions on (1) statistical strategies and methods to efficiently identify genetic and environmental factors contributing to the risk of complex disease; and (2) how to develop, apply, and evaluate these strategies for the design, analysis, and interpretation of large-scale complex disease association studies in order to guide NIH in setting the future agenda in this area of research. The workshop was organized as a series of short presentations covering scientific (gene-gene and gene-environment interaction, complex phenotypes, and rare variants and next generation sequencing) and methodological (simulation modeling and computational resources and data management) topic areas. Specific needs to advance the field were identified during each session and are summarized.
© 2011 Wiley Periodicals, Inc.
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10 MeSH Terms
Genetic determinants of lipid traits in diverse populations from the population architecture using genomics and epidemiology (PAGE) study.
Dumitrescu L, Carty CL, Taylor K, Schumacher FR, Hindorff LA, Ambite JL, Anderson G, Best LG, Brown-Gentry K, Bůžková P, Carlson CS, Cochran B, Cole SA, Devereux RB, Duggan D, Eaton CB, Fornage M, Franceschini N, Haessler J, Howard BV, Johnson KC, Laston S, Kolonel LN, Lee ET, MacCluer JW, Manolio TA, Pendergrass SA, Quibrera M, Shohet RV, Wilkens LR, Haiman CA, Le Marchand L, Buyske S, Kooperberg C, North KE, Crawford DC
(2011) PLoS Genet 7: e1002138
MeSH Terms: Adolescent, Adult, Aged, Aged, 80 and over, Continental Population Groups, Female, Gene Frequency, Genetics, Population, Genome-Wide Association Study, Humans, Linkage Disequilibrium, Lipid Metabolism, Lipoproteins, HDL, Lipoproteins, LDL, Male, Middle Aged, Molecular Epidemiology, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Risk Factors, Triglycerides, Young Adult
Show Abstract · Added December 10, 2013
For the past five years, genome-wide association studies (GWAS) have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE) study was established in 2008 to characterize GWAS-identified variants in diverse population-based studies. We genotyped 49 GWAS-identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG) levels in self-identified European American (~20,000), African American (~9,000), American Indian (~6,000), Mexican American/Hispanic (~2,500), Japanese/East Asian (~690), and Pacific Islander/Native Hawaiian (~175) adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92%) SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05) and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG) in European Americans generalized to African Americans (48%, 61%, and 57%), American Indians (45%, 64%, and 77%), and Mexican Americans/Hispanics (57%, 56%, and 86%). Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits.
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22 MeSH Terms
Disclosing individual CDKN2A research results to melanoma survivors: interest, impact, and demands on researchers.
Christensen KD, Roberts JS, Shalowitz DI, Everett JN, Kim SY, Raskin L, Gruber SB
(2011) Cancer Epidemiol Biomarkers Prev 20: 522-9
MeSH Terms: Adult, Aged, Disclosure, Female, Genes, p16, Genetic Predisposition to Disease, Genetic Testing, Humans, Male, Melanoma, Middle Aged, Molecular Epidemiology, Risk Factors, Survivors
Show Abstract · Added March 5, 2014
BACKGROUND - Whether to return individual research results from cancer genetics studies is widely debated, but little is known about how participants respond to results disclosure or about its time and cost burdens on investigators.
METHODS - We recontacted participants at one site of a multicenter genetic epidemiologic study regarding their CDKN2A gene test results and implications for melanoma risk. Interested participants were disclosed their results by telephone and followed for 3 months.
RESULTS - Among 39 patients approached, 27 were successfully contacted, and 19 (70% uptake) sought results, including three with mutations. Prior to disclosure, participants endorsed numerous benefits of receiving results (mean=7.7 of 9 posed), including gaining information relevant to their children's disease risk. Mean psychological well-being scores did not change from baseline, and no decreases to melanoma prevention behaviors were noted. Fifty-nine percent of participants reported that disclosure made participation in future research more likely. Preparation for disclosure required 40 minutes and $611 per recontact attempt. An additional 78 minutes and $68 was needed to disclose results.
CONCLUSION - Cancer epidemiology research participants who received their individual genetic research results showed no evidence of psychological harm or false reassurance from disclosure and expressed strong trust in the accuracy of results. Burdens to our investigators were high, but protocols may differ in their demands and disclosure may increase participants' willingness to enroll in future studies.
IMPACT - Providing individual study results to cancer genetics research participants poses potential challenges for investigators, but many participants desire and respond positively to this information.
©2011 AACR.
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14 MeSH Terms