Research Topics
Genomes and Genes
Species | E J van den OordSummaryAffiliation: Virginia Commonwealth University Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
Estimation of CpG coverage in whole methylome next-generation sequencing studiesEdwin J C G van den Oord
Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, P O Box 980533, Richmond, VA 23298, USA
BMC Bioinformatics 14:50. 2013..This hampers several aspects of the data analysis such as the calculation of enrichment measures that are based on the number of fragments covering the CpGs...- Estimating the number and size of the main effects in genome-wide case-control association studiesPo Hsiu Kuo
Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, 800 East Leigh Street, Biotech 1, VIPBG, Suite 1 130, Richmond, Virginia 23219, USA
BMC Proc 1:S143. 2007..Further improvements and extensions of the proposed methods are conceivable, such as estimating the distribution of effect sizes and taking population stratification into account when obtain estimates of p0 and effect size... - A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profilingHailong Meng
Altria Client Services, Research Development and Engineering, Richmond, VA 23219, USA
BMC Bioinformatics 11:227. 2010..Inclusion of these so-called "non-variable sites" will increase the risk of false discoveries and reduce statistical power to detect biologically relevant methylation markers... 
Identification of a high-risk haplotype for the dystrobrevin binding protein 1 (DTNBP1) gene in the Irish study of high-density schizophrenia familiesE J C G van den Oord
Department of Psychiatry and Virginia Institute for Psychiatric and Behavioral Genetics, Medical College of Virginia, Virginia Commonwealth University, Richmond, VA 23298 0126, USA
Mol Psychiatry 8:499-510. 2003..Implications of these findings for follow-up and replication studies are discussed...- False discoveries and models for gene discoveryEdwin J C G van den Oord
Virginia Institute for Psychiatric and Behavioral Genetics, Medical College of Virginia, Virginia Commonwealth University, Richmond, VA 23298 0126, USA
Trends Genet 19:537-42. 2003..This raises the question of whether current models for gene discovery are shaped excessively by a fear of false discoveries... - Controlling false discoveries in genetic studiesEdwin J C G van den Oord
Center for Biomarker Research and Personalized Medicine, Medical College of Virginia, Virginia Commonwealth University, Richmond, Virginia 23298 0533, USA
Am J Med Genet B Neuropsychiatr Genet 147:637-44. 2008..The final section discusses the role of replication studies for eliminating false discoveries and the complexities associated with the definition of what constitutes a replication and the design of these studies... - Genetics and diagnostic refinementEdwin van den Oord
Center for Biomarker Research and Personalized Medicine, Department of Pharmacy, Medical College of Virginia, Virginia Commonwealth University, 980533, Richmond, VA 23298 0533, USA
Behav Genet 37:535-45. 2007.... - Will haplotype maps be useful for finding genes?E J C G van den Oord
Virginia Institute for Psychiatric and Behavioral Genetics, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA, USA
Mol Psychiatry 9:227-36. 2004..In the final section, we summarize our main conclusions and comment on the usefulness of haplotype maps for finding genes... - Modeling with measured genotypes: effects of the vitamin D receptor gene, age, and latent genetic and environmental factors on bone mineral densityEdwin J C G van den Oord
Virginia Institute for Psychiatric and Behavioral Genetics, Medical College of Virginia, PO Box 980126, Richmond, VA 23298 0126, USA
Behav Genet 34:197-206. 2004.... - A framework for controlling false discovery rates and minimizing the amount of genotyping in the search for disease mutationsEdwin J C G van den Oord
Virginia Institute for Psychiatric and Behavioral Genetics, Medical College of Virginia Virginia Commonwealth University, PO Box 980126, Richmond, VA 23298 0126, USA
Hum Hered 56:188-99. 2003..To develop a method for designing studies to find disease mutations that can achieve a set of goals with respect to proportions of false and true discoveries with the minimum amount of genotyping... - Ethnic differences in birth weight: maternal effects emerge from an analysis involving mixed-race us couplesEdwin J C G van den Oord
Medical College of Virginia of Virginia Commonwealth University, Richmond, Virginia 23298 0126, USA
Ethn Dis 16:706-11. 2006..Specific candidates include cultural differences in lifestyle that are traditionally not measured in large-scale surveys. Multiple lines of evidence in the literature also suggest that maternal genes are involved... - FP-TDI SNP scoring by manual and statistical procedures: a study of error rates and typesE J C G van den Oord
Department of Psychiatry, Virginia Commonwealth University, P O Box 980126, Richmond, VA 23298 0126, USA
Biotechniques 34:610-6, 618-20, 622 passim. 2003..There were 3.3% more missing genotypes in the manual scoring due to errors in data manipulation (1.7%) and conservative scoring (1.6%)... - Normal variation and abnormality: an empirical study of the liability distributions underlying depression and delinquencyEdwin J C G van den Oord
Department of Psychiatry, Medical College of Virginia of Virginia Commonwealth University, Richmond 23298 0126, USA
J Child Psychol Psychiatry 44:180-92. 2003..This invites an interpretation of their forming an abnormal group, one that may be qualitatively distinct... 
Genomewide association analysis followed by a replication study implicates a novel candidate gene for neuroticismEdwin J C G van den Oord
Center for Biomarker Research and Personalized Medicine, Medical College of Virginia, Virginia Commonwealth University, PO Box 980533, Richmond, VA 23298 0533, USA
Arch Gen Psychiatry 65:1062-71. 2008..It has long been linked to internalizing psychiatric conditions, such as anxiety and depression, and it accounts for much of the substantial comorbidity seen between these disorders...- Estimating effect sizes in genome-wide association studiesJozsef Bukszar
Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Medical College of Virginia, Virginia Commonwealth University, P O Box 980533, Richmond, VA 23298 0533, USA
Behav Genet 40:394-403. 2010..Simulations suggest that the effects are estimated precisely with only a small upward bias. The R codes that compute the effect estimates are freely downloadable from the website: http://www.people.vcu.edu/~jbukszar/... - Factor structure and external validity of the PANSS revisitedEdwin J C G van den Oord
Virginia Institute for Psychiatric and Behavioral Genetics, Medical College of Virginia of Virginia Commonwealth University, P O Box 980126, Richmond VA 23298 0126, USA
Schizophr Res 82:213-23. 2006..Our analyses also suggested that some of the controversy about the PANSS can possibly be attributed to methodological factors where the substantial cross-loadings of some PANSS items may play an important role... - A systematic method for estimating individual responses to treatment with antipsychotics in CATIEEdwin J C G van den Oord
Center for Biomarker Research and Personalized Medicine, Medical College of Virginia of Virginia Commonwealth University, Richmond VA, USA
Schizophr Res 107:13-21. 2009..A major challenge, however, is how to estimate the individual responses to treatments. For this purpose, we propose a systematic method that condenses all information collected during the trials in an optimal, empirical fashion... - A step in another direction: looking for maternal genetic and environmental effects on racial differences in birth weightE J van den Oord
Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, P O Box 980126, Richmond, VA 23298 0126, USA
Demography 38:573-6. 2001.... - Estimating effects of latent and measured genotypes in multilevel modelsE J van den Oord
Utrecht University, Utrecht, The Netherlands
Stat Methods Med Res 10:393-407. 2001..To illustrate the approach we used birth weight data of 5562 children from 3643 fathers from 3186 mothers in 2873 extended families to which simulated genotypes of a hypothetical locus were added... - Including measured genotypes in statistical models to study the interplay of multiple factors affecting complex traitsEdwin J van den Oord
Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond 23298 0126, USA
Behav Genet 32:1-22. 2002..An example is also given that illustrates how the model could be applied to real data... - Association study between GABA receptor genes and anxiety spectrum disordersXuan Pham
Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia 23298 0126, USA
Depress Anxiety 26:998-1003. 2009..In this investigation, we explored four GABA receptor genes for their possible associations with genetic risk for anxiety disorders and depression... - Framework for identifying quantitative trait loci in association studies using structural equation modelingE J van den Oord
Institute of Psychiatry, London, UK, and Utrecht University, Utrecht, The Netherlands
Genet Epidemiol 18:341-59. 2000..This suggested that in the extreme and very specific conditions in which population admixture may cause false-positive findings, admixture can often be detected... - Differences between school classes in preschoolers' psychosocial adjustment: evidence for the importance of children's interpersonal relationsE J van den Oord
Utrecht University, The Netherlands
J Child Psychol Psychiatry 40:417-30. 1999.... - Continuity and change in children's social maladjustment: a developmental behavior genetic studyE J van den Oord
Department of Family Studies, Utrecht University, The Netherlands
Dev Psychol 33:319-32. 1997..To represent the genetic and shared environmental mechanisms underlying stability in problem behavior, the authors preffered liability models without time specific effects... - Racial differences in birth health risk: a quantitative genetic approachE J van den Oord
Utrecht University, Department of Child and Adolescent Psychology, The Netherlands
Demography 37:285-98. 2000.... - The use of mixture models to perform quantitative tests for linkage disequilibrium, maternal effects, and parent-of-origin effects with incomplete subject-parent triadsE J van den Oord
Department of Child and Adolescent Psychology, Utrecht University, The Netherlands
Behav Genet 30:335-43. 2000..Extensions of the model to nuclear families, multiple loci, and multiple outcome variables are briefly discussed... - Multivariate adaptive regression splines: a powerful method for detecting disease-risk relationship differences among subgroupsTimothy P York
Massey Cancer Center, Virginia Commonwealth University, Virginia Institute for Psychiatric and Behavioral Genetics, P O Box 980003, Richmond, VA 23298 0003, USA
Stat Med 25:1355-67. 2006..It was shown that power was higher even if the regression curve was linear, that gains increased with the complexity of the curve, and that for highly non-linear curves model-free methods such as MARS might be the only alternative... - Genomewide association study of movement-related adverse antipsychotic effectsKarolina Aberg
Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Medical College of Virginia of Virginia Commonwealth University, Richmond, Virginia 23298, USA
Biol Psychiatry 67:279-82. 2010..Understanding individual differences in the development of extrapyramidal side effects (EPS) as a response to antipsychotic therapy is essential to individualize treatment... - Model-based gene selection shows engrailed 1 is associated with antipsychotic responseBradley Todd Webb
Center for Biomarker Research and Personalized Medicine, Department of Pharmacy, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298, USA
Pharmacogenet Genomics 18:751-9. 2008..We sought to find genes that may influence treatment response in a less biased manner, after integrating heterogeneous data sources related to schizophrenia... - Association study of CREB1 with Major Depressive Disorder and related phenotypesJohn M Hettema
Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, 23298 0126, USA
Am J Med Genet B Neuropsychiatr Genet 150:1128-32. 2009..However, none of these markers were significant in stage 2 in either sex individually or combined. Our data suggests that common variations in the CREB1 gene do not appear to increase susceptibility for MDD or related phenotypes... - In silico whole genome association scan for murine prepulse inhibitionBradley Todd Webb
Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond, VA, USA
PLoS ONE 4:e5246. 2009.... - Estimating the posterior probability that genome-wide association findings are true or falseJozsef Bukszar
Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Medical College of Virginia, Virginia Commonwealth University, 1112 East Clay Street, PO Box 980533, Richmond, Virginia 23298, USA
Bioinformatics 25:1807-13. 2009..This lack of information increases the chance of false discoveries and may result in real effects being missed... - Asthma pharmacogenetic study using finite mixture models to handle drug-response heterogeneityTimothy P York
Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298 0003, USA
Pharmacogenomics 10:753-67. 2009..In this paper, we estimate drug nonresponse in a clinical trial for the asthma drug montelukast as either the result of an inactive genetic variant or the presence of subgroups of patients not responding to the drug... - (1)H nuclear magnetic resonance metabolomics analysis identifies novel urinary biomarkers for lung functionJoseph L McClay
Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, USA
J Proteome Res 9:3083-90. 2010..Our results will require replication and validation, but demonstrate the utility of NMR metabolomics as a screening tool for identifying novel biomarkers of pulmonary outcomes... - High-resolution mass spectrometry proteomics for the identification of candidate plasma protein biomarkers for chronic obstructive pulmonary diseaseTimothy P York
Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298 0003, USA
Biomarkers 15:367-77. 2010..This research demonstrates the utility of proteomic profiling to improve the understanding of molecular mechanisms involved in cigarette smoking-related COPD by identifying plasma proteins that correlate with decline in lung function... - Genome-wide pharmacogenomic study of neurocognition as an indicator of antipsychotic treatment response in schizophreniaJoseph L McClay
Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298 0533, USA
Neuropsychopharmacology 36:616-26. 2011..This study has generated several novel candidate genes for antipsychotic response. However, our findings will require replication and functional validation. To facilitate replication efforts, we provide all GWAS p-values for download... - Catechol-O-methyltransferase contributes to genetic susceptibility shared among anxiety spectrum phenotypesJohn M Hettema
Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, 23298 0126, USA
Biol Psychiatry 64:302-10. 2008..Catechol-O-methyltransferase (COMT) has been investigated for its possible role in a wide range of psychiatric phenotypes. In particular, several studies support association of this gene with panic disorder and other anxiety-related traits... - Lack of association between the amiloride-sensitive cation channel 2 (ACCN2) gene and anxiety spectrum disordersJohn M Hettema
Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia 23298 0126, USA
Psychiatr Genet 18:73-9. 2008..In this study, we examined, for the first time, the human analog of ASIC1, the amiloride-sensitive cation channel 2 (ACCN2) gene, for its association with genetic risk across a range of anxiety spectrum phenotypes... - Accurate and efficient power calculations for 2 x m tables in unmatched case-control designsJozsef Bukszar
Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, 23298 0126, USA
Stat Med 25:2632-46. 2006..This suggests that CE can be used to calculate power for tables where researchers would feel comfortable using Pearson's chi-square test... - AKT1 is associated with schizophrenia across multiple symptom dimensions in the Irish study of high density schizophrenia familiesDawn L Thiselton
Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia 23298 0424, USA
Biol Psychiatry 63:449-57. 2008..The AKT1 gene has also been implicated in schizophrenia by association studies and decreased protein expression in the brains of schizophrenic patients... - Variance component analysis of polymorphic metabolic systemsJoseph L McClay
Virginia Institute for Psychiatric and Behavioral Genetics, Medical College of Virginia, Virginia Commonwealth University, Biotech 1, 800 East Leigh Street, Richmond, VA 23298 0126, USA
J Theor Biol 240:149-59. 2006..We believe that implementation of this approach holds promise of a better understanding of the genotype to phenotype transition, particularly in integrating small allelic effects into larger frameworks... - lga972: a cross-platform application for optimizing LD studies using a genetic algorithmJaime R Robles
Virginia Institute for Psychiatric and Behavioral Genetics, Medical College of Virginia of Virginia Commonwealth University, Richmond, VA 23298 0126, USA
Bioinformatics 20:3244-5. 2004..lga972 is a user-friendly cross-platform application with a graphical interface for determining the design features of two-stage genetic linkage disequilibrium studies that minimize the genotyping burden... - A method for analyzing strain differences in acquisition of IV cocaine self-administration in miceCristina Vargas-Irwin
Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298 0126 USA
Behav Genet 36:525-35. 2006..In a second stage, strains differences in these indexes were assessed. This two-stage approach is illustrated with drug self-administration data and through a computer simulation... - Optimization of two-stage genetic designs where data are combined using an accurate and efficient approximation for Pearson's statisticJozsef Bukszar
Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Medical College of Virginia of Virginia Commonwealth University, P O Box 980126, Richmond, Virginia 23298 0126, U S A
Biometrics 62:1132-7. 2006..Compared to not combining data, combining the data decreases the required sample sizes on average by 15% and the genotyping burden by 5%... - A cautionary note on the use of simulation procedures for analyzing contingency tables containing small expected cell frequenciesJaime R Robles
Virginia Institute for Psychiatric and Behavioral Genetics, Medical College of Virginia, Virginia Commonwealth University, Richmond, 23298 0126, USA
Am J Med Genet B Neuropsychiatr Genet 141:414-7. 2006..Exact tests are recommended as an alternative to naive simulation for evaluating the statistical significance of contingency tables with small expected cell counts... - Genomewide linkage study in the Irish affected sib pair study of alcohol dependence: evidence for a susceptibility region for symptoms of alcohol dependence on chromosome 4C A Prescott
Department of Psychology, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, USA
Mol Psychiatry 11:603-11. 2006..The results of this study suggest the importance of genetic variation in chromosome 4 in the etiology and severity of alcoholism in Caucasian populations... - WISC profiles in child psychiatric diagnosis: sense or nonsense?J Rispens
Department of Child and Adolescent Psychiatry, Utrecht University, The Netherlands
J Am Acad Child Adolesc Psychiatry 36:1587-94. 1997..WISC factor structure, the specificity of WISC factors, and diagnostic correlates of WISC profiles were studied to investigate the contribution of WISC profile analysis to child psychiatric diagnosis... - An evaluation of nonresponse bias in peer, self, and teacher ratings of children's psychosocial adjustmentM H Gerrits
Utrecht University, The Netherlands
J Child Psychol Psychiatry 42:593-602. 2001..Instead, we argue that to assess nonresponse bias the specific conditions and analyses of the study will need to be considered and special measures may be required... - Disentangling genetic, environmental, and rater effects on internalizing and externalizing problem behavior in 10-year-old twinsMeike Bartels
Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
Twin Res 7:162-75. 2004..Significant influences of additive genetic, shared environmental and unique environmental factors were found for internalizing and externalizing syndromes... - Growth of left ventricular mass in African American and European American youthCaroline Dekkers
Georgia Prevention Institute, Medical College of Georgia, Augusta
Hypertension 39:943-51. 2002..Apart from these ethnicity and gender effects, individual differences in cardiac growth can mainly be explained by body growth and increases in general adiposity... - Genetic and environmental contributions to stability and change in children's internalizing and externalizing problemsJolande C van der Valk
Department of Biological Psychology, Vrije Universiteit, Van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
J Am Acad Child Adolesc Psychiatry 42:1212-20. 2003..To estimate genetic, shared environmental, and nonshared environmental contributions to stability and change in internalizing and externalizing problems... - A study of parent ratings of internalizing and externalizing problem behavior in 12-year-old twinsMeike Bartels
Department of Biological Psychiatry, Vrije Universiteit, Room 1F 66, Van der Boechorststraat 1, 1081 BT Amsterdam, The Netherlands
J Am Acad Child Adolesc Psychiatry 42:1351-9. 2003..This study investigates two models that have been used to explain the agreement and disagreement between mothers and fathers in the ratings of their children... - Pharmacogenetics of the 5-lipoxygenase biosynthetic pathway and variable clinical response to montelukastMichael Klotsman
GlaxoSmithKline, Research Triangle Park, North Carolina 27709 3398, USA
Pharmacogenet Genomics 17:189-96. 2007..Genetic variability in 5-lipoxygenase biosynthetic and receptor pathway gene loci may influence cysteinyl-leukotriene production and subsequent response to leukotriene modifiers... - Moderators of blood pressure development from childhood to adulthood: a 10-year longitudinal studyJ Caroline Dekkers
Georgia Prevention Institute, Medical College of Georgia, Augusta 30912, USA
J Pediatr 141:770-9. 2002..The ethnic differences cannot be entirely explained by individual differences in SES, growth, or adiposity. Identification of mechanisms responsible for increase of BP in childhood will improve prevention of hypertension in adulthood... - Twins and the study of rater (dis)agreementMeike Bartels
Department of Biological Psychology, VU University
Psychol Methods 12:451-66. 2007..Rater-specific shared environmental factors show substantial influence on stability. This could mean that rater bias may be persistent and affect longitudinal studies...
Research Grants
- Candidate Genes in Models of Mental HealthEdwin van den Oord; Fiscal Year: 2003..Furthermore, the empirical applications will not only have been of scientific importance but, e.g. by refining diagnostic classification, also have implications for prevention and clinical intervention. ..
- Design and analysis of adaptive multistage genetic association studiesEdwin van den Oord; Fiscal Year: 2010..The goal of this project is to develop a flexible framework for designing these studies in a cost-effective way and optimize subsequent replication efforts. ..
- A genome-wide association study to detect genetic variation for schizophreniaEdwin van den Oord; Fiscal Year: 2010..We attempt to contribute to the rigorous evaluation of the common disease/common genetic variant model for schizophrenia, which is key to further understand its pathophysiology and develop effective treatments. ..
- In silico genome scan with high-throughput addiction related phenotypes in miceEdwin van den Oord; Fiscal Year: 2007....
- Design and analysis of adaptive multistage genetic association studiesEdwin van den Oord; Fiscal Year: 2009..The goal of this project is to develop a flexible framework for designing these studies in a cost-effective way and optimize subsequent replication efforts. ..