Marylyn D Ritchie

Summary

Affiliation: Vanderbilt University
Country: USA

Publications

  1. pmc Optimization of neural network architecture using genetic programming improves detection and modeling of gene-gene interactions in studies of human diseases
    Marylyn D Ritchie
    Program in Human Genetics and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN, 37232 0700, USA
    BMC Bioinformatics 4:28. 2003
  2. pmc Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record
    Marylyn D Ritchie
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    Am J Hum Genet 86:560-72. 2010
  3. ncbi request reprint Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy
    Asha R Kallianpur
    Department of Medicine, Divisions of General Internal Medicine and Public Health, Nashville, TN, USA
    AIDS 20:1503-13. 2006
  4. pmc Genetic variation in the rhythmonome: ethnic variation and haplotype structure in candidate genes for arrhythmias
    William S Bush
    Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
    Pharmacogenomics 10:1043-53. 2009
  5. pmc Pitfalls of merging GWAS data: lessons learned in the eMERGE network and quality control procedures to maintain high data quality
    Rebecca L Zuvich
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
    Genet Epidemiol 35:887-98. 2011
  6. pmc Genetic determinants of response to warfarin during initial anticoagulation
    Ute I Schwarz
    Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
    N Engl J Med 358:999-1008. 2008
  7. pmc Assessing the accuracy of observer-reported ancestry in a biorepository linked to electronic medical records
    Logan Dumitrescu
    Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
    Genet Med 12:648-50. 2010
  8. pmc African mitochondrial DNA subhaplogroups and peripheral neuropathy during antiretroviral therapy
    Jeffrey A Canter
    Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 345 24th Ave North, Nashville, TN 37203, USA
    J Infect Dis 201:1703-7. 2010
  9. pmc Relative contribution of CYP2C9 and VKORC1 genotypes and early INR response to the prediction of warfarin sensitivity during initiation of therapy
    Chun Li
    Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
    Blood 113:3925-30. 2009
  10. pmc Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome science
    Joshua C Denny
    Office of Personalized Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232 0575, USA
    Circulation 122:2016-21. 2010

Detail Information

Publications91

  1. pmc Optimization of neural network architecture using genetic programming improves detection and modeling of gene-gene interactions in studies of human diseases
    Marylyn D Ritchie
    Program in Human Genetics and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN, 37232 0700, USA
    BMC Bioinformatics 4:28. 2003
    ....
  2. pmc Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record
    Marylyn D Ritchie
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    Am J Hum Genet 86:560-72. 2010
    ....
  3. ncbi request reprint Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy
    Asha R Kallianpur
    Department of Medicine, Divisions of General Internal Medicine and Public Health, Nashville, TN, USA
    AIDS 20:1503-13. 2006
    ..Since iron deficiency is associated with some types of PN, and iron is essential for mitochondrial function, we tested the hypothesis that hemochromatosis (HFE) gene mutations influence susceptibility to NRTI-induced PN...
  4. pmc Genetic variation in the rhythmonome: ethnic variation and haplotype structure in candidate genes for arrhythmias
    William S Bush
    Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
    Pharmacogenomics 10:1043-53. 2009
    ..Here, we report an evaluation of the variation and haplotype structure in six key components of the rhythmonome...
  5. pmc Pitfalls of merging GWAS data: lessons learned in the eMERGE network and quality control procedures to maintain high data quality
    Rebecca L Zuvich
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
    Genet Epidemiol 35:887-98. 2011
    ..Our experience demonstrates that merging multiple datasets after additional QC can be an efficient use of genotype data despite new challenges that appear in the process...
  6. pmc Genetic determinants of response to warfarin during initial anticoagulation
    Ute I Schwarz
    Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
    N Engl J Med 358:999-1008. 2008
    ....
  7. pmc Assessing the accuracy of observer-reported ancestry in a biorepository linked to electronic medical records
    Logan Dumitrescu
    Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
    Genet Med 12:648-50. 2010
    ....
  8. pmc African mitochondrial DNA subhaplogroups and peripheral neuropathy during antiretroviral therapy
    Jeffrey A Canter
    Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 345 24th Ave North, Nashville, TN 37203, USA
    J Infect Dis 201:1703-7. 2010
    ..7 [95% confidence interval, 1.1-12.0]). An African mtDNA subhaplogroup is for the first time implicated in susceptibility to nucleoside reverse-transcriptase inhibitor-associated toxicity...
  9. pmc Relative contribution of CYP2C9 and VKORC1 genotypes and early INR response to the prediction of warfarin sensitivity during initiation of therapy
    Chun Li
    Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
    Blood 113:3925-30. 2009
    ..08) and VKORC1 (P = .30) were not associated with stable warfarin dose. Thus, much of the information provided by CYP2C9 and VKORC1 genotypes during warfarin initiation is captured by the early INR response...
  10. pmc Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome science
    Joshua C Denny
    Office of Personalized Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232 0575, USA
    Circulation 122:2016-21. 2010
    ..The extent to which this can be demonstrated in cohorts derived from electronic medical records is unknown...
  11. pmc Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER
    Emily R Holzinger
    Vanderbilt University, Nashville, TN 37232, USA
    J Neurovirol 18:511-20. 2012
    ....
  12. pmc Mitochondrial genomics and CD4 T-cell count recovery after antiretroviral therapy initiation in AIDS clinical trials group study 384
    Benjamin J Grady
    Vanderbilt University Center for Human Genetics Research, Nashville, TN, USA
    J Acquir Immune Defic Syndr 58:363-70. 2011
    ..In this study, full mitochondrial DNA (mtDNA) sequence data from US-based adult participants in the AIDS Clinical Trials Group study 384 was used to assess associations between mtDNA variants and CD4 T-cell recovery with ART...
  13. ncbi request reprint Multilocus genetic interactions and response to efavirenz-containing regimens: an adult AIDS clinical trials group study
    Alison A Motsinger
    Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
    Pharmacogenet Genomics 16:837-45. 2006
    ..We examined whether long-term responses to efavirenz, and/or plasma efavirenz exposure, are better predicted by multilocus genetic interactions than by individual polymorphisms...
  14. ncbi request reprint Human genomic association studies: a primer for the infectious diseases specialist
    Alison A Motsinger
    School of Medicine, Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
    J Infect Dis 195:1737-44. 2007
    ..Our goal is to provide the infectious diseases specialist with information that will aid in the critical evaluation of publications that include human genomic analyses...
  15. pmc An association analysis of Alzheimer disease candidate genes detects an ancestral risk haplotype clade in ACE and putative multilocus association between ACE, A2M, and LRRTM3
    Todd L Edwards
    Department of Molecular Physiology and Biophysics and Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee 37232, USA
    Am J Med Genet B Neuropsychiatr Genet 150:721-35. 2009
    ....
  16. pmc Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies
    Joshua C Denny
    Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA
    Am J Hum Genet 89:529-42. 2011
    ..Our findings indicate that EMR-linked genomic data could allow discovery of genes associated with many diseases without additional genotyping cost...
  17. pmc Machine learning for detecting gene-gene interactions: a review
    Brett A McKinney
    Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical School, Nashville, Tennessee, USA
    Appl Bioinformatics 5:77-88. 2006
    ..We conclude with some ideas about how these methods and others can be integrated into a comprehensive and flexible framework for data mining and knowledge discovery in human genetics...
  18. pmc PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations
    Joshua C Denny
    Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
    Bioinformatics 26:1205-10. 2010
    ..The primary outcome of this study was replication of seven previously known SNP-disease associations for these SNPs...
  19. ncbi request reprint Drug transporter and metabolizing enzyme gene variants and nonnucleoside reverse-transcriptase inhibitor hepatotoxicity
    Marylyn D Ritchie
    Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    Clin Infect Dis 43:779-82. 2006
    ..Decreased risk of hepatotoxicity was associated with MDR1 3435C-->T (odds ratio, 0.254; P=.021). An interaction between MDR1 and hepatitis B surface antigen status predicted risk with 82% accuracy (P<.001)...
  20. pmc Exploring the performance of Multifactor Dimensionality Reduction in large scale SNP studies and in the presence of genetic heterogeneity among epistatic disease models
    Todd L Edwards
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tenn, USA
    Hum Hered 67:183-92. 2009
    ..Previously unknown aspects of MDR performance were the power to detect interactive effects given large numbers of non-model loci or varying degrees of heterogeneity among multiple epistatic disease models...
  21. pmc Interaction between interleukin 3 and dystrobrevin-binding protein 1 in schizophrenia
    Todd L Edwards
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
    Schizophr Res 106:208-17. 2008
    ..We also observed a significant main effect in DTNBP1, which survived correction for multiple comparisons, and numerous nominally significant effects in several genes...
  22. pmc Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records
    Matthew T Oetjens
    Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University, 2215 Garland Avenue, 519 Light Hall, Nashville, TN 37232 0700, USA
    Pharmacogenomics 14:735-44. 2013
    ..The ADME Core Panel assays 184 variants across 34 pharmacogenes, many of which are difficult to accurately genotype with standard multiplexing methods...
  23. pmc Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus
    William S Bush
    Department of Molecular Physiology, Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA
    Bioinformatics 26:578-9. 2010
    ....
  24. doi request reprint Genome simulation approaches for synthesizing in silico datasets for human genomics
    Marylyn D Ritchie
    Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
    Adv Genet 72:1-24. 2010
    ..Many of the hallmark features of biological datasets can be synthesized in silico; still much research is needed to enhance our capabilities to create datasets that capture the natural complexity of biological datasets...
  25. ncbi request reprint Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions
    Lance W Hahn
    Program in Human Genetics and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232 0700, USA
    Bioinformatics 19:376-82. 2003
    ..In this paper, we describe the MDR approach and an MDR software package...
  26. ncbi request reprint Clinical applications of whole-genome association studies: future applications at the bedside
    Alison A Motsinger
    Vanderbilt University, Center for Human Genetics Research Department of Molecular Physiology and Biophysics, 519 Light Hall, Nashville, TN 37232, USA
    Expert Rev Mol Diagn 6:551-65. 2006
    ....
  27. pmc Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin
    Hua Xu
    Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 18:387-91. 2011
    ..This study sought to develop natural-language-processing algorithms to extract drug-dose information from clinical text, and to assess the capabilities of such tools to automate the data-extraction process for pharmacogenetic studies...
  28. doi request reprint Evidence for extensive pleiotropy among pharmacogenes
    Matthew T Oetjens
    Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
    Pharmacogenomics 17:853-66. 2016
    ..We sought to identify potential pleiotropy involving pharmacogenes...
  29. pmc Genome-wide association study of plasma efavirenz pharmacokinetics in AIDS Clinical Trials Group protocols implicates several CYP2B6 variants
    Emily R Holzinger
    Center for Human Genetics Research bDepartments of Medicine, Pharmacology, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37204, USA
    Pharmacogenet Genomics 22:858-67. 2012
    ..Prior candidate gene studies have associated CYP2B6 516G→T [rs3745274] and 983T→C [rs28399499] with increased plasma efavirenz exposure. We sought to identify novel variants associated with efavirenz pharmacokinetics...
  30. pmc Chromosome 4q25 variants are genetic modifiers of rare ion channel mutations associated with familial atrial fibrillation
    Marylyn D Ritchie
    Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
    J Am Coll Cardiol 60:1173-81. 2012
    ..The aim of this study was to test the hypothesis that 2 common polymorphisms in the chromosome 4q25 region that have been associated with atrial fibrillation (AF) contribute to the variable penetrance of familial AF...
  31. pmc Enabling high-throughput genotype-phenotype associations in the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) project as part of the Population Architecture using Genomics and Epidemiology (PAGE) study
    William S Bush
    Department of Biomedical Informatics, Center for Human Genetics Research, Vanderbilt University, 2215 Garland Avenue, 519 Light Hall, Nashville, TN 37232, USA
    Pac Symp Biocomput . 2013
    ....
  32. ncbi request reprint Multilocus analysis of hypertension: a hierarchical approach
    Scott M Williams
    Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
    Hum Hered 57:28-38. 2004
    ..5% of the time. Thus, our data indicate epistatic interactions play a major role in hypertension susceptibility. Our data also support a model where multiple pathways need to be affected in order to predispose to hypertension...
  33. pmc BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge
    Carrie B Moore
    Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
    BMC Med Genomics 6:S6. 2013
    ..The novelty of BioBin is access to comprehensive knowledge-guided multi-level binning. For example, bin boundaries can be formed using genomic locations from: functional regions, evolutionary conserved regions, genes, and/or pathways...
  34. pmc Multifactor dimensionality reduction: an analysis strategy for modelling and detecting gene-gene interactions in human genetics and pharmacogenomics studies
    Alison A Motsinger
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232 0700, USA
    Hum Genomics 2:318-28. 2006
    ..MDR can be a powerful tool in reaching these goals when used appropriately...
  35. pmc Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction
    William S Bush
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
    BMC Bioinformatics 9:238. 2008
    ..We sought to improve the ability of MDR to detect gene-gene interactions by replacing classification error with a different measure to score model quality...
  36. ncbi request reprint The effect of reduction in cross-validation intervals on the performance of multifactor dimensionality reduction
    Alison A Motsinger
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee 37232 0700, USA
    Genet Epidemiol 30:546-55. 2006
    ..The validity of this reduction was confirmed with data from an Alzheimer's disease (AD) study...
  37. ncbi request reprint Immunogenetics of CD4 lymphocyte count recovery during antiretroviral therapy: An AIDS Clinical Trials Group study
    David W Haas
    Center for Human Genetics Research, Vanderbilt University, Nashville, TN, 37203, USA
    J Infect Dis 194:1098-107. 2006
    ..Immune recovery during antiretroviral therapy is a complex phenotype that is influenced by multiple genetic variants. Future studies should validate these tentative associations and define underlying mechanisms...
  38. pmc European mitochondrial DNA haplogroups and metabolic changes during antiretroviral therapy in AIDS Clinical Trials Group Study A5142
    Todd Hulgan
    Vanderbilt University, Nashville, Tennessee, USA
    AIDS 25:37-47. 2011
    ..Mitochondrial DNA (mtDNA) influences metabolic diseases and perhaps antiretroviral therapy (ART) complications. We explored associations between European mtDNA haplogroups and metabolic changes among A5142 participants...
  39. pmc Quality control procedures for genome-wide association studies
    Stephen Turner
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
    Curr Protoc Hum Genet . 2011
    ..We propose best practices and discuss areas of ongoing and future research...
  40. pmc Characterization of the Metabochip in diverse populations from the International HapMap Project in the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) project
    Dana C Crawford
    Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, 2215 Garland Avenue, 519 Light Hall, Nashville, TN 37232, USA
    Pac Symp Biocomput . 2013
    ....
  41. pmc Multiphenotype association study of patients randomized to initiate antiretroviral regimens in AIDS Clinical Trials Group protocol A5202
    Anurag Verma
    aThe Center for Systems Genomics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park bBiomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania cLos Angeles Biomedical Research Institute at Harbor, UCLA Medical Center, Torrance, California dUniversity of Rochester Medical Center, Rochester eDepartment of Pharmacy Practice, Center for Integrated Global Biomedical Sciences, University at Buffalo, SUNY, Buffalo, New York fVanderbilt University School of Medicine gMeharry Medical College, Nashville, Tennessee, USA
    Pharmacogenet Genomics . 2017
    ....
  42. pmc The use of a DNA biobank linked to electronic medical records to characterize pharmacogenomic predictors of tacrolimus dose requirement in kidney transplant recipients
    Kelly A Birdwell
    Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennesse, USA
    Pharmacogenet Genomics 22:32-42. 2012
    ..The importance of other drug absorption, distribution, metabolism, and elimination (ADME) gene variants has not been well characterized...
  43. pmc Polymorphism modulates symptomatic response to antiarrhythmic drug therapy in patients with lone atrial fibrillation
    Dawood Darbar
    Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37323 6602, USA
    Heart Rhythm 4:743-9. 2007
    ....
  44. pmc Genetic analysis of biological pathway data through genomic randomization
    Brian L Yaspan
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
    Hum Genet 129:563-71. 2011
    ..Using the KEGG database as an example, we apply PARIS to the publicly available Autism Genetic Resource Exchange GWAS dataset, revealing pathways with a significant enrichment of positive association results...
  45. ncbi request reprint Risk factor interactions and genetic effects associated with post-operative atrial fibrillation
    Alison A Motsinger
    Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
    Pac Symp Biocomput . 2006
    ..Applying this approach, we were able to elucidate potential associations with postoperative atrial fibrillation...
  46. pmc Using BioBin to explore rare variant population stratification
    Carrie B Moore
    Center for Human Genetics Research, Vanderbilt University, 519 Light Hall, Nashville, TN 37232, USA
    Pac Symp Biocomput . 2013
    ..Our results show interesting variant differences between two ancestral populations and demonstrate that population stratification is a pervasive concern for sequence analyses...
  47. pmc Genetic variants associated with serum thyroid stimulating hormone (TSH) levels in European Americans and African Americans from the eMERGE Network
    Jennifer R Malinowski
    Center for Human Genetics Research, Vanderbilt University, Nashville, TN, United States of America
    PLoS ONE 9:e111301. 2014
    ..These results support the previously reported association between PDE8B and serum TSH levels in European Americans and emphasize the need for additional genetic studies in more diverse populations. ..
  48. pmc Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans
    Janina M Jeff
    Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
    Ann Hum Genet 77:321-32. 2013
    ..This work provides a catalogue of generalized versus nongeneralized associations, a necessary step in prioritizing GWAS-identified regions for further fine-mapping in diverse populations. ..
  49. pmc A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data
    Carrie C Buchanan
    Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
    J Am Med Inform Assoc 19:289-94. 2012
    ..In 2008 the 1000 Genomes Project aimed to sequence 2500 individuals and identify rare variants and 99% of variants with a MAF of <1%...
  50. ncbi request reprint Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an adult AIDS clinical trials group study
    Todd Hulgan
    Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
    AIDS 19:1341-9. 2005
    ..The objective of this study was to determine if NRTI-associated peripheral neuropathy is associated with European mitochondrial haplogroups...
  51. ncbi request reprint Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity
    Marylyn D Ritchie
    Program in Human Genetics and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232 0700, USA
    Genet Epidemiol 24:150-7. 2003
    ..Extending MDR to address genetic heterogeneity should be a priority for the continued methodological development of this new approach...
  52. ncbi request reprint Bioinformatics approaches for detecting gene-gene and gene-environment interactions in studies of human disease
    Marylyn D Ritchie
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee 37232 0700, USA
    Neurosurg Focus 19:E2. 2005
    ..Finally, the author describes the future directions for this technique and related methodologies...
  53. pmc Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions
    William S Bush
    Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
    Bioinformatics 22:2173-4. 2006
    ..AVAILABILITY: Parallel MDR is freely available for non-commercial research institutions. For full details see http://chgr.mc.vanderbilt.edu/ritchielab/pMDR. An open-source version of MDR software is available at http://www.epistasis.org...
  54. pmc GPNN: power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease
    Alison A Motsinger
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232 0700, USA
    BMC Bioinformatics 7:39. 2006
    ..The goal of this study was to evaluate the power of GPNN for identifying high-order gene-gene interactions. We were also interested in applying GPNN to a real data analysis in Parkinson's disease...
  55. pmc Persistent atrial fibrillation is associated with reduced risk of torsades de pointes in patients with drug-induced long QT syndrome
    Dawood Darbar
    Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37323 6602, USA
    J Am Coll Cardiol 51:836-42. 2008
    ..The goal of this study was to identify markers of torsades de pointes (TdP) in patients with drug-associated long QT syndrome (LQTS)...
  56. pmc Identifying the genotype behind the phenotype: a role model found in VKORC1 and its association with warfarin dosing
    Dana C Crawford
    Vanderbilt University, Center for Human Genetics Research, 519 Light Hall, Nashville, TN 37232, USA
    Pharmacogenomics 8:487-96. 2007
    ..These future avenues will be best explored using diverse approaches encompassing clinical, statistical and genomic methods currently being developed for genotype-phenotype studies in human populations...
  57. pmc Using prior knowledge and genome-wide association to identify pathways involved in multiple sclerosis
    Marylyn D Ritchie
    Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, 519 Light Hall, Nashville, TN 37232 0700, USA
    Genome Med 1:65. 2009
    ..This and other pathway-based approaches are likely to continue to emerge in the GWAS literature, as they provide a powerful strategy to detect important modest single-locus effects and gene-gene interaction effects...
  58. pmc Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis
    Sarah A Pendergrass
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville TN, USA
    BioData Min 3:10. 2010
    ....
  59. pmc ATHENA: a tool for meta-dimensional analysis applied to genotypes and gene expression data to predict HDL cholesterol levels
    Emily R Holzinger
    Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
    Pac Symp Biocomput . 2013
    ..Additionally, our modeling method was able to capture more of the HDL-C variation than a linear regression model that included the same variables...
  60. pmc Visual integration of results from a large DNA biobank (BioVU) using synthesis-view
    Sarah Pendergrass
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, 507D Light Hall, Nashville, TN 37205, USA
    Pac Symp Biocomput . 2011
    ..Synthesis-View is freely available for non-commercial research institutions, for full details see https://chgr.mc.vanderbilt.edu/synthesisview...
  61. pmc Discovery of gene-gene interactions across multiple independent data sets of late onset Alzheimer disease from the Alzheimer Disease Genetics Consortium
    Timothy J Hohman
    Vanderbilt Memory and Alzheimer s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
    Neurobiol Aging 38:141-50. 2016
    ..Further, our results highlight the utility of evaluating genetic interactions to explain additional variance in AD risk and identify novel molecular mechanisms of AD pathogenesis. ..
  62. pmc Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies
    Emily R Holzinger
    Center for Human Genetics Research, Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN, USA
    Pharmacogenomics 13:213-22. 2012
    ..For this article, we examine two major categories of approaches for integrated data analysis, give examples of their use in experimental and in silico datasets, and assess the limitations of each method...
  63. ncbi request reprint Multifactor dimensionality reduction for detecting gene-gene and gene-environment interactions in pharmacogenomics studies
    Marylyn D Ritchie
    Vanderbilt University Medical Center, Department of Molecular Physiology and Biophysics, 519 Light Hall, Center for Human Genetics Research, Nashville, TN 37232 0700, USA
    Pharmacogenomics 6:823-34. 2005
    ..This computational technology is described in detail in this review, and its application in pharmacogenomic studies is demonstrated...
  64. ncbi request reprint STUDENTJAMA. The challenges of whole-genome approaches to common diseases
    Jason H Moore
    Vanderbilt University Medical School, Nashville, Tenn, USA
    JAMA 291:1642-3. 2004
  65. ncbi request reprint Complex gene-gene interactions in multiple sclerosis: a multifactorial approach reveals associations with inflammatory genes
    Alison A Motsinger
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, 519 Light Hall, Vanderbilt University Medical School, Nashville, TN 37232 0700, USA
    Neurogenetics 8:11-20. 2007
    ..These results suggest that significant epistasis, or gene-gene interactions, may exist even in the absence of statistically significant individual main effects...
  66. pmc Exploring epistasis in candidate genes for rheumatoid arthritis
    Marylyn D Ritchie
    Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical Center, 21st Avenue South and Garland Avenue, Nashville, Tennessee 37232, USA
    BMC Proc 1:S70. 2007
    ..This comparison should be extended in future studies with both simulated and real data...
  67. pmc Genetic variation in the mitochondrial enzyme carbamyl-phosphate synthetase I predisposes children to increased pulmonary artery pressure following surgical repair of congenital heart defects: a validated genetic association study
    Jeffrey A Canter
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
    Mitochondrion 7:204-10. 2007
    ..In conclusion, the CPSI T1405N genotype appears to be an important new factor in predicting susceptibility to increased PAP following surgical repair of congenital cardiac defects in children...
  68. ncbi request reprint Estrogens, enzyme variants, and breast cancer: a risk model
    Philip S Crooke
    Department of Pathology, TVC 4918, Vanderbilt University, Nashville, TN 37232, USA
    Cancer Epidemiol Biomarkers Prev 15:1620-9. 2006
    ..The model offers the opportunity to combine metabolic, genetic, and lifetime exposure data in assessing estrogens as a breast cancer risk factor...
  69. ncbi request reprint Trends in genomic variation: a view of some of the latest technologies
    Marylyn D Ritchie
    Vanderbilt University, Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Nashville, TN 37232, USA
    Drug Discov Today 10:1417-8. 2005
  70. pmc LD-spline: mapping SNPs on genotyping platforms to genomic regions using patterns of linkage disequilibrium
    William S Bush
    Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
    BioData Min 2:7. 2009
    ..SNPs in the genome can represent broader genomic regions via linkage disequilibrium (LD), and population-specific patterns of LD can be exploited to generate a data-driven map of SNPs to genes...
  71. pmc The effects of linkage disequilibrium in large scale SNP datasets for MDR
    Benjamin J Grady
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
    BioData Min 4:11. 2011
    ..In this study, we examined the effect of LD on the sensitivity of the Multifactor Dimensionality Reduction (MDR) software package...
  72. doi request reprint Basic statistics
    Jason H Moore
    Vanderbilt University Medical School, Nashville, Tennessee, USA
    Curr Protoc Hum Genet . 2003
    ..Also provided is a list of references and software for commonly used statistical methods...
  73. pmc ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci
    Stephen D Turner
    Center for Human Genetics Research, Departments of Molecular Physiology and Biophysics and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
    BioData Min 3:5. 2010
    ..Non-additive gene-gene interactions, which are not often explored, are thought to be one source of this "missing" heritability...
  74. ncbi request reprint Nephrocystin-conserved domains involved in targeting to epithelial cell-cell junctions, interaction with filamins, and establishing cell polarity
    John C Donaldson
    Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    J Biol Chem 277:29028-35. 2002
    ....
  75. ncbi request reprint Subsets of the major tyrosine phosphorylation sites in Crk-associated substrate (CAS) are sufficient to promote cell migration
    Nah Young Shin
    Department of Cell and Developmental Biology, Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    J Biol Chem 279:38331-7. 2004
    ..Effective wound healing was achieved by CAS variants containing as few as four of the major sites, indicating sufficiency of partial SD signaling function in this cell migration response...
  76. ncbi request reprint Renin-angiotensin system gene polymorphisms and coronary artery disease in a large angiographic cohort: detection of high order gene-gene interaction
    Chia Ti Tsai
    Division of Cardiology, Department of Internal Medicine, National Taiwan, University Hospital, Taipei, Taiwan
    Atherosclerosis 195:172-80. 2007
    ..These results are compatible with the concept of multilocus and multi-gene effects in complex diseases that would be missed with conventional approaches...
  77. ncbi request reprint Renin-angiotensin system gene polymorphisms and atrial fibrillation
    Chia Ti Tsai
    Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
    Circulation 109:1640-6. 2004
    ..We hypothesized that RAS genes might be among the susceptibility genes of nonfamilial structural AF and conducted a genetic case-control study to demonstrate this...
  78. ncbi request reprint ABCB1 and GST polymorphisms associated with TP53 status in breast cancer
    Silje H Nordgard
    Department of Genetics, The Norwegian Radium Hospital, University of Oslo, Oslo, Norway
    Pharmacogenet Genomics 17:127-36. 2007
    ..The goal of this study was to characterize the genetic variation in the ABCB1, GSTM1, GSTT1 and GSTP1 genes, as well as the haplotype structure in the ABCB1 gene...
  79. ncbi request reprint A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction
    Digna R Velez
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee
    Genet Epidemiol 31:306-15. 2007
    ..These results suggest that balanced accuracy should be used instead of accuracy for the MDR analysis of epistasis in imbalanced datasets...
  80. pmc An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene interactions on risk of myocardial infarction: the importance of model validation
    Christopher S Coffey
    Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294 0022, USA
    BMC Bioinformatics 5:49. 2004
    ..One advantage of the MDR method is that it provides an internal prediction error for validation. We summarize our use of this internal prediction error for model validation...
  81. pmc A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose
    Gregory M Cooper
    Department of Genome Sciences, University of Washington, Seattle, WA98195, USA
    Blood 112:1022-7. 2008
    ..Randomized clinical trials that account for these 2 genes should therefore produce results that are definitive and broadly applicable...
  82. ncbi request reprint Susceptibility and modifier genes in Portuguese transthyretin V30M amyloid polyneuropathy: complexity in a single-gene disease
    Miguel L Soares
    Department of Molecular and Experimental Medicine, Division of Rheumatology Research and the WM Keck Autoimmune Disease Center, The Scripps Research Institute, La Jolla, CA 92037, USA
    Hum Mol Genet 14:543-53. 2005
    ..Thus, although the TTR V30M mutation is required for the disease in Portuguese patients, different genetic factors may govern the age of onset, as well as the occurrence of anticipation...
  83. doi request reprint Comparison of approaches for machine-learning optimization of neural networks for detecting gene-gene interactions in genetic epidemiology
    Alison A Motsinger-Reif
    Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
    Genet Epidemiol 32:325-40. 2008
    ..Finally, we demonstrate the scalability of the GENN method with increasing numbers of variables--as many as 500,000 single nucleotide polymorphisms...
  84. ncbi request reprint Pacific Symposium on Biocomputing--computational approaches for pharmacogenomics
    Russell A Wilke
    Marshfield Clinic, Center for Human Genetics, and Department of Internal Medicine, 1000 N Oak Ave, Marshfield, WI 54449, and Department of Genetics, Stanford University, CA 94305 5120, USA
    Pharmacogenomics 6:111-3. 2005
  85. ncbi request reprint Discussing gene-gene interaction: warning--translating equations to English may result in jabberwocky
    Christopher W Bartlett
    Center for Quantitative and Computational Biology and Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, USA
    Genet Epidemiol 31:S61-7. 2007
    ..The difficulty of using (primarily) affected sib pair data in a gene x gene interaction analysis is explored...
  86. ncbi request reprint Problems with genome-wide association studies
    Scott M Williams
    Science 316:1840-2. 2007
  87. ncbi request reprint Different contributions of polymorphisms in VKORC1 and CYP2C9 to intra- and inter-population differences in maintenance dose of warfarin in Japanese, Caucasians and African-Americans
    Harumi Takahashi
    Department of Pharmacotherapy, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan
    Pharmacogenet Genomics 16:101-10. 2006
    ....
  88. ncbi request reprint Investigation of potential gene-gene interactions between APOE and RELN contributing to autism risk
    Allison E Ashley-Koch
    Center for Human Genetics, Department of Medicine, Duke University Medical Center, Snyderman Genomic Sciences Building, Durham, NC 27710, USA
    Psychiatr Genet 17:221-6. 2007
    ..RELN shares a common biological pathway with APOE, and Persico et al. have observed transmission distortion of the APOE-2 allele in autism families...
  89. ncbi request reprint Single-nucleotide polymorphisms for diagnosis of salt-sensitive hypertension
    Hironobu Sanada
    Third Department of Internal Medicine, Fukushima Medical University, School of Medicine, Fukushima City, Japan
    Clin Chem 52:352-60. 2006
    ..Salt-sensitive (SS) hypertension affects >30 million Americans and is often associated with low plasma renin activity. We tested the diagnostic validity of several candidate genes for SS and low-renin hypertension...
  90. ncbi request reprint Novel methods for detecting epistasis in pharmacogenomics studies
    Alison A Motsinger
    North Carolina State University, Bioinformatics Research Center, Department of Statistics, Raleigh, NC 27695, USA
    Pharmacogenomics 8:1229-41. 2007
    ..The overall goal of this paper is to aid researchers in developing an analysis plan that accounts for gene-gene and gene-environment in their own work...
  91. ncbi request reprint Genetic heterogeneity is not as threatening as you might think
    Marylyn D Ritchie
    Genet Epidemiol 31:797-800. 2007