Identifying the genotype behind the phenotype: a role model found in VKORC1 and its association with warfarin dosing.

PubWeight™: 1.12‹?› | Rank: Top 10%

🔗 View Article (PMC 3112050)

Published in Pharmacogenomics on May 01, 2007

Authors

Dana C Crawford1, Marylyn D Ritchie, Mark J Rieder

Author Affiliations

1: Vanderbilt University, Center for Human Genetics Research, 519 Light Hall, Nashville, TN 37232, USA. crawford@chgr.mc.vanderbilt.edu

Articles cited by this

A haplotype map of the human genome. Nature (2005) 105.70

The sequence of the human genome. Science (2001) 101.55

Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature (1953) 47.27

Whole-genome re-sequencing. Curr Opin Genet Dev (2006) 35.24

Complement factor H polymorphism in age-related macular degeneration. Science (2005) 31.10

A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science (2006) 27.49

Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet (2001) 17.43

A comprehensive review of genetic association studies. Genet Med (2002) 16.75

Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet (2003) 16.51

Replication validity of genetic association studies. Nat Genet (2001) 16.30

Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28

A common genetic variant is associated with adult and childhood obesity. Science (2006) 14.95

Population stratification and spurious allelic association. Lancet (2003) 10.53

Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet (2002) 9.18

Association study designs for complex diseases. Nat Rev Genet (2001) 8.91

Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. N Engl J Med (2005) 8.77

The importance of race and ethnic background in biomedical research and clinical practice. N Engl J Med (2003) 7.94

The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered (2003) 7.42

Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction. Nat Genet (2002) 6.46

Race and genomics. N Engl J Med (2003) 6.19

Mutations in VKORC1 cause warfarin resistance and multiple coagulation factor deficiency type 2. Nature (2004) 5.95

The complex interplay among factors that influence allelic association. Nat Rev Genet (2004) 5.26

The impact of CYP2C9 and VKORC1 genetic polymorphism and patient characteristics upon warfarin dose requirements: proposal for a new dosing regimen. Blood (2005) 4.91

A polymorphism in the VKORC1 gene is associated with an interindividual variability in the dose-anticoagulant effect of warfarin. Blood (2004) 4.70

Toward the 1,000 dollars human genome. Pharmacogenomics (2005) 4.68

Identification of the gene for vitamin K epoxide reductase. Nature (2004) 4.52

Genes, environment and the value of prospective cohort studies. Nat Rev Genet (2006) 4.33

Highly parallel genomic assays. Nat Rev Genet (2006) 4.24

Recent developments in genomewide association scans: a workshop summary and review. Am J Hum Genet (2005) 3.76

Common VKORC1 and GGCX polymorphisms associated with warfarin dose. Pharmacogenomics J (2005) 3.75

What makes a good genetic association study? Lancet (2005) 3.46

Genetic associations in large versus small studies: an empirical assessment. Lancet (2003) 3.41

Association of warfarin dose with genes involved in its action and metabolism. Hum Genet (2006) 3.27

BiDil for heart failure in black patients: The U.S. Food and Drug Administration perspective. Ann Intern Med (2007) 3.13

Influence of coagulation factor, vitamin K epoxide reductase complex subunit 1, and cytochrome P450 2C9 gene polymorphisms on warfarin dose requirements. Clin Pharmacol Ther (2006) 3.06

Detection of gene x gene interactions in genome-wide association studies of human population data. Hum Hered (2007) 2.97

A novel functional VKORC1 promoter polymorphism is associated with inter-individual and inter-ethnic differences in warfarin sensitivity. Hum Mol Genet (2005) 2.97

Drug reactions enzymes, and biochemical genetics. J Am Med Assoc (1957) 2.67

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. Pharmacogenet Genomics (2006) 2.66

Priorities and standards in pharmacogenetic research. Nat Genet (2005) 2.65

Use of pharmacogenetics and clinical factors to predict the maintenance dose of warfarin. Thromb Haemost (2004) 2.64

Optimization of neural network architecture using genetic programming improves detection and modeling of gene-gene interactions in studies of human diseases. BMC Bioinformatics (2003) 2.47

Pharmacogenetics of warfarin: current status and future challenges. Pharmacogenomics J (2006) 2.40

Congenital deficiency of vitamin K dependent coagulation factors in two families presents as a genetic defect of the vitamin K-epoxide-reductase-complex. Thromb Haemost (2000) 2.34

Testing for population subdivision and association in four case-control studies. Am J Hum Genet (2002) 2.26

Combined genetic profiles of components and regulators of the vitamin K-dependent gamma-carboxylation system affect individual sensitivity to warfarin. Thromb Haemost (2006) 2.22

The patterns of natural variation in human genes. Annu Rev Genomics Hum Genet (2005) 2.12

Comment on "A common genetic variant is associated with adult and childhood obesity". Science (2007) 2.04

Warfarin response and vitamin K epoxide reductase complex 1 in African Americans and Caucasians. Clin Pharmacol Ther (2007) 2.01

Pharmacogenetics goes genomic. Nat Rev Genet (2003) 2.00

Patient-specific factors predictive of warfarin dosage requirements. Ann Pharmacother (2002) 1.96

Pharmacogenomics: challenges and opportunities. Ann Intern Med (2006) 1.96

A coding VKORC1 Asp36Tyr polymorphism predisposes to warfarin resistance. Blood (2006) 1.94

Comment on "A common genetic variant is associated with adult and childhood obesity". Science (2007) 1.93

Comment on "A common genetic variant is associated with adult and childhood obesity". Science (2007) 1.86

Interethnic variability of warfarin maintenance requirement is explained by VKORC1 genotype in an Asian population. Clin Pharmacol Ther (2006) 1.84

Apolipoprotein E genotype and warfarin dosing among Caucasians and African Americans. Pharmacogenomics J (2007) 1.78

Genotypes of vitamin K epoxide reductase, gamma-glutamyl carboxylase, and cytochrome P450 2C9 as determinants of daily warfarin dose in Japanese patients. Thromb Res (2006) 1.78

Genotypes of the cytochrome p450 isoform, CYP2C9, and the vitamin K epoxide reductase complex subunit 1 conjointly determine stable warfarin dose: a prospective study. J Thromb Thrombolysis (2006) 1.78

Heritable resistance to warfarin in rats. Nature (1967) 1.77

Role of dietary vitamin K intake in chronic oral anticoagulation: prospective evidence from observational and randomized protocols. Am J Med (2004) 1.73

Association of Vitamin K epoxide reductase complex 1 (VKORC1) variants with warfarin dose in a Hong Kong Chinese patient population. Pharmacogenet Genomics (2005) 1.72

Deeper into the genome. Nature (2005) 1.70

Shaking the tree: mapping complex disease genes with linkage disequilibrium. Lancet (2005) 1.67

Will tomorrow's medicines work for everyone? Nat Genet (2004) 1.61

What makes a good case-control study? Design issues for complex traits such as endometriosis. Hum Reprod (2002) 1.59

VKORC1 haplotypes and their impact on the inter-individual and inter-ethnical variability of oral anticoagulation. Thromb Haemost (2005) 1.55

Pharmacodynamic resistance to warfarin associated with a Val66Met substitution in vitamin K epoxide reductase complex subunit 1. Thromb Haemost (2005) 1.54

Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions. Bioinformatics (2006) 1.53

Warfarin dose and the pharmacogenomics of CYP2C9 and VKORC1 - rationale and perspectives. Thromb Res (2006) 1.43

Race-based therapeutics. N Engl J Med (2004) 1.41

Polymorphisms in the VKORC1 gene are strongly associated with warfarin dosage requirements in patients receiving anticoagulation. J Med Genet (2006) 1.38

Interaction of warfarin with drugs, natural substances, and foods. J Clin Pharmacol (2005) 1.31

Pharmacogenomics: from bedside to clinical practice. Hum Mol Genet (2006) 1.28

GPNN: power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease. BMC Bioinformatics (2006) 1.26

VKORC1 gene variations are the major contributors of variation in warfarin dose in Japanese patients. Clin Pharmacol Ther (2006) 1.22

Lymphotoxin-alpha gene and risk of myocardial infarction in 6,928 cases and 2,712 controls in the ISIS case-control study. PLoS Genet (2006) 1.16

A new vitamin K epoxide reductase complex subunit-1 (VKORC1) mutation in a patient with decreased stability of CYP2C9 enzyme. J Thromb Haemost (2006) 0.99

Homozygosity mapping of a second gene locus for hereditary combined deficiency of vitamin K-dependent clotting factors to the centromeric region of chromosome 16. Blood (2002) 0.94

Misreading race and genomics after BiDil. Nat Genet (2005) 0.93

A vitamin K epoxide reductase complex subunit-1 (VKORC1) mutation in a patient with vitamin K antagonist resistance. J Thromb Haemost (2005) 0.92

A number no greater than the sum of its parts: the use and abuse of heritability. Hum Biol (2003) 0.88

A gene-anchored map position of the rat warfarin-resistance locus, Rw, and its orthologs in mice and humans. Blood (2000) 0.87

Articles by these authors

Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet (2003) 21.52

Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet (2008) 20.73

Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science (2012) 17.12

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature (2012) 14.76

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet (2010) 12.63

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet (2011) 11.94

Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics (2003) 9.91

The eMERGE Network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies. BMC Med Genomics (2011) 9.20

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature (2012) 8.91

Genetic determinants of response to warfarin during initial anticoagulation. N Engl J Med (2008) 7.13

Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol (2004) 7.11

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics (2010) 7.07

Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet (2004) 6.99

Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. Am J Hum Genet (2012) 5.48

Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet (2003) 5.30

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nat Biotechnol (2013) 4.85

Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res (2005) 4.81

The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future. Genet Med (2013) 4.37

Common missense variant in the glucokinase regulatory protein gene is associated with increased plasma triglyceride and C-reactive protein but lower fasting glucose concentrations. Diabetes (2008) 4.20

A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction. Genet Epidemiol (2007) 4.15

A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose. Blood (2008) 4.02

Pattern of sequence variation across 213 environmental response genes. Genome Res (2004) 3.93

Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet (2004) 3.91

Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies. Am J Hum Genet (2011) 3.85

Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet (2004) 3.73

Meta-analysis identifies six new susceptibility loci for atrial fibrillation. Nat Genet (2012) 3.71

Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. Am J Hum Genet (2008) 3.61

Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. Proc Natl Acad Sci U S A (2011) 3.54

Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome science. Circulation (2010) 3.35

Return of individual research results from genome-wide association studies: experience of the Electronic Medical Records and Genomics (eMERGE) Network. Genet Med (2012) 3.29

Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study. Lancet (2013) 3.21

Renin-angiotensin system gene polymorphisms and atrial fibrillation. Circulation (2004) 3.02

The Next PAGE in understanding complex traits: design for the analysis of Population Architecture Using Genetics and Epidemiology (PAGE) Study. Am J Epidemiol (2011) 2.98

Estimating coverage and power for genetic association studies using near-complete variation data. Nat Genet (2008) 2.80

Using synthetic templates to design an unbiased multiplex PCR assay. Nat Commun (2013) 2.72

Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet (2011) 2.68

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. Pharmacogenet Genomics (2006) 2.66

Polymorphism modulates symptomatic response to antiarrhythmic drug therapy in patients with lone atrial fibrillation. Heart Rhythm (2007) 2.62

Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus. Bioinformatics (2010) 2.59

Machine learning for detecting gene-gene interactions: a review. Appl Bioinformatics (2006) 2.56

TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome. Nat Genet (2012) 2.50

Data simulation software for whole-genome association and other studies in human genetics. Pac Symp Biocomput (2006) 2.49

Quality control procedures for genome-wide association studies. Curr Protoc Hum Genet (2011) 2.48

A statin-dependent QTL for GATM expression is associated with statin-induced myopathy. Nature (2013) 2.46

Genome-wide association of lipid-lowering response to statins in combined study populations. PLoS One (2010) 2.43

Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy. Am J Hum Genet (2011) 2.38

Detection of structural variants and indels within exome data. Nat Methods (2011) 2.27

Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pac Symp Biocomput (2009) 2.26

Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Nat Genet (2012) 2.14

Assessing the accuracy of observer-reported ancestry in a biorepository linked to electronic medical records. Genet Med (2010) 2.09

Generalization and dilution of association results from European GWAS in populations of non-European ancestry: the PAGE study. PLoS Biol (2013) 2.08

Genetic variation is associated with C-reactive protein levels in the Third National Health and Nutrition Examination Survey. Circulation (2006) 2.00

Genetic variants associated with the white blood cell count in 13,923 subjects in the eMERGE Network. Hum Genet (2011) 2.00

Relative contribution of CYP2C9 and VKORC1 genotypes and early INR response to the prediction of warfarin sensitivity during initiation of therapy. Blood (2008) 1.99

STUDENTJAMA. The challenges of whole-genome approaches to common diseases. JAMA (2004) 1.95

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. BMC Bioinformatics (2004) 1.95

Exome sequencing identifies SMAD3 mutations as a cause of familial thoracic aortic aneurysm and dissection with intracranial and other arterial aneurysms. Circ Res (2011) 1.93

CYP4F2 is a vitamin K1 oxidase: An explanation for altered warfarin dose in carriers of the V433M variant. Mol Pharmacol (2009) 1.92

Effect of CYP2B6, ABCB1, and CYP3A5 polymorphisms on efavirenz pharmacokinetics and treatment response: an AIDS Clinical Trials Group study. J Infect Dis (2010) 1.91

Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Circ Cardiovasc Genet (2008) 1.89

Multilocus analysis of hypertension: a hierarchical approach. Hum Hered (2004) 1.82

Evaluating pathogenicity of rare variants from dilated cardiomyopathy in the exome era. Circ Cardiovasc Genet (2012) 1.78

An analysis of the relative effects of VKORC1 and CYP2C9 variants on anticoagulation related outcomes in warfarin-treated patients. Thromb Haemost (2008) 1.76

Comparison of approaches for machine-learning optimization of neural networks for detecting gene-gene interactions in genetic epidemiology. Genet Epidemiol (2008) 1.75

Subsets of the major tyrosine phosphorylation sites in Crk-associated substrate (CAS) are sufficient to promote cell migration. J Biol Chem (2004) 1.74

Association of Vitamin K epoxide reductase complex 1 (VKORC1) variants with warfarin dose in a Hong Kong Chinese patient population. Pharmacogenet Genomics (2005) 1.72

Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network. PLoS Genet (2013) 1.70

Variation in the 3-hydroxyl-3-methylglutaryl coenzyme a reductase gene is associated with racial differences in low-density lipoprotein cholesterol response to simvastatin treatment. Circulation (2008) 1.68

Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin. J Am Med Inform Assoc (2011) 1.67

Complement receptor 1 gene variants are associated with erythrocyte sedimentation rate. Am J Hum Genet (2011) 1.66

Predicting warfarin dosage in European-Americans and African-Americans using DNA samples linked to an electronic health record. Pharmacogenomics (2012) 1.66

Efficient selection of tagging single-nucleotide polymorphisms in multiple populations. Hum Genet (2006) 1.66

VKORC1 polymorphisms, haplotypes and haplotype groups on warfarin dose among African-Americans and European-Americans. Pharmacogenomics (2008) 1.65

Finding unique filter sets in PLATO: a precursor to efficient interaction analysis in GWAS data. Pac Symp Biocomput (2010) 1.64

A comparison of analytical methods for genetic association studies. Genet Epidemiol (2008) 1.61

High-throughput genotyping of intermediate-size structural variation. Hum Mol Genet (2006) 1.61

Variation in the 4q25 chromosomal locus predicts atrial fibrillation after coronary artery bypass graft surgery. Circ Cardiovasc Genet (2009) 1.59

Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions. Bioinformatics (2006) 1.53

Routine Discovery of Complex Genetic Models using Genetic Algorithms. Appl Soft Comput (2004) 1.53

Genome-wide association study of plasma efavirenz pharmacokinetics in AIDS Clinical Trials Group protocols implicates several CYP2B6 variants. Pharmacogenet Genomics (2012) 1.52

Single-nucleotide polymorphisms for diagnosis of salt-sensitive hypertension. Clin Chem (2006) 1.51

Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction. BMC Bioinformatics (2008) 1.50

Lack of associations of ten candidate coronary heart disease risk genetic variants and subclinical atherosclerosis in four US populations: the Population Architecture using Genomics and Epidemiology (PAGE) study. Atherosclerosis (2013) 1.48

A large candidate gene survey identifies the KCNE1 D85N polymorphism as a possible modulator of drug-induced torsades de pointes. Circ Cardiovasc Genet (2011) 1.48

Functional polymorphism in human CYP4F2 decreases 20-HETE production. Physiol Genomics (2007) 1.47

A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. Hum Genet (2013) 1.47

Next generation analytic tools for large scale genetic epidemiology studies of complex diseases. Genet Epidemiol (2011) 1.47

Renin-angiotensin system gene polymorphisms and coronary artery disease in a large angiographic cohort: detection of high order gene-gene interaction. Atherosclerosis (2006) 1.46

Application of Genetic Algorithms to the Discovery of Complex Models for Simulation Studies in Human Genetics. Proc Genet Evol Comput Conf (2002) 1.46

Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks. PLoS One (2011) 1.42

Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections. Am J Hum Genet (2013) 1.40

Problems with genome-wide association studies. Science (2007) 1.39

Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an adult AIDS clinical trials group study. AIDS (2005) 1.39

Susceptibility and modifier genes in Portuguese transthyretin V30M amyloid polyneuropathy: complexity in a single-gene disease. Hum Mol Genet (2005) 1.38

Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis. BioData Min (2010) 1.37

Multifactor dimensionality reduction: an analysis strategy for modelling and detecting gene-gene interactions in human genetics and pharmacogenomics studies. Hum Genomics (2006) 1.37

A phenomics-based strategy identifies loci on APOC1, BRAP, and PLCG1 associated with metabolic syndrome phenotype domains. PLoS Genet (2011) 1.35

FAM-MDR: a flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals. PLoS One (2010) 1.34

Genome-wide association study of plasma lipoprotein(a) levels identifies multiple genes on chromosome 6q. J Lipid Res (2009) 1.34