Research Topics
Genomes and GenesSpecies | Mark RiederSummaryAffiliation: University of Washington Country: USA Publications
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Publications
Sequence variation in the human transcription factor gene POU5F1Shehnaz K Hussain
University of California, Los Angeles, Division of Cancer Prevention and Control Research, School of Public Health and Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095 6900, USA
BMC Genet 9:15. 2008..3 kb region containing POU5F1, and to describe the linkage disequilibrium patterns, using DNA from individuals of African-descent (AD) and European-descent (ED)...
Gamma-glutamyl carboxylase (GGCX) tagSNPs have limited utility for predicting warfarin maintenance doseM J Rieder
Department of Genome Sciences, Epidemiology, and Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
J Thromb Haemost 5:2227-34. 2007..Gamma-glutamyl carboxylase (GGCX), in its role as a key component of the vitamin K cycle, is a potential candidate gene associated with warfarin treatment...- Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genomeM J Rieder
Department of Molecular Biotechnology, Box 357730, University of Washington, Seattle, WA 98195 7730, USA
Nucleic Acids Res 26:967-73. 1998.... - The environmental genome project: reference polymorphisms for drug metabolism genes and genome-wide association studiesMark J Rieder
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Drug Metab Rev 40:241-61. 2008..Herein, we review a subset of Phase I cytochrome P450 genes studied by the EGP, approaches to GWAS, and the sensitivity of available genotyping platforms to capture common sequence variation in this subset of drug metabolism genes... - Sequence variation in the human angiotensin converting enzymeM J Rieder
University of Washington, Department of Molecular Biotechnology, Seattle 98195, USA
Nat Genet 22:59-62. 1999..The highly correlated structure in DCP1 raises important issues for the determination of functional DNA variants within genes and genetic studies in humans based on marker association... - TagSNP analyses of the PON gene cluster: effects on PON1 activity, LDL oxidative susceptibility, and vascular diseaseChristopher S Carlson
The Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, The University of Washington, Seattle, USA
J Lipid Res 47:1014-24. 2006.... - Population history and natural selection shape patterns of genetic variation in 132 genesJoshua M Akey
Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
PLoS Biol 2:e286. 2004..More generally, our results have important implications for mapping genes underlying complex human diseases... - Sequence-based linkage analysisItay Furman
Division of Human Biology, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109-1024, USA
Am J Hum Genet 75:647-53. 2004..We validate these results experimentally by implementing the sequence-based linkage approach for chromosome 19 in CEPH pedigrees... - In-vitro and in-vivo effects of the CYP2C9*11 polymorphism on warfarin metabolism and doseGuoying Tai
Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
Pharmacogenet Genomics 15:475-81. 2005..To determine the in-vitro and in-vivo effects of the CYP2C9*11 polymorphism on (S)-warfarin metabolism... - Effect of VKORC1 haplotypes on transcriptional regulation and warfarin doseMark J Rieder
Department of Genome Sciences, University of Washington, Seattle, USA
N Engl J Med 352:2285-93. 2005..The management of warfarin therapy is complicated by a wide variation among patients in drug response. Variants in the gene encoding vitamin K epoxide reductase complex 1 (VKORC1) may affect the response to warfarin... - A genome-wide scan for common genetic variants with a large influence on warfarin maintenance doseGregory 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... - CYP2C9 haplotype structure in European American warfarin patients and association with clinical outcomesDavid L Veenstra
Department of Pharmacy, Environmental Health, Genome Sciences, and Medicinal Chemistry, University of Washington, Seattle, USA
Clin Pharmacol Ther 77:353-64. 2005..The goal of this study was to define the haplotype structure of the cytochrome P450 (CYP) 2C9 gene in a European American population and evaluate associations between CYP2C9 haplotypes and anticoagulation-related outcomes... - Genetic variation is associated with C-reactive protein levels in the Third National Health and Nutrition Examination SurveyDana C Crawford
Department of Genome Sciences, University of Washington, Seattle, USA
Circulation 114:2458-65. 2006..Increased serum C-reactive protein (CRP) is an independent risk factor for cardiovascular disease. Previous studies have suggested that genetic variation within the CRP gene is associated with serum CRP... - Human liver expression of CYP2C8: gender, age, and genotype effectsSuresh Babu Naraharisetti
Departments of Medicinal Chemistry, University of Washington, Seattle, WA 98195 7610, USA
Drug Metab Dispos 38:889-93. 2010..CYP2C8 mRNA or protein expression levels were not significantly affected by CYP2C8*3 or *4 genotype, gender, or age, and variation observed clinically in CYP2C8 activity warrants further investigation... - CYP4F2 is a vitamin K1 oxidase: An explanation for altered warfarin dose in carriers of the V433M variantMatthew G McDonald
Department of Medicinal Chemistry, University of Washington, Seattle, 98195, USA
Mol Pharmacol 75:1337-46. 2009..Therefore, patients with the rs2108622 polymorphism are likely to have elevated hepatic levels of VK1, necessitating a higher warfarin dose to elicit the same anticoagulant response... - An analysis of the relative effects of VKORC1 and CYP2C9 variants on anticoagulation related outcomes in warfarin-treated patientsLisa M Meckley
University of Washington, Department of Pharmacy, Seattle, WA 98195, USA
Thromb Haemost 100:229-39. 2008..This difference may be due, in part, to pharmacokinetics factors (e.g. drug half-life), which are influenced primarily by CYP2C9; these findings should be confirmed in additional studies... - Direct detection of null alleles in SNP genotyping dataChristopher S Carlson
Department of Genome Sciences, University of Washington, Seattle, WA 98195-7730, USA
Hum Mol Genet 15:1931-7. 2006..Detecting unexpected null alleles not only has benefits in QC of genotype data but may also be valuable in detecting rare, functional null alleles that would otherwise be missed... - Efficient selection of tagging single-nucleotide polymorphisms in multiple populationsBryan N Howie
Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA
Hum Genet 120:58-68. 2006..Using populations of African, Asian, and European ancestry, we also show that an optimal multi-population set of tagSNPs can be substantially smaller (up to 44%) than a typical set obtained through independent or sequential selection... - Polymorphisms within the C-reactive protein (CRP) promoter region are associated with plasma CRP levelsChristopher S Carlson
Department of Genome Sciences, University of Washington, Seattle, WA, USA
Am J Hum Genet 77:64-77. 2005..We also demonstrate the functional importance of these SNPs in vitro... - Paraoxonase activity, but not haplotype utilizing the linkage disequilibrium structure, predicts vascular diseaseGail P Jarvik
Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Wash, USA
Arterioscler Thromb Vasc Biol 23:1465-71. 2003..The effects of paraoxonase (PON1) activity and of genetic variation in the PON1 promoter and coding region on carotid artery disease (CAAD) were investigated... - Renin-angiotensin system haplotypes and the risk of myocardial infarction and stroke in pharmacologically treated hypertensive patientsKristin D Marciante
Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
Am J Epidemiol 166:19-27. 2007..17). In this case-control study, RAS gene haplotypes were not significantly associated with increased risks of myocardial infarction or stroke... - Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive proteinAlexander P Reiner
University of Washington, Department of Epidemiology, Seattle, WA 98195, USA
Am J Hum Genet 82:1193-201. 2008.... - Polymorphisms of the IL1-receptor antagonist gene (IL1RN) are associated with multiple markers of systemic inflammationAlexander P Reiner
Department of Epidemiology, Box 357236, University of Washington, Seattle, Washington 98195, USA
Arterioscler Thromb Vasc Biol 28:1407-12. 2008..Circulating levels of acute phase reactant proteins such as plasma C-reactive protein (CRP) are likely influenced by multiple genes regulating the innate immune response... - TagSNP evaluation for the association of 42 inflammation loci and vascular disease: evidence of IL6, FGB, ALOX5, NFKBIA, and IL4R loci effectsChristopher S Carlson
Division of Public Health Sciences, The Fred Hutchinson Cancer Research Center, The University of Washington, Seattle, WA, USA
Hum Genet 121:65-75. 2007..The NFKBIA and IL10RA expression levels significantly differed between subjects with CAAD and controls. These results support a role for genetic variation related to inflammation in CAAD and a causal role for specific gene products... 
Estimating coverage and power for genetic association studies using near-complete variation dataTushar R Bhangale
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Nat Genet 40:841-3. 2008..We quantify the power offered by these arrays for a range of disease models...- Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibriumChristopher S Carlson
Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
Am J Hum Genet 74:106-20. 2004..We demonstrate that, although common variation tends to be shared between populations, tagSNPs should be selected separately for populations with different ancestries... - Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genomeMichael A Eberle
Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
PLoS Genet 2:e142. 2006..The SNP pairs exhibiting perfect LD showed a significant bias for derived, nonancestral alleles, providing evidence for positive natural selection in the human genome... - A case study of acenocoumarol sensitivity and genotype-phenotype discordancy explained by combinations of polymorphisms in VKORC1 and CYP2C9Allan E Rettie
Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
Br J Clin Pharmacol 62:617-20. 2006..The study provides additional data in support of diminished CYP2C9 activity due to the presence of the rare *11 allele... - Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genesTushar R Bhangale
Department of Bioengineering, University of Washington, Seattle, WA 98195-7730, USA
Hum Mol Genet 14:59-69. 2005.... - Novel paraoxonase (PON1) nonsense and missense mutations predicted by functional genomic assay of PON1 statusGail P Jarvik
Department of Medicine, Division of Medical Genetics, The University of Washington, Seattle, Washington 98195 7720, USA
Pharmacogenetics 13:291-5. 2003.... - Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humansChristopher S Carlson
Department of Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, Washington 98195-7730, USA
Nat Genet 33:518-21. 2003.... - Genomic regions exhibiting positive selection identified from dense genotype dataChristopher S Carlson
Department of Genome Sciences, University of Washington, Seattle, Washington 98195 7730, USA
Genome Res 15:1553-65. 2005.... - Common genetic variation in the prothrombin gene, hormone therapy, and incident nonfatal myocardial infarction in postmenopausal womenLucia A Hindorff
Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98101, USA
Am J Epidemiol 163:600-7. 2006..These preliminary results suggest that common genetic variants in the prothrombin gene or other variants in linkage disequilibrium are associated with myocardial infarction in postmenopausal women... - Allelic spectrum of the natural variation in CRPDana C Crawford
Department of Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, WA 98195 7730, USA
Hum Genet 119:496-504. 2006..Collectively, these data suggest that several different types re-sequencing and genotyping approaches may be required to fully understand the complete spectrum of alleles that impact human phenotypes... - Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populationsDana C Crawford
Department of Genome Sciences, University of Washington, Seattle 98195 7730, USA
Am J Hum Genet 74:610-22. 2004.... - Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsisMark M Wurfel
Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
Am J Respir Crit Care Med 178:710-20. 2008..Polymorphisms affecting Toll-like receptor (TLR)-mediated responses could predispose to excessive inflammation during an infection and contribute to an increased risk for poor outcomes in patients with sepsis... - Single nucleotide polymorphism discovery in TBX1 in individuals with and without 22q11.2 deletion syndromeCarrie L Heike
Department of Pediatrics, Division of Craniofacial Medicine, University of Washington and Seattle Children s Hospital, Seattle, Washington 98105 5371, USA
Birth Defects Res A Clin Mol Teratol 88:54-63. 2010..The purpose of this study was to further characterize the sequence variability in TBX1 by identifying all common SNPs in this gene... - High-throughput genotyping of intermediate-size structural variationTera L Newman
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
Hum Mol Genet 15:1159-67. 2006..The approach we describe may be used to characterize a large number of individuals in a cost-effective manner once the sequence organization of ISVs is known... - Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndromeSarah B Ng
Department of Genome Sciences, University of Washington, Seattle, Washington, USA
Nat Genet 42:790-3. 2010..Our results strongly suggest that mutations in MLL2 are a major cause of Kabuki syndrome... - Soluble P-selectin, SELP polymorphisms, and atherosclerotic risk in European-American and African-African young adults: the Coronary Artery Risk Development in Young Adults (CARDIA) StudyAlexander P Reiner
Departments of Epidemiology, University of Washington, Seattle, WA 98195, USA
Arterioscler Thromb Vasc Biol 28:1549-55. 2008..To characterize the genetic and clinical correlates of soluble P-selectin, and the relationship of P-selectin to atherosclerotic risk, in young European-American (EA) and African-American (AA) adults... - Mitochondrial genetic variants and Alzheimer disease: a case-control study of the T4336C and G5460A variantsSteven D Edland
Department of Epidemiology, University of Washington, Seattle, Washington, USA
Alzheimer Dis Assoc Disord 16:1-7. 2002..Substantially larger samples than are currently available would be required to resolve this question. G5460(A/T) variants were also investigated and found not to be associated with Alzheimer disease... - Evidence for substantial fine-scale variation in recombination rates across the human genomeDana C Crawford
Department of Genome Sciences, University of Washington, Box 354322, Seattle, Washington 98195, USA
Nat Genet 36:700-6. 2004..No primary sequence characteristics are consistently associated with precise hot-spot location, although G+C content and nucleotide diversity are correlated with local recombination rate... - Autosomal dominant familial dyskinesia and facial myokymia: single exome sequencing identifies a mutation in adenylyl cyclase 5Ying Zhang Chen
Department of Medicine Medical Genetics, University of Washington, Seattle, WA 98195, USA
Arch Neurol 69:630-5. 2012..In a 5-generation family of German ancestry, we previously mapped FDFM to chromosome band 3p21-3q21. The 72.5-Mb linkage region was too large for traditional positional mutation identification... - Targeted enrichment of specific regions in the human genome by array hybridizationCatherine Igartua
University of Washington, Seattle, Washington, USA
Curr Protoc Hum Genet . 2010.... - Variation in the 3-hydroxyl-3-methylglutaryl coenzyme a reductase gene is associated with racial differences in low-density lipoprotein cholesterol response to simvastatin treatmentRonald M Krauss
Children s Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
Circulation 117:1537-44. 2008..We hypothesized that single nucleotide polymorphisms in the gene encoding HMGCR, a rate-limiting enzyme in cholesterol synthesis and the direct enzymatic target of statins, contribute to variation in statin response... - Functional polymorphism in human CYP4F2 decreases 20-HETE productionDavid E Stec
Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi 39216 4505, USA
Physiol Genomics 30:74-81. 2007..In contrast these variants had no effect on the omega-hydroxylation of LTB(4). These findings are the first to identify a functional variant in the human CYP4F2 gene that alters the production of 20-HETE... - Identifying the genotype behind the phenotype: a role model found in VKORC1 and its association with warfarin dosingDana 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... - A common VLDLR polymorphism interacts with APOE genotype in the prediction of carotid artery disease riskDana C Crawford
Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
J Lipid Res 49:588-96. 2008..These findings may further our understanding of VLDLR function, its ligand APOE, and ultimately the pathogenesis of CAAD in the general population... - Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humansSekar Kathiresan
Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
Nat Genet 40:189-97. 2008..Understanding the molecular, cellular and clinical consequences of the newly identified loci may inform therapy and clinical care... - Novel CYP2C9 promoter variants and assessment of their impact on gene expressionMelissa A Kramer
Department of Pediatrics, Medical College of Wisconsin, Milwaukee WI 53226, USA
Mol Pharmacol 73:1751-60. 2008..These data suggest that genetic variation within CYP2C9 regulatory sequences is likely to contribute to differences in CYP2C9 phenotype both within and among different populations... - LPA and PLG sequence variation and kringle IV-2 copy number in two populationsDana C Crawford
Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
Hum Hered 66:199-209. 2008..African-descent populations have, on average, higher levels of Lp(a), suggesting other genetic factors contribute to Lp(a) level variability across populations... - Integrating host genomics with surveillance for invasive bacterial diseasesDana C Crawford
Vanderbilt University, Nashville, Tennessee, USA
Emerg Infect Dis 14:1138-40. 2008..Using nDBS specimens, we resequenced CD46, putative host gene receptor for Neisseria meningitidis, and identified variants associated with susceptibility to this disease... - Association of Vitamin K epoxide reductase complex 1 (VKORC1) variants with warfarin dose in a Hong Kong Chinese patient populationDavid L Veenstra
School of Pharmacy, The Chinese University of Hong Kong, Hong Kong
Pharmacogenet Genomics 15:687-91. 2005..To evaluate the association of VKORC1 genetic variants with warfarin dose requirements in a Hong Kong Chinese patient population... - Pattern of sequence variation across 213 environmental response genesRobert J Livingston
Department of Genome Sciences, University of Washington, Seattle, Washington 98195-7730, USA
Genome Res 14:1821-31. 2004..The implications for the use of these data in direct and indirect association studies of environmentally induced diseases are discussed...
Research Grants
- Genetic Factors Influencing Warfarin DoseMark Rieder; Fiscal Year: 2007..The long-term aim of this proposal is to account for 100% of the inter-individual variability in warfarin dosing. ..