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Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood

S.H. Lee, J. Yang, M.E. Goddard, P.M. Visscher, N.R. Wray
2012 Computer applications in the biosciences : CABIOS  
of complex diseases using population-based case-control studies with genome-wide SNP data.  ...  The method is validated in a simulation study and applied to estimate genetic correlation between various diseases from Wellcome Trust Case Control Consortium data in a series of bivariate analyses.  ...  US National Institute of Health (GM075091).  ... 
doi:10.1093/bioinformatics/bts474 pmid:22843982 pmcid:PMC3463125 fatcat:abadcvctvngctbtubi3ibs7lwy

Investigating the relationship between mitochondrial genetic variation and cardiovascular-related traits to develop a framework for mitochondrial phenome-wide association studies

Sabrina L Mitchell, Jacob B Hall, Robert J Goodloe, Jonathan Boston, Eric Farber-Eger, Sarah A Pendergrass, William S Bush, Dana C Crawford
2014 BioData Mining  
We employed both polygenic modeling and association testing with mitochondrial single nucleotide polymorphisms (mtSNPs) to explore the relationship between mtDNA variants and a group of eight cardiovascular-related  ...  To date, this approach has not been used to investigate the relationship between mtDNA variants and phenotypic variation.  ...  The Vanderbilt University Center for Human Genetics Research, Computational Genomics Core provided computational and/or analytical support for this work.  ... 
doi:10.1186/1756-0381-7-6 pmid:24731735 pmcid:PMC4021623 fatcat:kpanilsq5fg6pono3mopwhugk4

Methods and results from the genome-wide association group at GAW20

Xuexia Wang, Felix Boekstegers, Regina Brinster
2018 BMC Genetics  
This paper summarizes the contributions from the Genome-wide Association Study group (GWAS group) of the GAW20.  ...  The GWAS group contributions focused on topics such as association tests, phenotype imputation, and application of empirical kinships. The goals of the GWAS group contributions were varied.  ...  Analysis of Variance; MLE: Maximum Likelihood Estimator; pUSAT: Pedigree-based Unified Scorebases Association Test; SNP: Single Nucleotide Polymorphism; SOLAR: Sequential Oligogenic Linkage Analysis Routines  ... 
doi:10.1186/s12863-018-0649-0 pmid:30255814 pmcid:PMC6157187 fatcat:2icfq7ugxzbbtajz2pgm4ucruq

Genetic Factors Influencing Coagulation Factor XIII B-Subunit Contribute to Risk of Ischemic Stroke

Ken B. Hanscombe, Matthew Traylor, Pirro G. Hysi, Stephen Bevan, Martin Dichgans, Peter M. Rothwell, Bradford B. Worrall, Sudha Seshadri, Cathie Sudlow, Frances M.K. Williams, Hugh S. Markus, Cathryn M. Lewis
2015 Stroke  
multiple coagulation-associated single nucleotide polymorphisms in stroke, and (3) an evaluation of common genetic risk between coagulation and stroke.  ...  Effect directions for FXIIIB-associated single nucleotide polymorphisms were significantly discordant with cardioembolic disease (smallest P=5.7×10(-04)); the joint effect of FXIIIB-associated single nucleotide  ...  Estimation of SNP heritability and pleiotropy between complex traits using SNP-derived genomic relationships and restricted maximum likelihood is implemented in the program Genome-wide Complex Trait Analysis  ... 
doi:10.1161/strokeaha.115.009387 pmid:26159793 pmcid:PMC4512747 fatcat:xn6cq7y22bdv3n5o537cnxku2u

Shared genetic architecture in the relationship between adult stature and subclinical coronary artery atherosclerosis

Andrea E. Cassidy-Bushrow, Lawrence F. Bielak, Patrick F. Sheedy, Stephen T. Turner, Julia S. Chu, Patricia A. Peyser
2011 Atherosclerosis  
Pleiotropy between height and CAC was determined using maximum-likelihood estimation implemented in SOLAR. Results-Adult height was significantly and inversely associated with CAC score (P=0.01).  ...  Conclusions-Further studies of shared genetic factors between height and CAC may provide important insight into the complex genetic architecture of CHD, in part through increased understanding of the molecular  ...  Acknowledgments This research was supported by Grant R01 HL46292 from the NIH and by a General Clinic Research Center Grant from the NIH (MO1-RR00585) awarded to Mayo Clinic Rochester.  ... 
doi:10.1016/j.atherosclerosis.2011.08.030 pmid:21937044 pmcid:PMC3226925 fatcat:kpmkiwaa2newvkfrekqttf5fle

Genetically determined blood pressure, antihypertensive medications, and risk of Alzheimer's disease: a Mendelian randomization study

Ya-Nan Ou, Yu-Xiang Yang, Xue-Ning Shen, Ya-Hui Ma, Shi-Dong Chen, Qiang Dong, Lan Tan, Jin-Tai Yu
2021 Alzheimer's Research & Therapy  
Results There was limited evidence that genetically predicted SBP/diastolic BP level affected AD risk based on 400/398 single nucleotide polymorphisms (SNPs), respectively (all P > 0.05).  ...  Background Observational studies suggest that the use of antihypertensive medications (AHMs) is associated with a reduced risk of Alzheimer's disease (AD); however, these findings may be biased by confounding  ...  We thank the International Genomics of Alzheimer's Project (IGAP) for providing summary results data for these analyses.  ... 
doi:10.1186/s13195-021-00782-y pmid:33563324 fatcat:znhv46w3rnd5zgywl2gh2yivpi

SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes

Reedik Mägi, Yury V. Suleimanov, Geraldine M. Clarke, Marika Kaakinen, Krista Fischer, Inga Prokopenko, Andrew P. Morris
2017 BMC Bioinformatics  
Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative  ...  to diseases and quantitative traits.  ...  Availability of data and materials We do not have ethical approval to share individual level genotype and phenotype data from the Estonian Biobank.  ... 
doi:10.1186/s12859-016-1437-3 pmid:28077070 pmcid:PMC5225593 fatcat:qzokpha46ng3vle5ufnahmhnku

The roles of pleiotropy and close linkage as revealed by association mapping of yield and correlated traits of wheat (Triticum aestivum L.)

Albert W Schulthess, Jochen C Reif, Jie Ling, Jörg Plieske, Sonja Kollers, Erhard Ebmeyer, Viktor Korzun, Odile Argillier, Gunther Stiewe, Martin W Ganal, Marion S Röder, Yong Jiang
2017 Journal of Experimental Botany  
Most quantitative genetics studies assessed the multiple-trait (MT) complex of GY-syndrome using single-trait approaches, and little is known about its underlying pleiotropic architecture.  ...  We investigated the pleiotropic architecture of wheat GY-syndrome through MT association mapping (MT-GWAS) using 372 varieties phenotyped in up to eight environments and genotyped with 18 832 single nucleotide  ...  Acknowledgements This research project was financially supported by the Plant Biotechnology program of the German Federal Ministry of Education and Research (BMBF) within the framework of projects GABI-WHEAT-Wheat  ... 
doi:10.1093/jxb/erx214 pmid:28922760 pmcid:PMC5853857 fatcat:i4shxuilxfg7zmembntapexn7i

Dissecting the genetics of complex traits using summary association statistics

Bogdan Pasaniuc, Alkes L. Price
2016 Nature reviews genetics  
| During the past decade, genome-wide association studies (GWAS) have been used to successfully identify tens of thousands of genetic variants associated with complex traits and diseases.  ...  Here, we review recent progress on statistical methods that leverage summary association data to gain insights into the genetic basis of complex traits and diseases.  ...  The work of the authors is funded by US National Institutes of Health grants R01 HG006399, R01 MH101244, R01 GM105857 and R01 MH107649.  ... 
doi:10.1038/nrg.2016.142 pmid:27840428 pmcid:PMC5449190 fatcat:4pmrqfltnzbihcfackcvniorai

Bayesian methods for instrumental variable analysis with genetic instruments ('Mendelian randomization'): example with urate transporter SLC2A9 as an instrumental variable for effect of urate levels on metabolic syndrome

Paul M McKeigue, Harry Campbell, Sarah Wild, Veronique Vitart, Caroline Hayward, Igor Rudan, Alan F Wright, James F Wilson
2010 International Journal of Epidemiology  
To demonstrate the approach, we examined the relationship of plasma urate levels to metabolic syndrome in the ORCADES study of a Scottish population isolate, using genotype at six single-nucleotide polymorphisms  ...  We describe a Bayesian approach that overcomes these limitations, using the JAGS program to compute the log-likelihood ratio (lod score) between causal and non-causal explanations of a biomarker-disease  ...  uncertain whether this relationship is causal. 2 This has been investigated using a single-nucleotide polymorphism (SNP) in the promoter region of the -fibrinogen gene FGB, which is known to affect plasma  ... 
doi:10.1093/ije/dyp397 pmid:20348110 pmcid:PMC2878456 fatcat:adqosafuvveshjhytdxvft43ha

The MR-Base platform supports systematic causal inference across the human phenome

Gibran Hemani, Jie Zheng, Benjamin Elsworth, Kaitlin H Wade, Valeriia Haberland, Denis Baird, Charles Laurin, Stephen Burgess, Jack Bowden, Ryan Langdon, Vanessa Y Tan, James Yarmolinsky (+8 others)
2018 eLife  
Results from genome-wide association studies (GWAS) can be used to infer causal relationships between phenotypes, using a strategy known as 2-sample Mendelian randomization (2SMR) and bypassing the need  ...  The database currently comprises 11 billion single nucleotide polymorphism-trait associations from 1673 GWAS and is updated on a regular basis.  ...  Tang, Merce Garcia-Barcelo and Paul KH Tam on behalf of the Hirschsprung's disease GWAS; Kaya Kvarme Jacobsen on behalf  ... 
doi:10.7554/elife.34408 pmid:29846171 pmcid:PMC5976434 fatcat:osgm5ofbpvex3f4mzqeurp4psq

Response to Lee et al.: SNP-Based Heritability Analysis with Dense Data

Doug Speed, Gibran Hemani, Michael R. Johnson, David J. Balding
2013 American Journal of Human Genetics  
Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism -derived genomic relationships and restricted maximum likelihood.  ...  calculating the genomic-relationship matrix (GRM), and (2) the accuracy of h 2 estimates depends on how closely the assumed relationship between a causal variant's minor allele frequency (MAF) and effect  ... 
doi:10.1016/j.ajhg.2013.10.016 pmid:24314551 pmcid:PMC3852920 fatcat:p7vaoxnxlvbrfma2ty7nqjnkwa

Genetic variation, brain, and intelligence differences

Ian J. Deary, Simon R. Cox, W. David Hill
2021 Molecular Psychiatry  
We attempt to identify growing points that might contribute toward a more integrated 'systems biology' account of some of the between-individual differences in intelligence.  ...  From this solid phenotypic foundation and importance for life, comes an interest in the environmental, social, and genetic aetiologies of intelligence, and in the foundations of intelligence differences  ...  The statistical-genetic method used to estimate heritability is called genome-based restricted maximum likelihood single component (GREML-SC) (Box 2).  ... 
doi:10.1038/s41380-021-01027-y pmid:33531661 pmcid:PMC8960418 fatcat:h2hzx6lal5ai3gsndvokusngny

Quantitative trait locus analyses and the study of evolutionary process

DAVID L. ERICKSON, CHARLES B. FENSTER, HANS K. STENOIEN, DONALD PRICE
2004 Molecular Ecology  
of individual genes or nucleotide differences within genes (QTN).  ...  We highlight representative issues in ecology and evolutionary biology and discuss the range of questions that can be addressed satisfactorily using QTL approaches.  ...  Shaw and B. Walsh and the contributions of three anonymous reviewers. We appreciate the support of funding from the US NSF (9815780 to C. Fenster, 9972366 to D. Price), US NIH (5S06Gm008073-24 to D.  ... 
doi:10.1111/j.1365-294x.2004.02254.x pmid:15315666 fatcat:krahtdsxozerdifx5twxkj5yze

Sleep Disordered Breathing, Obesity and Atrial Fibrillation: A Mendelian Randomisation Study

Maddalena Ardissino, Rohin K. Reddy, Eric A. W. Slob, Kiran H. K. Patel, David K. Ryan, Dipender Gill, Fu Siong Ng
2022 Genes  
Single-nucleotide polymorphisms associated with SDB (n = 29) and BMI (n = 453) were selected as instrumental variables to investigate the effects of SDB and BMI on AF, using genetic association data on  ...  We performed Mendelian randomisation (MR) to investigate the causal relationships between SDB, body mass index (BMI) and AF.  ...  A recent univariable MR study reported a causal association between five single-nucleotide polymorphisms (SNPs) associated with OSA and AF [20] .  ... 
doi:10.3390/genes13010104 pmid:35052444 pmcid:PMC8774383 fatcat:sx54xtgrp5aszi3f6krrbmusvi
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