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Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies
2012
PLoS Computational Biology
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In contrast to previous methods, PANAMA learns hidden factors jointly with the effect of prominent genetic regulators. ...
Here, we report PANAMA (Probabilistic ANAlysis of genoMic dAta), a novel probabilistic model to account for confounding factors within an eQTL analysis. ...
Acknowledgments The authors would like to thank Leonid Kruglyak, Erin Smith and Rachel Brem for access to gene expression and genotype data as well as permission to include the primary data alongside with ...
doi:10.1371/journal.pcbi.1002330
pmid:22241974
pmcid:PMC3252274
fatcat:ozz2kxje2jbzjff5d63x7k2zgq
Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects
2011
Nature Precedings
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In contrast to previous methods, PANAMA learns hidden factors jointly with the effect of prominent genetic regulators. ...
Here, we report PANAMA (Probabilistic ANAlysis of genoMic dAta), a novel probabilistic model to account for confounding factors within an eQTL analysis. ...
Acknowledgments This research was supported by the FP7 PASCAL II Network of Excellence. NF was supported by PhD scolarships from the University of Sheffield and the University of Manchester. ...
doi:10.1038/npre.2011.5995.1
fatcat:dvekebbgi5btnbt7ixu5es2aha
On Using Local Ancestry to Characterize the Genetic Architecture of Human Traits: Genetic Regulation of Gene Expression in Multiethnic or Admixed Populations
2019
American Journal of Human Genetics
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By using simulations of diverse genetic architectures and degrees of confounding, we show improved accuracy in estimating heritability when accounting for local ancestry similarity. ...
We provide a computationally efficient approach to local ancestry analysis in eQTL mapping while increasing control of type I and type II error over traditional approaches. ...
We thank Tanima De, Zhou Zhang, Yiben The American Journal of Human Genetics 104, 1097-1115, June 6, 2019 1113 Yang, and Jun Xiong for helpful discussion. ...
doi:10.1016/j.ajhg.2019.04.009
pmid:31104770
pmcid:PMC6562007
fatcat:7scf3lgatrhtdcu75recwjeoee
48th European Mathematical Genetics Meeting (EMGM) 2020
2020
Human Heredity
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We considered various combinations of factors, including varying effect sizes, variant allele frequencies, numbers of disease SNPs, varying sample sizes and the degree of genetic overlap between the phenotypes ...
of European ancestry based on the 1000 Genomes project. ...
in sequencing accuracy across the genome, and the efficacy of quality control measures. ...
doi:10.1159/000507248
pmid:32268327
fatcat:3aneluafpnes3a2ayzn53uffca
Detecting regulatory gene–environment interactions with unmeasured environmental factors
2013
Computer applications in the biosciences : CABIOS
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To fully understand the genetic regulation of gene expression variability, it is important to study the effect of genotype in the context of external factors such as alternative environmental conditions ...
Motivation: Genomic studies have revealed a substantial heritable component of the transcriptional state of the cell. ...
Funding: FP7 PASCAL II Network of Excellence; University of Sheffield doctoral training award (to N.F.); Volkswagen Foundation and a Marie Curie FP7 grant (to O.S.). ...
doi:10.1093/bioinformatics/btt148
pmid:23559640
fatcat:n24ytrgecnhmvjthheers2q3pa
On Using Local Ancestry to Characterize the Genetic Architecture of Human Phenotypes: Genetic Regulation of Gene Expression in Multiethnic or Admixed Populations as a Model
[article]
2018
bioRxiv
pre-print
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Using simulations of diverse genetic architectures to estimate trait heritability and the level of confounding, we show improved accuracy given individual-level data and evaluate a summary statistics based ...
Furthermore, we provide a computationally efficient approach to local ancestry analysis in eQTL mapping while increasing control of type I and type II error over traditional approaches. ...
Taken together, 406 these results substantially extend existing approaches and provide a framework for future large-scale studies of genetic 407 regulation of gene expression in multiethnic or admixed ...
doi:10.1101/483107
fatcat:ip4sez2zdrhgtnfqtmpfyfdwbq
Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality
2020
G3: Genes, Genomes, Genetics
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Useful insights were provided on the genetic architecture of apricot fruit quality whose integration in prediction models improved their performance, notably for traits governed by major QTLs. ...
Genomic selection (GS) is a breeding approach which exploits genome-wide information and whose unprecedented success has shaped several animal and plant breeding schemes through delivering their genetic ...
Therefore, higher degree of IBD sharing between full-sibs is likely to provide accurate estimation of genetic variation for quantitative traits exempt from confounding nongenetic factors in comparison ...
doi:10.1534/g3.120.401452
pmid:33067307
pmcid:PMC7718743
fatcat:ov2ws3xkzzguhhttfo7ikak3sy
Pathogenetic Overview of Psoriatic Disease
2012
Journal of Rheumatology Supplement
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Similarly, there are important new genetic observations focusing on the HLA region, and genome-wide association that confirms the genetic heterogeneity of patients with psoriasis and patients with PsA. ...
Apart from peripheral joint involvement, the musculoskeletal lesions in PsA include enthesitis and involvement of the distal interphalangeal joint (frequently associated with nail involvement, dactylitis ...
There are many factors that can confound identifying susceptibility genes in PsA. ...
doi:10.3899/jrheum.120232
pmid:22751581
fatcat:dftfaquiofhujmedc3x6tsngge
Synergistic Association of Genetic Variants with Environmental Risk Factors in Susceptibility to Essential Hypertension
2017
Genetic Testing and Molecular Biomarkers
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This study was designed to identify the interaction model between genetic variants and environmental risk factors that most highly potentiates EH development. ...
Traditional risk factors, biochemical and genetic parameters, including the genotypic discrimination of 14 genetic variants previously associated with EH, were investigated. ...
Acknowledgment This study was supported by the European Regional Development Fund's Operational Program for the Enhancement of Economic Potential and Territorial Cohesion for the Autonomous Region of Madeira ...
doi:10.1089/gtmb.2017.0048
pmid:28872890
fatcat:xaqwcnvqkff6fbgtg5up6cdote
Gene-gene interaction of BLK, TNFSF4, TRAF1, TNFAIP3, and REL in systemic lupus erythematosus
2011
Arthritis & Rheumatism
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Recent genome-wide association studies (GWAS) in SLE have produced renewed interest in B cell/T cell responses and the NF-κB signaling pathway. ...
Objective-Although the number of convincingly established genetic associations with systemic lupus erythematosus (SLE) has increased sharply over the last few years, refinement of these associations is ...
In the Chinese population, the regression models were adjusted for the potential confounders, including age and sex. ...
doi:10.1002/art.33318
pmid:21905002
pmcid:PMC3994469
fatcat:ols2gilf7fftjg3desoqernv3u
Biodemographic Analyses of Longitudinal Data on Aging, Health, and Longevity: Recent Advances and Future Perspectives
2014
Advances in Geriatrics
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using Medicare claims data; (2) methodological advances in genetic and genomic biodemography and applications to research on genetic determinants of longevity and health; and (3) biodemographic models ...
for joint analyses of time-to-event data and longitudinal measurements of biomarkers collected in longitudinal studies on aging. ...
Acknowledgments Research reported in this publication was partly supported by the National Institute on Aging of the National Institutes of Health under Awards nos. R01AG046860 and R21AG045245. ...
doi:10.1155/2014/957073
pmid:25590047
pmcid:PMC4290867
fatcat:26oj35e6prcuxnv5obijbpzae4
Gene–environment-wide association studies: emerging approaches
2010
Nature reviews genetics
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Acknowledgements S u p p o r t e d i n p a r t b y g r a n t s 5 P 3 0 E S 0 070 4 3 , 1U01 ES15090 and 1R01 ES016813 from the US National Institute of Environmental Health Sciences. ...
Gilliland and R. Haile for many helpful suggestions. ...
Confounder A spurious association between a risk factor (a gene, exposure or interaction) and disease induced by the joint associations of some other variable with the risk factor and the disease that ...
doi:10.1038/nrg2764
pmid:20212493
pmcid:PMC2891422
fatcat:hsbxlwi5dzfttidv2kbvxtzmoi
44th European Mathematical Genetics Meeting (EMGM) 2016. Newcastle upon Tyne, UK, May 11-12, 2016: Abstracts
2015
Human Heredity
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Complex diseases are supposed to be driven by multiple interactions between genetic factors and environmental exposures. ...
Then, in a second part, the method is used in a complex simulation scenario attempting to mimic the GxE interaction between a dominant genetic factor and a treatment with appetite suppressant effect. ...
assigned to genes based on the locations in build 37.3 of the human reference genome. ...
doi:10.1159/000445228
pmid:27111916
fatcat:553k64equ5f7lkbhpwun7nbgkm
The landscape of microbial phenotypic traits and associated genes
2016
Nucleic Acids Research
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Moreover, the Pro-Traits pipeline assigns phenotypes by drawing extensively on comparative genomics, capturing patterns in gene repertoires, codon usage biases, proteome composition and co-occurrence in ...
A global analysis of trait interrelatedness outlined clusters in the microbial phenotype network, suggesting common genetic underpinnings. ...
There is a known confounding effect of genome size with the other genetic determinants of spore-forming ability (52) . ...
doi:10.1093/nar/gkw964
pmid:27915291
pmcid:PMC5137458
fatcat:xnrilp536japlcojdc3xysfl3m
OATargets: a knowledge base of genes associated with osteoarthritis joint damage in animals
2020
Annals of the Rheumatic Diseases
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and online resource for understanding gene regulation of animal model OA pathogenesis. ...
Several discrepancies between different studies were identified, providing lessons on interpretation of these data. ...
Acknowledgements The authors thank Louise Reynard, Newcastle University for helpful discussions regarding the database and the manuscript. ...
doi:10.1136/annrheumdis-2020-218344
pmid:33077471
pmcid:PMC7892386
fatcat:ijvatzbq7jddnkkroz4heen2vm
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