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Bayesian nonparametric clustering and association studies for candidate SNP observations
2017
International Journal of Approximate Reasoning
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AperTO -Archivio Istituzionale Open Access dell'Università di Torino Bayesian nonparametric clustering and association studies for candidate SNP observations / Wang, C.; Ruggeri, F.; Hsiao, C.K.; Argiento ...
We exemplify this Bayesian nonparametric strategy in a genome-wide association study of Crohn's * Corresponding author. disease in a case-control setting. ...
Acknowledgements The research was performed with the support of the joint CNR (National Research Council of Italy) -MOST (Ministry of Science and Technology of Taiwan) programme on scientific and technological ...
doi:10.1016/j.ijar.2016.07.014
fatcat:svh7szvlejgk7bmijsciiwv6vq
Network-based Nonparametric Tests to Identify Genetic Modifiers of Rare Diseases
[article]
2020
Figshare
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One reason is that current use of genome-wide association study (GWAS) utilize narrow sense heritability estimates and do not include assessment of epistasis and other components of broad-sense heritability1 ...
clustering. ...
More realistic Genotype-Phenotype models To develop a fast and scalable software to study genetic variation IV. Retain data resolution while controlling for noise V. ...
doi:10.6084/m9.figshare.11929557.v1
fatcat:ftef5v37vrc4zh7kw4gpj6ltle
Modeling Population Structure Under Hierarchical Dirichlet Processes
2018
Bayesian Analysis
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We propose a Bayesian nonparametric model to infer population admixture, extending the hierarchical Dirichlet process to allow for correlation between loci due to linkage disequilibrium. ...
We present a Markov chain Monte Carlo (MCMC) algorithm to perform posterior inference from the model and we discuss some methods to summarize the MCMC output for the analysis of population admixture. ...
In particular the associated admixture analysis of individuals is important in correcting the confounding effects of population ancestry on gene mapping (Zhu et al., 2008) and association studies (Price ...
doi:10.1214/17-ba1093
fatcat:hskzmxjrgnarjmsw3fxvv6cadu
Modeling population structure under hierarchical Dirichlet processes
[article]
2015
arXiv
pre-print
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We propose a Bayesian nonparametric model to infer population admixture, extending the Hierarchical Dirichlet Process to allow for correlation between loci due to Linkage Disequilibrium. ...
We present a MCMC algorithm to perform posterior inference from the model and discuss methods to summarise the MCMC output for the analysis of population admixture. ...
The associated admixture analysis of individuals is important in correcting the confounding effects of population ancestry on gene mapping [60] and association studies [42] . ...
arXiv:1503.08278v1
fatcat:j6zw5pswjvcajkg3rjqzfaqqq4
Evaluation of novel candidate variations and their interactions related to bipolar disorders: Analysis of GWAS data
2016
Neuropsychiatric Disease and Treatment
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Samples and associated phenotype data for the Collaborative Genomic Study of Bipolar Disorder were provided by the NIMH Genetics Initiative for Bipolar Disorder. ...
Acknowledgments Funding support for the Whole-Genome Association Study of Bipolar Disorder was provided by NIMH, and the genotyping of samples was provided through the Genetic Association Information Network ...
associations, implement pattern-based cluster analysis, analyze pathways, and visualize results and data. 17 Nevertheless, limitations remain. ...
doi:10.2147/ndt.s112558
pmid:27920536
pmcid:PMC5127431
fatcat:yfyz6pcfwfecznyto6bgi3poca
Learning Densities Conditional on Many Interacting Features
[article]
2013
arXiv
pre-print
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We demonstrate a novel nonparametric Bayes method based upon a tensor factorization of feature-dependent weights for Gaussian kernels. ...
The method makes use of multistage feature selection for dimension reduction. The resulting conditional density morphs flexibly with the selected features. ...
The associated challenges of variable selection and dimensionality reduction have been explored in Bayesian density regression. ...
arXiv:1304.7230v2
fatcat:3eunpq7twfdspg5sjeq2ork6xa
Molecular Proxies for Climate Maladaptation in a Long-Lived Tree (Pinus pinaster Aiton, Pinaceae)
2014
Genetics
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A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses ...
Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. ...
Third, a covariance matrix was built based on the control SNP data set (1745 SNPs) and used as a null model to further test for candidate SNP-climate correlations with the geographical Bayesian association ...
doi:10.1534/genetics.114.173252
pmid:25549630
pmcid:PMC4349072
fatcat:x2ufkcuqyvhfpjikur4xzwvgp4
Classification and Clustering Methods for Multiple Environmental Factors in Gene–Environment Interaction
2016
Epidemiology
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First, we utilize common clustering and classification strategies (e.g., k-means, latent class analysis, classification and regression trees, Bayesian clustering using Dirichlet Process) to define subgroups ...
Using the data from the Multi-Ethnic Study of Atherosclerosis, we illustrate a two-step approach for modeling G×E with multiple environmental factors. ...
Genotyping was performed at Affymetrix (Santa Clara, California, USA) and the Broad Institute of Harvard and MIT (Boston, Massachusetts, USA) using the Affymetrix Genome-Wide Human SNP Array 6.0. ...
doi:10.1097/ede.0000000000000548
pmid:27479650
pmcid:PMC5039086
fatcat:k4nynx24wrfujcvbr64tishx7i
Machine learning in genome-wide association studies
2009
Genetic Epidemiology
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ACKNOWLEDGMENTS The authors thank all GAW16 Group 8b participants for interesting discussions and helpful comments. The work of Silke Szymczak and Inke R. ...
Kö nig was supported by the German Ministry of Education and Science, grant 01GS0831, and an intramural grant of the University at Lü beck, Germany. ...
An ANN was used in a candidate gene study to identify SNPs with major effects as well as two-and threeway interactions [Tomita et al., 2004] . ...
doi:10.1002/gepi.20473
pmid:19924717
fatcat:ln5mdwsnaza2thmaorpq7sshnq
Signatures of adaptive divergence among populations of an avian species of conservation concern
2019
Evolutionary Applications
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Here, we use 15,033 SNP loci in genomic outlier analyses, genotype-environment association analyses, and gene ontology enrichment tests to examine patterns of putatively adaptive genetic differentiation ...
We found 411 loci within 5 kbp of 289 putative genes associated with biological functions or pathways that were overrepresented in the assemblage of outlier SNPs. ...
Restricting the distance between candidate SNPs and gene regions increased our confidence that the association between candidate SNP and gene was nonrandom although it ensures that many potential targets ...
doi:10.1111/eva.12825
pmid:31462921
pmcid:PMC6708427
fatcat:fkulejjmejhjxbctsbpkyhuyqm
Recombination Hotspots and Population Structure in Plasmodium falciparum
2005
PLoS Biology
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This study supports the feasibility of genome-wide association studies in some parasite populations. ...
Here we describe the first (to our knowledge) chromosome-wide SNP haplotype and population recombination maps for a global collection of malaria parasites, including the 3D7 isolate, whose genome has been ...
Tim Anderson and Matthew Hahn for critical reading of the manuscript, Ms. Brenda Rae Marshall for editorial assistance, and the Wellcome Trust for financial support for PA. Competing interests. ...
doi:10.1371/journal.pbio.0030335
pmid:16144426
pmcid:PMC1201364
fatcat:lpwma7pi3rdylkkeuohlsrdnwi
The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae)
2017
Molecular Ecology
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A FST -based outlier search among the 1659 SNPs revealed that 34 SNPs (2.05%) were likely to be under divergent selection and the allele frequencies of 21 of them were associated with environmental changes ...
All rights reserved. divergent selection and the allele frequencies of 21 of them were associated with environmental changes along elevations, such as temperature and precipitation. ...
ACKNOWLEDGMENTS We thank Michimasa Yamasaki for his help with the statistical analyses and Ichiro Tamaki for his advice on the coalescent simulations. ...
doi:10.1111/mec.14016
pmid:28099775
fatcat:ezgpqv3jovaxzn66ixecaxoweq
Adaptations to Climate in Candidate Genes for Common Metabolic Disorders
2008
PLoS Genetics
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analysis and a newly developed method termed Bayesian geographic analysis. ...
Among our strongest signals were several SNPs (e.g., LEPR R109K, FABP2 A54T) that had previously been associated with phenotypes directly related to cold tolerance. ...
Scanu, and R. Watanabe. H. Norton kindly provided the genotype data for the six skin pigmentation SNPs. Author contributions. AMH, JKP, GC, and AD conceived and designed the study. ...
doi:10.1371/journal.pgen.0040032
pmid:18282109
pmcid:PMC2242814
fatcat:5yzp7hdxy5cilcemsnhl3ybo7e
A nonparametric spatial test to identify factors that shape a microbiome
[article]
2018
arXiv
pre-print
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In this paper, we propose a flexible Bayesian spike-and-slab variable selection model for presence-absence indicators that accounts for spatial dependence and cross-dependence between taxa while reducing ...
Recently, methods have been developed to model the abundance of taxa in a community, but they can be computationally intensive and do not account for spatial effects underlying microbial settlement. ...
The proposed nonparametric model reduces the dimensionality of the problem for both large numbers of observations and a large number of observed taxa without sacrificing its aptitude to discern influential ...
arXiv:1806.06297v1
fatcat:ikdydnaqzfdmnbrhwbhwup6aay
A Review of Statistical Methods in Imaging Genetics
[article]
2018
arXiv
pre-print
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and theoretical challenges for existing analytical methods. ...
Such understanding is critical for diagnosis, prevention, and treatment of numerous complex brain-related disorders (e.g., schizophrenia and Alzheimer). ...
The resulting 'eigenSNPs' approximate the information in the collection of observed SNPs for a given gene. ...
arXiv:1707.07332v2
fatcat:ykdjy3dxsrdaffcvv2hwfgan4u
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