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Bayesian nonparametric clustering and association studies for candidate SNP observations

Charlotte Wang, Fabrizio Ruggeri, Chuhsing K. Hsiao, Raffaele Argiento
2017 International Journal of Approximate Reasoning  
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]

Eliatan Niktab, Stephen Sturley, Ingrid Winship, Mark Walterfang, Paul Atkinson, Andrew Munkacsi
2020 Figshare  
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

Lloyd T. Elliott, Maria De Iorio, Stefano Favaro, Kaustubh Adhikari, Yee Whye Teh
2018 Bayesian Analysis  
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]

M. De Iorio, L.T. Elliott, S. Favaro, K. Adhikari, Y.W. Teh
2015 arXiv   pre-print
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

Cengizhan Acikel, Yesim Aydin Son, Cemil Celik, Husamettin Gul
2016 Neuropsychiatric Disease and Treatment  
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]

David C. Kessler and Jack Taylor and David B. Dunson
2013 arXiv   pre-print
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)

J.-P. Jaramillo-Correa, I. Rodriguez-Quilon, D. Grivet, C. Lepoittevin, F. Sebastiani, M. Heuertz, P. H. Garnier-Gere, R. Alia, C. Plomion, G. G. Vendramin, S. C. Gonzalez-Martinez
2014 Genetics  
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

Yi-An Ko, Bhramar Mukherjee, Jennifer A. Smith, Sharon L. R. Kardia, Matthew Allison, Ana V. Diez Roux
2016 Epidemiology  
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

Silke Szymczak, Joanna M. Biernacka, Heather J. Cordell, Oscar González-Recio, Inke R. König, Heping Zhang, Yan V. Sun
2009 Genetic Epidemiology  
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

Shawna J. Zimmerman, Cameron L. Aldridge, Kevin P. Oh, R. Scott Cornman, Sara J. Oyler‐McCance
2019 Evolutionary Applications  
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

Jianbing Mu, Philip Awadalla, Junhui Duan, Kate M McGee, Deirdre A Joy, Gilean A. T McVean, Xin-zhuan Su, Jody Hey
2005 PLoS Biology  
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)

Ayako Izuno, Kanehiro Kitayama, Yusuke Onoda, Yuki Tsujii, Masaomi Hatakeyama, Atsushi J. Nagano, Mie N. Honjo, Rie Shimizu-Inatsugi, Hiroshi Kudoh, Kentaro K. Shimizu, Yuji Isagi
2017 Molecular Ecology  
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

Angela M. Hancock, David B. Witonsky, Adam S. Gordon, Gidon Eshel, Jonathan K. Pritchard, Graham Coop, Anna Di Rienzo
2008 PLoS Genetics  
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]

Susheela P. Singh, Ana-Maria Staicu, Robert R. Dunn, Noah Fierer and Brian J. Reich
2018 arXiv   pre-print
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]

Farouk S. Nathoo, Linglong Kong, Hongtu Zhu
2018 arXiv   pre-print
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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