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Probabilistic graphical models for genetic association studies

R. Mourad, C. Sinoquet, P. Leray
2011 Briefings in Bioinformatics  
Probabilistic graphical models have been widely recognized as a powerful formalism in the bioinformatics field, especially in gene expression studies and linkage analysis.  ...  In this review article, we cover the applications of these models to the population association studies' context, such as linkage disequilibrium modeling, fine mapping and candidate gene studies, and genome-scale  ...  GENOME-WIDE ASSOCIATION STUDIES Novel high-throughput technologies now make the analysis of the entire human genome variability feasible through the generation of hundreds of thousands of SNPs, thus posing  ... 
doi:10.1093/bib/bbr015 pmid:21450805 fatcat:yh3v7vyopngczbqtmcqfs73rbm

Genotype-Based Ancestral Background Consistently Predicts Efficacy and Side Effects across Treatments in CATIE and STAR*D

Daniel E. Adkins, Renan P. Souza, Karolina Åberg, Shaunna L. Clark, Joseph L. McClay, Patrick F. Sullivan, Edwin J. C. G. van den Oord, Chuhsing Kate Hsiao
2013 PLoS ONE  
We first estimated each patient's unique mosaic of ancestral backgrounds using genome-wide SNP data collected in the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) (n = 765) and the  ...  Comparison of the marginal predictive power of MDS ancestral dimensions and self-reported race indicated significant improvements to model fit with the inclusion of MDS dimensions, but mixed evidence for  ...  (South San Francisco) on the Human Mapping 500 K Array Set and another 979 samples were genotyped using the Affymetrix Genome-Wide Human SNP Array 5.0.  ... 
doi:10.1371/journal.pone.0055239 pmid:23405125 pmcid:PMC3566192 fatcat:zi3ray4fvnelfkxkclo5j573eq

Population genetic considerations for using biobanks as international resources in the pandemic era and beyond

Hannah Carress, Daniel John Lawson, Eran Elhaik
2021 BMC Genomics  
Here, we evaluate the appropriateness of the most common genomic tools used to depict population structure in a standardized and comparable manner.  ...  The end goal is to reduce the effects of confounding and learn from genuine variation in genetic effects on phenotypes across populations, which will improve the value of biobanks (locally and internationally  ...  The funders had no role in the study. Open Access funding provided by Lund University.  ... 
doi:10.1186/s12864-021-07618-x pmid:34001009 fatcat:ycxels4hwzcgpojykja7demj2i

Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk

Minta Thomas, Lori C. Sakoda, Michael Hoffmeister, Elisabeth A. Rosenthal, Jeffrey K. Lee, Franzel J.B. van Duijnhoven, Elizabeth A. Platz, Anna H. Wu, Christopher H. Dampier, Albert de la Chapelle, Alicja Wolk, Amit D. Joshi (+85 others)
2020 American Journal of Human Genetics  
(3) LDpred, a Bayesian approach for genome-wide risk prediction.  ...  to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group).  ...  Acknowledgments A full list of funding and acknowledgments is provided in the Supplemental Data.  ... 
doi:10.1016/j.ajhg.2020.07.006 pmid:32758450 pmcid:PMC7477007 fatcat:hpturkdy3zf3lgiiavpl23ceua

Genomweite Assoziationsstudien

D Grimm, H Blum, R Thimme
2011 Deutsche Medizinische Wochenschrift  
For the first, we describe implicit causal models, a class of causal models that leverages neural architectures with an implicit density.  ...  However, there has been limited progress in models that capture causal relationships, for example, how individual genetic factors cause major human diseases.  ...  Causality with population-confounders has primarily been studied for genome-wide association studies (GWAS).  ... 
doi:10.1055/s-0030-1269446 pmid:21225557 fatcat:fodl7ef35fafxbav7kde47v3mu

Localization of adaptive variants in human genomes using averaged one-dependence estimation

Lauren Alpert Sugden, Elizabeth G. Atkinson, Annie P. Fischer, Stephen Rong, Brenna M. Henn, Sohini Ramachandran
2018 Nature Communications  
posterior probability of a sweep at each genomic site.  ...  Using array and exome data from 45 ‡Khomani San hunter-gatherers of southern Africa, we identify an enrichment of adaptive signals in genes associated with metabolism and obesity.  ...  mutations in the human genome using data from the 1000 Genomes Project.  ... 
doi:10.1038/s41467-018-03100-7 pmid:29459739 pmcid:PMC5818606 fatcat:xadvvke23zbrrcei3bnf65hqum

47th European Mathematical Genetics Meeting (EMGM) 2019, Dublin, Ireland, April 8-9, 2019

2018 Human Heredity  
to be confirmed in a cross-validation scenario.  ...  Continuous advances in massively parallel sequencing technologies make large whole-genome sequencing studies increasingly feasible.  ...  Genome wide association studies (GWASs) are sometimes performed as a secondary analysis in clinical studies with a different objective.  ... 
doi:10.1159/000499459 fatcat:g6uvxea32jcgzjdt6oxzui3mly

Is population structure in the genetic biobank era irrelevant, a challenge, or an opportunity?

Daniel John Lawson, Neil Martin Davies, Simon Haworth, Bilal Ashraf, Laurence Howe, Andrew Crawford, Gibran Hemani, George Davey Smith, Nicholas John Timpson
2019 Human Genetics  
Replicable genetic association signals have consistently been found through genome-wide association studies in recent years.  ...  The recent dramatic expansion of study sizes improves power of estimation of effect sizes, genomic prediction, causal inference, and polygenic selection, but it simultaneously increases susceptibility  ...  arrival of the genome-wide association study (GWAS) (Pe'er et al. 2008 ) and consequent adoption of stringent genome-wide significance levels.  ... 
doi:10.1007/s00439-019-02014-8 pmid:31030318 pmcid:PMC6942007 fatcat:7behwtignffudemybajk6qu63i

Perspectives on Human Population Structure at the Cusp of the Sequencing Era

John Novembre, Sohini Ramachandran
2011 Annual review of genomics and human genetics (Print)  
SNPs represent the first dense genome-wide markers, and as such, their analysis has raised many challenges and insights relevant to the study of population genetics with whole-genome sequences.  ...  Human groups show structured levels of genetic similarity as a consequence of factors such as geographical subdivision and genetic drift.  ...  near genes and a genome-wide effect of a higher variance in reproductive success for males compared with females.  ... 
doi:10.1146/annurev-genom-090810-183123 pmid:21801023 fatcat:cayycwjnordpjarzvvl34sbwo4

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

Damian Smedley, Max Schubach, Julius O.B. Jacobsen, Sebastian Köhler, Tomasz Zemojtel, Malte Spielmann, Marten Jäger, Harry Hochheiser, Nicole L. Washington, Julie A. McMurry, Melissa A. Haendel, Christopher J. Mungall (+4 others)
2016 American Journal of Human Genetics  
The interpretation of non-coding variants still constitutes a major challenge in the application of whole-genome sequencing in Mendelian disease, especially for single-nucleotide and other small non-coding  ...  Genomiser scores variants through either existing methods such as CADD or a bespoke machine learning method and combines these with allele frequency, regulatory sequences, chromosomal topological domains  ...  The hand-curated set of Mendelian mutations was used as a positive training set, and non-coding nucleotides that have diverged in humans as compared with the inferred ancestral primate genome sequence  ... 
doi:10.1016/j.ajhg.2016.07.005 pmid:27569544 pmcid:PMC5011059 fatcat:eph7w5sgmvbefgyyqvpaqzqwlm

Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies

Anand Bhaskar, Adel Javanmard, Thomas A. Courtade, David Tse
2016 Bioinformatics  
Our spatial inference algorithm can also be effectively applied to the problem of population stratification in genome-wide association studies (GWAS), where hidden population structure can create fictitious  ...  Motivation: Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns.  ...  Funding A.J. was partially supported by a CSoI fellowship during the course of this work (NSF Grant CCF-0939370). A.B. was supported in part by NIH grant HG008140 to Jonathan K.  ... 
doi:10.1093/bioinformatics/btw720 pmid:28025204 pmcid:PMC5860619 fatcat:m44ibfhxcff6jpv6krw7loglru

A Prism Vote Framework for Individualized Risk Prediction of Traits in Genome-wide Sequencing Data of Multiple Populations [article]

Xiaoxuan Xia, Rui Sun, Yexian Zhang, Ying Ying Wei, Qi Li, Marc Ka Chun Chong, William Ka Kei Wu, Benny Chung-Ying Zee, Hua Tang, Maggie Haitian Wang
2022 bioRxiv   pre-print
In two real genome-wide association data consists of multiple populations, we showed that the framework enhanced prediction accuracy of the linear mixed model by up to 12.1% in five-group cross validations  ...  The proposed framework offers a new aspect to analyze individual's disease risk and improve accuracy for predicting complex traits in genome data.  ...  Introduction Genome-wide genetic markers encode a considerable portion of common human traits heritability (1) .  ... 
doi:10.1101/2022.02.02.478767 fatcat:sx7u7yhx5zeb3epxbmceio7uy4

Integrating Genomes

D. R. Zerbino, B. Paten, D. Haussler
2012 Science  
In addition to other medical applications, similar scenarios are playing out in applications of genomics in a wide range of fields, such as agriculture (2) and the study of human prehistory (2) .  ...  This phenomenon is exploited in correlating specific segregating variants with phenotypic traits or diseases-for example, in genome-wide association studies conducted with microarrays or incomplete sequencing  ... 
doi:10.1126/science.1216830 pmid:22499938 fatcat:pkraq26dpzehreooeka2k7tlyi

A hierarchical Bayesian network approach for linkage disequilibrium modeling and data-dimensionality reduction prior to genome-wide association studies

Raphaël Mourad, Christine Sinoquet, Philippe Leray
2011 BMC Bioinformatics  
Discovering the genetic basis of common genetic diseases in the human genome represents a public health issue.  ...  In order to tackle the learning of both forest structure and probability distributions, a generic algorithm has been proposed.  ...  RM's work was supported by a grant from the BIL Bioinformatics Research Project of Pays de la Loire Region, France.  ... 
doi:10.1186/1471-2105-12-16 pmid:21226914 pmcid:PMC3033325 fatcat:dbgrxmj46zcn5cr52e2x47hrsa

EVOLUTION OF RELIGIOUS CAPACITY IN THE GENUS HOMO: COGNITIVE TIME SEQUENCE

Margaret Boone Rappaport, Christopher Corbally
2018 Zygon: Journal of Religion and Science  
The result is a logical, and even a likely story 55-65 million years long, which leads to the evolution of religious capacity in modern human beings.  ...  Intrigued by the possible paths that the evolution of religious capacity may have taken, the authors identify a series of six major building blocks that form a foundation for religious capacity in genus  ...  We note that, as with the FOXP2 gene, humans appear to use a type of genomic material widely found in other animals, but their own version of it.  ... 
doi:10.1111/zygo.12387 fatcat:zuzafqcwingqvf6rm47pwj3t6u
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