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Probabilistic ancestry maps: a method to assess and visualize population substructures in genetics [article]

Héléna A Gaspar, Gerome Breen
2018 bioRxiv   pre-print
Principal component analysis (PCA) is a standard method to correct for population stratification in ancestry-specific genome-wide association studies (GWASs) and is used to cluster individuals by ancestry  ...  used to provide improved ancestry maps by accounting for a higher percentage of explained variance in ancestry, and how they can help to estimate the number of principal components necessary to account  ...  Acknowledgments 297 The ugtm python package used to build the GTM models was implemented by HG and accessible at https://github.com/hagax8/ugtm with a tutorial for reproducing the analyses presented  ... 
doi:10.1101/362343 fatcat:j37qikbcgrdjjafgolwebxwxcm

Probabilistic ancestry maps: a method to assess and visualize population substructures in genetics

Héléna A. Gaspar, Gerome Breen
2019 BMC Bioinformatics  
The main interest of probabilistic GTM maps is to attain two objectives with only one map: provide a better visualization that separates populations efficiently, and infer genetic ancestry for individuals  ...  Principal component analysis (PCA) is a standard method to correct for population stratification in ancestry-specific genome-wide association studies (GWASs) and is used to cluster individuals by ancestry  ...  On the other hand, both t-SNE and GTM provide a way to cluster and visualize more complex population substructures.  ... 
doi:10.1186/s12859-019-2680-1 pmid:30845922 pmcid:PMC6407257 fatcat:6oacejfpojd5zpkalzpucxensm

Mapping asthma-associated variants in admixed populations

Tesfaye B. Mersha
2015 Frontiers in Genetics  
Acknowledgments This work was supported by NIH Grant K01HL103165 and Diversity and Health Disparities Award of the Cincinnati Children's Research Foundation. We thank Dr. Ranajit Chakraborty and Dr.  ...  Admixture Mapping in Admixed Populations Admixture mapping (AM) is a gene mapping method used for persons of mixed ancestry to identify genomic segments in which the proportion of a particular ancestry  ...  Understanding the consequences of admixture based population substructure in admixed populations is important, because admixture can be both a confounding factor and a source of statistical power to map  ... 
doi:10.3389/fgene.2015.00292 pmid:26483834 pmcid:PMC4586512 fatcat:ewwo7x26vra4hk5on47y7iwj4y

Association Mapping and Disease: Evolutionary Perspectives [chapter]

Søren Besenbacher, Thomas Mailund, Bjarni J. Vilhjálmsson, Mikkel H. Schierup
2019 Msphere  
In this chapter, we give a short introduction to the genetics of complex diseases emphasizing evolutionary models for disease genes and the effect of different models on the genetic architecture, and we  ...  give a survey of the state-of-the-art of genome-wide association studies (GWASs).  ...  in a population of European ancestry [35] .  ... 
doi:10.1007/978-1-4939-9074-0_17 pmid:31278676 fatcat:be4xwoykzzceratsa3g53c5o2a

Nonmetric Multidimensional Scaling Corrects for Population Structure in Association Mapping With Different Sample Types

C. Zhu, J. Yu
2009 Genetics  
Recent research has developed various promising methods to control for population structure in genomewide association mapping of complex traits, but systematic examination of how well these methods perform  ...  Further, the nMDS technique of correcting for genetic relationship proved to be a powerful complement to other existing methods.  ...  We concluded that the nMDS method is a powerful method for association mapping in populations with either subtle or complex genetic structure.  ... 
doi:10.1534/genetics.108.098863 pmid:19414565 pmcid:PMC2710166 fatcat:tmsexhsnfrcrhjncrbfulii5qu

Softwares and methods for estimating genetic ancestry in human populations

Yushi Liu, Toru Nyunoya, Shuguang Leng, Steven A Belinsky, Yohannes Tesfaigzi, Shannon Bruse
2013 Human Genomics  
Genetic ancestry is used to control for population stratification in genetic association studies, and is used to understand the genetic basis for ethnic differences in disease susceptibility.  ...  In this review, we present an overview of genetic ancestry estimation in human disease studies, followed by a review of popular softwares and methods used for this estimation.  ...  Direct estimates of genetic ancestry based on genotype data are therefore preferred as a control for population substructure, given the advantage in precision and informativeness over self-identified ethnicity  ... 
doi:10.1186/1479-7364-7-1 pmid:23289408 pmcid:PMC3542037 fatcat:2ve77wuwyzft5d443owmuw7n2i

Cross-sex shifts in two brain imaging phenotypes and their relation to polygenic scores for same-sex sexual behavior: A study of 18,645 individuals from the UK Biobank

Christoph Abé, Alexander Lebedev, Ruyue Zhang, Lina Jonsson, Sarah E Bergen, Martin Ingvar, Mikael Landén, Qazi Rahman
2021 Human Brain Mapping  
These findings support a neurobiological basis to the differences in human sexuality.  ...  Genetic and hormonal factors have been suggested to influence human sexual orientation.  ...  We thank the UK Biobank members for their participation in the study and the UK Biobank team, who collected, processed, and made available the data for analysis.  ... 
doi:10.1002/hbm.25370 pmid:33635603 pmcid:PMC8046142 fatcat:ga2debv3pjcitnuqigy4lr6k5i

The fine-scale genetic structure of the British population

Stephen Leslie, Bruce Winney, Garrett Hellenthal, Dan Davison, Abdelhamid Boumertit, Tammy Day, Katarzyna Hutnik, Ellen C. Royrvik, Barry Cunliffe, Daniel J. Lawson, Daniel Falush, Colin Freeman (+5 others)
2015 Nature  
but post--Mesolithic movement into SE England from the Continent, and show that in non--Saxon parts of the UK there exist genetically differentiated subgroups rather than a general "Celtic" population  ...  Fine--scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies.  ...  PD was supported in part by a Wolfson--Royal Society Merit Award.  ... 
doi:10.1038/nature14230 pmid:25788095 pmcid:PMC4632200 fatcat:bsigwtw2nvfj7jvmgd327yxyem

High Differentiation among Eight Villages in a Secluded Area of Sardinia Revealed by Genome-Wide High Density SNPs Analysis

Giorgio Pistis, Ignazio Piras, Nicola Pirastu, Ivana Persico, Alessandro Sassu, Andrea Picciau, Dionigio Prodi, Cristina Fraumene, Evelina Mocci, Maria Teresa Manias, Rossano Atzeni, Massimiliano Cosso (+3 others)
2009 PLoS ONE  
These isolates showed differences in LD values and LD map length. Five of these villages show high LD values probably due to their reduced population size and extreme isolation.  ...  To better design association studies for complex traits in isolated populations it's important to understand how history and isolation moulded the genetic features of different communities.  ...  Acknowledgments We thank the Ogliastra population and all the individuals who participated in this study.  ... 
doi:10.1371/journal.pone.0004654 pmid:19247500 pmcid:PMC2646134 fatcat:636arxuiundarnilab5utw5nfy

Combined linkage disequilibrium and linkage mapping: Bayesian multilocus approach

P Pikkuhookana, M J Sillanpää
2013 Heredity  
The 27 pedigrees encompass 212 people, range in size from 1 to 36 people and from 1 to 5 generations, and contain sibships of 1 to 5 children.  ...  The selected Framingham pedigrees were chosen to reflect the kind of pedigrees commonly collected in family-based genetic studies.  ...  methods, and construction of classroom exercises in statistical genetics.  ... 
doi:10.1038/hdy.2013.111 pmid:24253936 pmcid:PMC3931163 fatcat:i3jslsqvqjgdjdmvaxalhrxqwe

Non-Darwinian estimation: My ancestors, my genes' ancestors

K. M. Weiss, J. C. Long
2009 Genome Research  
0321610) and the University of Michigan Medical School (J.C.L.).  ...  This work was supported by funding from the National Institutes of Health (MH063749) and the Penn State Evan Pugh Professors research fund (K.M.W.), and funding from the National Science Foundation (NSF  ...  Genetic methods assess the similarity relationship between individuals on the basis of sharing alleles at polymorphic loci.  ... 
doi:10.1101/gr.076539.108 pmid:19411595 pmcid:PMC3647532 fatcat:dsl2okb6src7nb6k36ve3ow7ku

Discovery of novel hepatocyte eQTLs in African Americans

Yizhen Zhong, Tanima De, Cristina Alarcon, C. Sehwan Park, Bianca Lec, Minoli A. Perera, Christopher R. Gignoux
2020 PLoS Genetics  
These AA-specific eQTLs are less correlated to GTEx eQTL in effect sizes and have larger Fst values compared to eQTLs found in both cohorts (overlapping eQTLs).  ...  ancestry genome.  ...  Acknowledgments The authors appreciate Yilin Xu and Eric Gamazon for the critical reading of the manuscript and Yinan Zheng for the helpful discussions.  ... 
doi:10.1371/journal.pgen.1008662 pmid:32310939 fatcat:sih567twjjc5lbpwgrw7xwcqzq

Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure

David Mimno, David M. Blei, Barbara E. Engelhardt
2015 Proceedings of the National Academy of Sciences of the United States of America  
Admixture models are a ubiquitous approach to capture latent population structure in genetic samples.  ...  Here we develop methods for validating admixture models based on posterior predictive checks (PPCs), a Bayesian method for assessing the quality of a statistical model.  ...  We believe that methods to control for population stratification in association mapping will benefit from application of the mapping PPC, including linear mixed models and nongenerative methods such as  ... 
doi:10.1073/pnas.1412301112 pmid:26071445 pmcid:PMC4491772 fatcat:txix7krb4zfwlnmjo33tg4ngt4

The genetic architecture of Parkinson disease in Spain: characterizing population-specific risk, differential haplotype structures, and providing etiologic insight [article]

Sara Bandres Ciga, Sarah Ahmed, Marya Sabir, Cornelis Blauwendraat, Astrid Adarmes-Gomez, Inmaculada Bernal-Bernal, Marta Bonilla-Toribio, Dolores Buiza-Rueda, Fatima Carrillo, Mario Carrion-Claro, Pilar Gomez-Garre, Silvia Jesus (+80 others)
2019 bioRxiv   pre-print
Methods: We performed a GWAS for both risk of PD and age at onset (AAO) in 7,849 Spanish individuals.  ...  Conclusions: Our data demonstrate the utility of the Spanish risk haplotype substructure for future fine-mapping efforts, showing how leveraging unique and diverse population histories can benefit genetic  ...  Here, we dissect population-specific differences in risk and AAO from a genetic perspective and highlight the utility of the Spanish risk haplotype substructure for future fine-mapping efforts.  ... 
doi:10.1101/609016 fatcat:lbiejvqdvndotm4kias6lkfbxy

42nd European Mathematical Genetics Meeting (EMGM) 2014, April 1-2, 2014, Cologne, Germany: Abstracts

2013 Human Heredity  
In population genetics one aim is to identify population stratification, and I will argue in the second part that the study of religious, cultural, and political differences between groups can be helpful  ...  The aim of most genetic epidemiological studies is to identify an association between a disease and a chromosomal region.  ...  The approach is compared to state-of-the-art methods in the context of population substructure and admixture analysis.  ... 
doi:10.1159/000360587 fatcat:nc5mdmjfrfc2tfwa3tbmwj2nmm
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