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Probabilistic ancestry maps: a method to assess and visualize population substructures in genetics
[article]
2018
bioRxiv
pre-print
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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
2019
BMC Bioinformatics
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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
2015
Frontiers in Genetics
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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]
2019
Msphere
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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
2009
Genetics
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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
2013
Human Genomics
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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
2021
Human Brain Mapping
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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
2015
Nature
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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
2009
PLoS ONE
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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
2013
Heredity
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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
2009
Genome Research
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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
2020
PLoS Genetics
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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
2015
Proceedings of the National Academy of Sciences of the United States of America
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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]
2019
bioRxiv
pre-print
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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
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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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