The impact of a fine-scale population stratification on rare variant association test results
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pone.0207677
Download full text from publisher
References listed on IDEAS
- Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
- Timothy D O’Connor & Adam Kiezun & Michael Bamshad & Stephen S Rich & Joshua D Smith & Emily Turner & NHLBIGO Exome Sequencing Project & ESP Population Genetics, Statistical Analysis Working Group & S, 2013. "Fine-Scale Patterns of Population Stratification Confound Rare Variant Association Tests," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-10, July.
- Elodie Persyn & Matilde Karakachoff & Solena Le Scouarnec & Camille Le Clézio & Dominique Campion & French Exome Consortium & Jean-Jacques Schott & Richard Redon & Lise Bellanger & Christian Dina, 2017. "DoEstRare: A statistical test to identify local enrichments in rare genomic variants associated with disease," PLOS ONE, Public Library of Science, vol. 12(7), pages 1-20, July.
- Benjamin M Neale & Manuel A Rivas & Benjamin F Voight & David Altshuler & Bernie Devlin & Marju Orho-Melander & Sekar Kathiresan & Shaun M Purcell & Kathryn Roeder & Mark J Daly, 2011. "Testing for an Unusual Distribution of Rare Variants," PLOS Genetics, Public Library of Science, vol. 7(3), pages 1-8, March.
- Yun-Ching Chen & Hannah Carter & Jennifer Parla & Melissa Kramer & Fernando S Goes & Mehdi Pirooznia & Peter P Zandi & W Richard McCombie & James B Potash & Rachel Karchin, 2013. "A Hybrid Likelihood Model for Sequence-Based Disease Association Studies," PLOS Genetics, Public Library of Science, vol. 9(1), pages 1-18, January.
- Wan-Yu Lin, 2014. "Association Testing of Clustered Rare Causal Variants in Case-Control Studies," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-6, April.
- Dajiang J Liu & Suzanne M Leal, 2010. "A Novel Adaptive Method for the Analysis of Next-Generation Sequencing Data to Detect Complex Trait Associations with Rare Variants Due to Gene Main Effects and Interactions," PLOS Genetics, Public Library of Science, vol. 6(10), pages 1-14, October.
- Robert B. Davies, 1980. "The Distribution of a Linear Combination of χ2 Random Variables," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 29(3), pages 323-333, November.
- Marie-Claude Babron & Marie de Tayrac & Douglas N Rutledge & Eleftheria Zeggini & Emmanuelle Génin, 2012. "Rare and Low Frequency Variant Stratification in the UK Population: Description and Impact on Association Tests," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-9, October.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Chung-Feng Kao & Jia-Rou Liu & Hung Hung & Po-Hsiu Kuo, 2015. "A Robust GWSS Method to Simultaneously Detect Rare and Common Variants for Complex Disease," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-14, April.
- Gyaneshwer Chaubey & Anurag Kadian & Saroj Bala & Vadlamudi Raghavendra Rao, 2015. "Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-11, June.
- Daniel Svensson & Matilda Rentoft & Anna M Dahlin & Emma Lundholm & Pall I Olason & Andreas Sjödin & Carin Nylander & Beatrice S Melin & Johan Trygg & Erik Johansson, 2020. "A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences," PLOS ONE, Public Library of Science, vol. 15(9), pages 1-18, September.
- Estavoyer, Maxime & François, Olivier, 2022. "Theoretical analysis of principal components in an umbrella model of intraspecific evolution," Theoretical Population Biology, Elsevier, vol. 148(C), pages 11-21.
- Felsenstein, Joseph, 2015. "Covariation of gene frequencies in a stepping-stone lattice of populations," Theoretical Population Biology, Elsevier, vol. 100(C), pages 88-97.
- Yaron Granot & Omri Tal & Saharon Rosset & Karl Skorecki, 2016. "On the Apportionment of Population Structure," PLOS ONE, Public Library of Science, vol. 11(8), pages 1-24, August.
- Escanciano, Juan Carlos & Jacho-Chávez, David T., 2010. "Approximating the critical values of Cramér-von Mises tests in general parametric conditional specifications," Computational Statistics & Data Analysis, Elsevier, vol. 54(3), pages 625-636, March.
- Özkan İş & Xue Wang & Joseph S. Reddy & Yuhao Min & Elanur Yilmaz & Prabesh Bhattarai & Tulsi Patel & Jeremiah Bergman & Zachary Quicksall & Michael G. Heckman & Frederick Q. Tutor-New & Birsen Can De, 2024. "Gliovascular transcriptional perturbations in Alzheimer’s disease reveal molecular mechanisms of blood brain barrier dysfunction," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
- Pötscher, Benedikt M. & Preinerstorfer, David, 2021.
"Valid Heteroskedasticity Robust Testing,"
MPRA Paper
107420, University Library of Munich, Germany.
- Pötscher, Benedikt M. & Preinerstorfer, David, 2021. "Valid Heteroskedasticity Robust Testing," MPRA Paper 117855, University Library of Munich, Germany, revised Jul 2023.
- Benedikt M. Potscher & David Preinerstorfer, 2021. "Valid Heteroskedasticity Robust Testing," Papers 2104.12597, arXiv.org, revised Jul 2023.
- Hyosik Jang & Ian M Ehrenreich, 2012. "Genome-Wide Characterization of Genetic Variation in the Unicellular, Green Alga Chlamydomonas reinhardtii," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-9, July.
- Mathieu Gautier & Denis Laloë & Katayoun Moazami-Goudarzi, 2010. "Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-11, September.
- Xiaofeng Cai & Xuepeng Sun & Chenxi Xu & Honghe Sun & Xiaoli Wang & Chenhui Ge & Zhonghua Zhang & Quanxi Wang & Zhangjun Fei & Chen Jiao & Quanhua Wang, 2021. "Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
- Lee, Anthony J. & Hibbs, Courtney & Wright, Margaret J. & Martin, Nicholas G. & Keller, Matthew C. & Zietsch, Brendan P., 2017. "Assessing the accuracy of perceptions of intelligence based on heritable facial features," Intelligence, Elsevier, vol. 64(C), pages 1-8.
- Thompson Katherine L. & Linnen Catherine R. & Kubatko Laura, 2016. "Tree-based quantitative trait mapping in the presence of external covariates," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(6), pages 473-490, December.
- Chin-Shang Li, 2016. "A test for the linearity of the nonparametric part of a semiparametric logistic regression model," Journal of Applied Statistics, Taylor & Francis Journals, vol. 43(3), pages 461-475, March.
- Taamouti, Abderrahim, 2009. "Analytical Value-at-Risk and Expected Shortfall under regime-switching," Finance Research Letters, Elsevier, vol. 6(3), pages 138-151, September.
- Matthieu Bouaziz & Caroline Paccard & Mickael Guedj & Christophe Ambroise, 2012. "SHIPS: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-17, October.
- Nicolas Städler & Sach Mukherjee, 2017. "Two-sample testing in high dimensions," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 79(1), pages 225-246, January.
- Jacobo Pardo-Seco & Alberto Gómez-Carballa & Jorge Amigo & Federico Martinón-Torres & Antonio Salas, 2014. "A Genome-Wide Study of Modern-Day Tuscans: Revisiting Herodotus's Theory on the Origin of the Etruscans," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-11, September.
- Mahmood Kharrati-Kopaei, 2021. "On the exact distribution of the likelihood ratio test statistic for testing the homogeneity of the scale parameters of several inverse Gaussian distributions," Computational Statistics, Springer, vol. 36(2), pages 1123-1138, June.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0207677. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.