Performance of Genotype Imputation for Low Frequency and Rare Variants from the 1000 Genomes
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pone.0116487
Download full text from publisher
References listed on IDEAS
- Martin Ladouceur & Zari Dastani & Yurii S Aulchenko & Celia M T Greenwood & J Brent Richards, 2012. "The Empirical Power of Rare Variant Association Methods: Results from Sanger Sequencing in 1,998 Individuals," PLOS Genetics, Public Library of Science, vol. 8(2), pages 1-11, February.
- Brendan Maher, 2008. "Personal genomes: The case of the missing heritability," Nature, Nature, vol. 456(7218), pages 18-21, November.
- Bryan N Howie & Peter Donnelly & Jonathan Marchini, 2009. "A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies," PLOS Genetics, Public Library of Science, vol. 5(6), pages 1-15, June.
- Yu-Fang Pei & Jian Li & Lei Zhang & Christopher J Papasian & Hong-Wen Deng, 2008. "Analyses and Comparison of Accuracy of Different Genotype Imputation Methods," PLOS ONE, Public Library of Science, vol. 3(10), pages 1-7, October.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Paul S de Vries & Maria Sabater-Lleal & Daniel I Chasman & Stella Trompet & Tarunveer S Ahluwalia & Alexander Teumer & Marcus E Kleber & Ming-Huei Chen & Jie Jin Wang & John R Attia & Riccardo E Mario, 2017. "Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study," PLOS ONE, Public Library of Science, vol. 12(1), pages 1-22, January.
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.- Emily Mathieu, 2016. "AGGrEGATOr: A Gene-based GEne-Gene interActTiOn test for case-control association studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(2), pages 151-171, April.
- Diana Chang & Feng Gao & Andrea Slavney & Li Ma & Yedael Y Waldman & Aaron J Sams & Paul Billing-Ross & Aviv Madar & Richard Spritz & Alon Keinan, 2014. "Accounting for eXentricities: Analysis of the X Chromosome in GWAS Reveals X-Linked Genes Implicated in Autoimmune Diseases," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-31, December.
- 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.
- Chuong B Do & David A Hinds & Uta Francke & Nicholas Eriksson, 2012. "Comparison of Family History and SNPs for Predicting Risk of Complex Disease," PLOS Genetics, Public Library of Science, vol. 8(10), pages 1-16, October.
- Chuan Gao & Nan Wang & Xiuqing Guo & Julie T Ziegler & Kent D Taylor & Anny H Xiang & Yang Hai & Steven J Kridel & Jerry L Nadler & Fouad Kandeel & Leslie J Raffel & Yii-Der I Chen & Jill M Norris & J, 2015. "A Comprehensive Analysis of Common and Rare Variants to Identify Adiposity Loci in Hispanic Americans: The IRAS Family Study (IRASFS)," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-17, November.
- Faming Liang & Momiao Xiong, 2013. "Bayesian Detection of Causal Rare Variants under Posterior Consistency," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-16, July.
- Iuliana Ionita-Laza & Joseph D Buxbaum & Nan M Laird & Christoph Lange, 2011. "A New Testing Strategy to Identify Rare Variants with Either Risk or Protective Effect on Disease," PLOS Genetics, Public Library of Science, vol. 7(2), pages 1-6, February.
- Paul S de Vries & Maria Sabater-Lleal & Daniel I Chasman & Stella Trompet & Tarunveer S Ahluwalia & Alexander Teumer & Marcus E Kleber & Ming-Huei Chen & Jie Jin Wang & John R Attia & Riccardo E Mario, 2017. "Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study," PLOS ONE, Public Library of Science, vol. 12(1), pages 1-22, January.
- Bo Jiang & Jun S. Liu, 2015. "Bayesian Partition Models for Identifying Expression Quantitative Trait Loci," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 110(512), pages 1350-1361, December.
- Rakesh Chettier & Lesa Nelson & James W Ogilvie & Hans M Albertsen & Kenneth Ward, 2015. "Haplotypes at LBX1 Have Distinct Inheritance Patterns with Opposite Effects in Adolescent Idiopathic Scoliosis," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-11, February.
- Michel S. Naslavsky & Marilia O. Scliar & Guilherme L. Yamamoto & Jaqueline Yu Ting Wang & Stepanka Zverinova & Tatiana Karp & Kelly Nunes & José Ricardo Magliocco Ceroni & Diego Lima Carvalho & Carlo, 2022. "Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
- Aida Bianco & Eusebio Chiefari & Carmelo G A Nobile & Daniela Foti & Maria Pavia & Antonio Brunetti, 2015. "The Association between HMGA1 rs146052672 Variant and Type 2 Diabetes: A Transethnic Meta-Analysis," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-15, August.
- Steinrücken, Matthias & Paul, Joshua S. & Song, Yun S., 2013. "A sequentially Markov conditional sampling distribution for structured populations with migration and recombination," Theoretical Population Biology, Elsevier, vol. 87(C), pages 51-61.
- Yumei Yang & Qishan Wang & Qiang Chen & Rongrong Liao & Xiangzhe Zhang & Hongjie Yang & Youmin Zheng & Zhiwu Zhang & Yuchun Pan, 2014. "A New Genotype Imputation Method with Tolerance to High Missing Rate and Rare Variants," PLOS ONE, Public Library of Science, vol. 9(6), pages 1-7, June.
- 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.
- Anshuman Sewda & A J Agopian & Elizabeth Goldmuntz & Hakon Hakonarson & Bernice E Morrow & Fadi Musfee & Deanne Taylor & Laura E Mitchell & on behalf of the Pediatric Cardiac Genomics Consortium, 2020. "Gene-based analyses of the maternal genome implicate maternal effect genes as risk factors for conotruncal heart defects," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-15, June.
- Lin Yuan & Chang-An Yuan & De-Shuang Huang, 2017. "FAACOSE: A Fast Adaptive Ant Colony Optimization Algorithm for Detecting SNP Epistasis," Complexity, Hindawi, vol. 2017, pages 1-10, September.
- Carl Nettelblad, 2013. "Breakdown of Methods for Phasing and Imputation in the Presence of Double Genotype Sharing," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-5, March.
- Viinikainen, Jutta & Bryson, Alex & Böckerman, Petri & Kari, Jaana T. & Lehtimäki, Terho & Raitakari, Olli & Viikari, Jorma & Pehkonen, Jaakko, 2022. "Does better education mitigate risky health behavior? A mendelian randomization study," Economics & Human Biology, Elsevier, vol. 46(C).
- Dominic Russ & John A Williams & Victor Roth Cardoso & Laura Bravo-Merodio & Samantha C Pendleton & Furqan Aziz & Animesh Acharjee & Georgios V Gkoutos, 2022. "Evaluating the detection ability of a range of epistasis detection methods on simulated data for pure and impure epistatic models," PLOS ONE, Public Library of Science, vol. 17(2), pages 1-19, February.
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:pone00:0116487. 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.