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A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

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Cited by:

  1. Urmo Võsa & Tõnu Esko & Silva Kasela & Tarmo Annilo, 2015. "Altered Gene Expression Associated with microRNA Binding Site Polymorphisms," PLOS ONE, Public Library of Science, vol. 10(10), pages 1-24, October.
  2. Myoung Keun Lee & John R Shaffer & Elizabeth J Leslie & Ekaterina Orlova & Jenna C Carlson & Eleanor Feingold & Mary L Marazita & Seth M Weinberg, 2017. "Genome-wide association study of facial morphology reveals novel associations with FREM1 and PARK2," PLOS ONE, Public Library of Science, vol. 12(4), pages 1-13, April.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. Hakhamanesh Mostafavi & Tomaz Berisa & Felix R Day & John R B Perry & Molly Przeworski & Joseph K Pickrell, 2017. "Identifying genetic variants that affect viability in large cohorts," PLOS Biology, Public Library of Science, vol. 15(9), pages 1-29, September.
  8. Sacco Chiara & Viroli Cinzia & Falchi Mario, 2017. "A statistical test for detecting parent-of-origin effects when parental information is missing," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 16(4), pages 275-289, September.
  9. Poojitha Balakrishnan & Miranda R. Jones & Dhananjay Vaidya & Maria Tellez-Plaza & Wendy S. Post & Joel D. Kaufman & Suzette J. Bielinski & Kent Taylor & Kevin Francesconi & Walter Goessler & Ana Nava, 2018. "Ethnic, Geographic, and Genetic Differences in Arsenic Metabolism at Low Arsenic Exposure: A Preliminary Analysis in the Multi-Ethnic Study of Atherosclerosis (MESA)," IJERPH, MDPI, vol. 15(6), pages 1-11, June.
  10. Steffan D Bos & Christian M Page & Bettina K Andreassen & Emon Elboudwarej & Marte W Gustavsen & Farren Briggs & Hong Quach & Ingvild S Leikfoss & Anja Bjølgerud & Tone Berge & Hanne F Harbo & Lisa F , 2015. "Genome-Wide DNA Methylation Profiles Indicate CD8+ T Cell Hypermethylation in Multiple Sclerosis," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-16, March.
  11. Wei-Yu Lin & Ian W Brock & Dan Connley & Helen Cramp & Rachel Tucker & Jon Slate & Malcolm W R Reed & Sabapathy P Balasubramanian & Lisa A Cannon-Albright & Nicola J Camp & Angela Cox, 2013. "Associations of ATR and CHEK1 Single Nucleotide Polymorphisms with Breast Cancer," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-1, July.
  12. Craig, Sarah J.C. & Kenney, Ana M. & Lin, Junli & Paul, Ian M. & Birch, Leann L. & Savage, Jennifer S. & Marini, Michele E. & Chiaromonte, Francesca & Reimherr, Matthew L. & Makova, Kateryna D., 2023. "Constructing a polygenic risk score for childhood obesity using functional data analysis," Econometrics and Statistics, Elsevier, vol. 25(C), pages 66-86.
  13. Ani Manichaikul & Xin-Qun Wang & Solomon K Musani & David M Herrington & Wendy S Post & James G Wilson & Stephen S Rich & Annabelle Rodriguez, 2015. "Association of the Lipoprotein Receptor SCARB1 Common Missense Variant rs4238001 with Incident Coronary Heart Disease," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-16, May.
  14. Morten Dybdahl Krebs & Gonçalo Espregueira Themudo & Michael Eriksen Benros & Ole Mors & Anders D. Børglum & David Hougaard & Preben Bo Mortensen & Merete Nordentoft & Michael J. Gandal & Chun Chieh F, 2021. "Associations between patterns in comorbid diagnostic trajectories of individuals with schizophrenia and etiological factors," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
  15. Susanna Lemmelä & Svetlana Solovieva & Rahman Shiri & Christian Benner & Markku Heliövaara & Johannes Kettunen & Verneri Anttila & Samuli Ripatti & Markus Perola & Ilkka Seppälä & Markus Juonala & Mik, 2016. "Genome-Wide Meta-Analysis of Sciatica in Finnish Population," PLOS ONE, Public Library of Science, vol. 11(10), pages 1-18, October.
  16. Heejung Shim & Daniel I Chasman & Joshua D Smith & Samia Mora & Paul M Ridker & Deborah A Nickerson & Ronald M Krauss & Matthew Stephens, 2015. "A Multivariate Genome-Wide Association Analysis of 10 LDL Subfractions, and Their Response to Statin Treatment, in 1868 Caucasians," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-20, April.
  17. Anshuman Sewda & A J Agopian & Elizabeth Goldmuntz & Hakon Hakonarson & Bernice E Morrow & Deanne Taylor & Laura E Mitchell & on behalf of the Pediatric Cardiac Genomics Consortium, 2019. "Gene-based genome-wide association studies and meta-analyses of conotruncal heart defects," PLOS ONE, Public Library of Science, vol. 14(7), pages 1-19, July.
  18. Harriëtte Riese & Loretto M Muñoz & Catharina A Hartman & Xiuhua Ding & Shaoyong Su & Albertine J Oldehinkel & Arie M van Roon & Peter J van der Most & Joop Lefrandt & Ron T Gansevoort & Pim van der H, 2014. "Identifying Genetic Variants for Heart Rate Variability in the Acetylcholine Pathway," PLOS ONE, Public Library of Science, vol. 9(11), pages 1-9, November.
  19. Thomas J Hoffmann & Bronya J Keats & Noriko Yoshikawa & Catherine Schaefer & Neil Risch & Lawrence R Lustig, 2016. "A Large Genome-Wide Association Study of Age-Related Hearing Impairment Using Electronic Health Records," PLOS Genetics, Public Library of Science, vol. 12(10), pages 1-20, October.
  20. Mette K Andersen & Emil Jørsboe & Line Skotte & Kristian Hanghøj & Camilla H Sandholt & Ida Moltke & Niels Grarup & Timo Kern & Yuvaraj Mahendran & Bolette Søborg & Peter Bjerregaard & Christina V L L, 2020. "The derived allele of a novel intergenic variant at chromosome 11 associates with lower body mass index and a favorable metabolic phenotype in Greenlanders," PLOS Genetics, Public Library of Science, vol. 16(1), pages 1-17, January.
  21. Gianmarco Mignogna & Caitlin E. Carey & Robbee Wedow & Nikolas Baya & Mattia Cordioli & Nicola Pirastu & Rino Bellocco & Kathryn Fiuza Malerbi & Michel G. Nivard & Benjamin M. Neale & Raymond K. Walte, 2023. "Patterns of item nonresponse behaviour to survey questionnaires are systematic and associated with genetic loci," Nature Human Behaviour, Nature, vol. 7(8), pages 1371-1387, August.
  22. Indra Adrianto & Chee Paul Lin & Jessica J Hale & Albert M Levin & Indrani Datta & Ryan Parker & Adam Adler & Jennifer A Kelly & Kenneth M Kaufman & Christopher J Lessard & Kathy L Moser & Robert P Ki, 2012. "Genome-Wide Association Study of African and European Americans Implicates Multiple Shared and Ethnic Specific Loci in Sarcoidosis Susceptibility," PLOS ONE, Public Library of Science, vol. 7(8), pages 1-10, August.
  23. Anu Loukola & Jadwiga Buchwald & Richa Gupta & Teemu Palviainen & Jenni Hällfors & Emmi Tikkanen & Tellervo Korhonen & Miina Ollikainen & Antti-Pekka Sarin & Samuli Ripatti & Terho Lehtimäki & Olli Ra, 2015. "A Genome-Wide Association Study of a Biomarker of Nicotine Metabolism," PLOS Genetics, Public Library of Science, vol. 11(9), pages 1-23, September.
  24. Xiaodong Cai & Juan Andrés Bazerque & Georgios B Giannakis, 2013. "Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations," PLOS Computational Biology, Public Library of Science, vol. 9(5), pages 1-13, May.
  25. Andrew A. Brown & Juan J. Fernandez-Tajes & Mun-gwan Hong & Caroline A. Brorsson & Robert W. Koivula & David Davtian & Théo Dupuis & Ambra Sartori & Theodora-Dafni Michalettou & Ian M. Forgie & Jonath, 2023. "Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  26. 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.
  27. Jennifer Zou & Farhad Hormozdiari & Brandon Jew & Stephane E Castel & Tuuli Lappalainen & Jason Ernst & Jae Hoon Sul & Eleazar Eskin, 2019. "Leveraging allelic imbalance to refine fine-mapping for eQTL studies," PLOS Genetics, Public Library of Science, vol. 15(12), pages 1-24, December.
  28. Maggie C Y Ng & Daniel Shriner & Brian H Chen & Jiang Li & Wei-Min Chen & Xiuqing Guo & Jiankang Liu & Suzette J Bielinski & Lisa R Yanek & Michael A Nalls & Mary E Comeau & Laura J Rasmussen-Torvik &, 2014. "Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes," PLOS Genetics, Public Library of Science, vol. 10(8), pages 1-14, August.
  29. Yee-Ling Wong & Pirro Hysi & Gemmy Cheung & Milly Tedja & Quan V Hoang & Stuart W J Tompson & Kristina N Whisenhunt & Virginie Verhoeven & Wanting Zhao & Moritz Hess & Chee-Wai Wong & Annette Kifley &, 2019. "Genetic variants linked to myopic macular degeneration in persons with high myopia: CREAM Consortium," PLOS ONE, Public Library of Science, vol. 14(8), pages 1-16, August.
  30. Bárbara Sousa da Mota & Simone Rubinacci & Diana Ivette Cruz Dávalos & Carlos Eduardo G. Amorim & Martin Sikora & Niels N. Johannsen & Marzena H. Szmyt & Piotr Włodarczak & Anita Szczepanek & Marcin M, 2023. "Imputation of ancient human genomes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  31. Hans M Albertsen & Rakesh Chettier & Pamela Farrington & Kenneth Ward, 2013. "Genome-Wide Association Study Link Novel Loci to Endometriosis," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-8, March.
  32. Gemma Cadby & Corey Giles & Phillip E. Melton & Kevin Huynh & Natalie A. Mellett & Thy Duong & Anh Nguyen & Michelle Cinel & Alex Smith & Gavriel Olshansky & Tingting Wang & Marta Brozynska & Mike Ino, 2022. "Comprehensive genetic analysis of the human lipidome identifies loci associated with lipid homeostasis with links to coronary artery disease," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  33. Andrew McDavid & Paul K Crane & Katherine M Newton & David R Crosslin & Wayne McCormick & Noah Weston & Kelly Ehrlich & Eugene Hart & Robert Harrison & Walter A Kukull & Carla Rottscheit & Peggy Peiss, 2013. "Enhancing the Power of Genetic Association Studies through the Use of Silver Standard Cases Derived from Electronic Medical Records," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-9, June.
  34. Oren E Livne & Lide Han & Gorka Alkorta-Aranburu & William Wentworth-Sheilds & Mark Abney & Carole Ober & Dan L Nicolae, 2015. "PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population," PLOS Computational Biology, Public Library of Science, vol. 11(3), pages 1-14, March.
  35. Fang Chen & Jing He & Jianqi Zhang & Gary K Chen & Venetta Thomas & Christine B Ambrosone & Elisa V Bandera & Sonja I Berndt & Leslie Bernstein & William J Blot & Qiuyin Cai & John Carpten & Graham Ca, 2015. "Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-17, June.
  36. Faheem Mitha & Herodotos Herodotou & Nedyalko Borisov & Chen Jiang & Josh Yoder & Kouros Owzar, 2011. "SNPpy - Database Management for SNP Data from Genome Wide Association Studies," PLOS ONE, Public Library of Science, vol. 6(10), pages 1-8, October.
  37. Qingqin S Li & Antonio R Parrado & Mahesh N Samtani & Vaibhav A Narayan & Alzheimer’s Disease Neuroimaging Initiative, 2015. "Variations in the FRA10AC1 Fragile Site and 15q21 Are Associated with Cerebrospinal Fluid Aβ1-42 Level," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-17, August.
  38. 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.
  39. Ayush Giri & Jennifer M Wu & Renee M Ward & Katherine E Hartmann & Amy J Park & Kari E North & Mariaelisa Graff & Robert B Wallace & Gihan Bareh & Lihong Qi & Mary J O'Sullivan & Alexander P Reiner & , 2015. "Genetic Determinants of Pelvic Organ Prolapse among African American and Hispanic Women in the Women’s Health Initiative," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-19, November.
  40. Akinori Miyashita & Asako Koike & Gyungah Jun & Li-San Wang & Satoshi Takahashi & Etsuro Matsubara & Takeshi Kawarabayashi & Mikio Shoji & Naoki Tomita & Hiroyuki Arai & Takashi Asada & Yasuo Harigaya, 2013. "SORL1 Is Genetically Associated with Late-Onset Alzheimer’s Disease in Japanese, Koreans and Caucasians," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-11, April.
  41. 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.
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