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Analyses and comparison of accuracy of different genotype imputation methods.

Pei YF, Li J, Zhang L, Papasian CJ, Deng HW.

PLoS One. 2008;3(10):e3551. doi: 10.1371/journal.pone.0003551. Epub 2008 Oct 29.


Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies.

Hao K, Chudin E, McElwee J, Schadt EE.

BMC Genet. 2009 Jun 16;10:27. doi: 10.1186/1471-2156-10-27.


Analyses and comparison of imputation-based association methods.

Pei YF, Zhang L, Li J, Deng HW.

PLoS One. 2010 May 26;5(5):e10827. doi: 10.1371/journal.pone.0010827.


A comprehensive evaluation of SNP genotype imputation.

Nothnagel M, Ellinghaus D, Schreiber S, Krawczak M, Franke A.

Hum Genet. 2009 Mar;125(2):163-71. doi: 10.1007/s00439-008-0606-5. Epub 2008 Dec 17.


Assessment of genotype imputation methods.

Biernacka JM, Tang R, Li J, McDonnell SK, Rabe KG, Sinnwell JP, Rider DN, de Andrade M, Goode EL, Fridley BL.

BMC Proc. 2009 Dec 15;3 Suppl 7:S5.


Imputation of missing genotypes: an empirical evaluation of IMPUTE.

Zhao Z, Timofeev N, Hartley SW, Chui DH, Fucharoen S, Perls TT, Steinberg MH, Baldwin CT, Sebastiani P.

BMC Genet. 2008 Dec 12;9:85. doi: 10.1186/1471-2156-9-85.


Simpute: an efficient solution for dense genotypic data.

Lin YJ, Chang CT, Tang CY, Hsieh WP.

Biomed Res Int. 2013;2013:813912. doi: 10.1155/2013/813912. Epub 2013 Feb 3.


Effect of genome-wide genotyping and reference panels on rare variants imputation.

Zheng HF, Ladouceur M, Greenwood CM, Richards JB.

J Genet Genomics. 2012 Oct 20;39(10):545-50. doi: 10.1016/j.jgg.2012.07.002. Epub 2012 Jul 24.


Analysis of untyped SNPs: maximum likelihood and imputation methods.

Hu YJ, Lin DY.

Genet Epidemiol. 2010 Dec;34(8):803-15. doi: 10.1002/gepi.20527.


Imputation of unordered markers and the impact on genomic selection accuracy.

Rutkoski JE, Poland J, Jannink JL, Sorrells ME.

G3 (Bethesda). 2013 Mar;3(3):427-39. doi: 10.1534/g3.112.005363. Epub 2013 Mar 1.


A new genotype imputation method with tolerance to high missing rate and rare variants.

Yang Y, Wang Q, Chen Q, Liao R, Zhang X, Yang H, Zheng Y, Zhang Z, Pan Y.

PLoS One. 2014 Jun 27;9(6):e101025. doi: 10.1371/journal.pone.0101025. eCollection 2014.


Genotype imputation in genome-wide association studies.

Porcu E, Sanna S, Fuchsberger C, Fritsche LG.

Curr Protoc Hum Genet. 2013 Jul;Chapter 1:Unit 1.25. doi: 10.1002/0471142905.hg0125s78. Review.


On combining reference data to improve imputation accuracy.

Chen J, Zhang JG, Li J, Pei YF, Deng HW.

PLoS One. 2013;8(1):e55600. doi: 10.1371/journal.pone.0055600. Epub 2013 Jan 30.


fcGENE: a versatile tool for processing and transforming SNP datasets.

Roshyara NR, Scholz M.

PLoS One. 2014 Jul 22;9(7):e97589. doi: 10.1371/journal.pone.0097589. eCollection 2014.


Genotype imputation for African Americans using data from HapMap phase II versus 1000 genomes projects.

Sung YJ, Gu CC, Tiwari HK, Arnett DK, Broeckel U, Rao DC.

Genet Epidemiol. 2012 Jul;36(5):508-16. doi: 10.1002/gepi.21647. Epub 2012 May 29.


Assessing accuracy of genotype imputation in American Indians.

Malhotra A, Kobes S, Bogardus C, Knowler WC, Baier LJ, Hanson RL.

PLoS One. 2014 Jul 11;9(7):e102544. doi: 10.1371/journal.pone.0102544. eCollection 2014.


The effect of reference panels and software tools on genotype imputation.

Nho K, Shen L, Kim S, Swaminathan S, Risacher SL, Saykin AJ; Alzheimer’s Disease Neuroimaging Initiative (ADNI).

AMIA Annu Symp Proc. 2011;2011:1013-8. Epub 2011 Oct 22.


Extent of linkage disequilibrium, consistency of gametic phase, and imputation accuracy within and across Canadian dairy breeds.

Larmer SG, Sargolzaei M, Schenkel FS.

J Dairy Sci. 2014 May;97(5):3128-41. doi: 10.3168/jds.2013-6826. Epub 2014 Feb 26.


LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms.

Money D, Gardner K, Migicovsky Z, Schwaninger H, Zhong GY, Myles S.

G3 (Bethesda). 2015 Sep 15;5(11):2383-90. doi: 10.1534/g3.115.021667.


Genotype determination for polymorphisms in linkage disequilibrium.

Yu Z, Garner C, Ziogas A, Anton-Culver H, Schaid DJ.

BMC Bioinformatics. 2009 Feb 20;10:63. doi: 10.1186/1471-2105-10-63.

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