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10.1186/s12711-015-0134-4 http://scihub22266oqcxt.onion/10.1186/s12711-015-0134-4 C4486706!4486706!26122927     free     free     free Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Genet+Sel+Evol 2015 ; 47 (1): ä Nephropedia Template TP {{tp|p=26122927|t=2015. Imputation of genotypes in Danish purebred and two-way crossbred pigs using low-density panels |pdf=|usr=}}{{26122927}} gab.com Text Imputation of genotypes in Danish purebred and two-way crossbred pigs using low-density panels JO: Genet Sel Evol http://www.kidney.de/pget.php?&tw=1&pmid=26122927 #FOAvip Background: Genotype imputation is commonly used as an initial step in genomic selection since the accuracy of genomic selection does not decline if accurately imputed genotypes are used instead of actual genotypes but for a lower cost. Performance of imputation has rarely been investigated in crossbred animals and, in particular, in pigs. The extent and pattern of linkage disequilibrium differ in crossbred versus purebred animals, which may impact the performance of imputation. In this study, first we compared different scenarios of imputation from 5 K to 8 K single nucleotide polymorphisms (SNPs) in genotyped Danish Landrace and Yorkshire and crossbred Landrace-Yorkshire datasets and, second, we compared imputation from 8 K to 60 K SNPs in genotyped purebred and simulated crossbred datasets. All imputations were done using software Beagle version 3.3.2. Then, we investigated the reasons that could explain the differences observed. Results: Genotype imputation performs as well in crossbred animals as in purebred animals when both parental breeds are included in the reference population. When the size of the reference population is very large, it is not necessary to use a reference population that combines the two breeds to impute the genotypes of purebred animals because a within-breed reference population can provide a very high level of imputation accuracy (correct rate???0.99, correlation???0.95). However, to ensure that similar imputation accuracies are obtained for crossbred animals, a reference population that combines both parental purebred animals is required. Imputation accuracies are higher when a larger proportion of haplotypes are shared between the reference population and the validation (imputed) populations. Conclusions: The results from both real data and pedigree-based simulated data demonstrate that genotype imputation from low-density panels to medium-density panels is highly accurate in both purebred and crossbred pigs. In crossbred pigs, combining the parental purebred animals in the reference population is necessary to obtain high imputation accuracy. Electronic supplementary material: The online version of this article (doi:10.1186/s12711-015-0134-4) contains supplementary material, which is available to authorized users. Twit Text FOAVip Imputation of genotypes in Danish purebred and two-way crossbred pigs using low-density panels ????Genet Sel Evol http://www.kidney.de/pget.php?&tw=1&pmid=26122927 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=26122927 #FOAvip English Wikipedia <ref>{{Cite pmid|26122927}}</ref> Imputation of genotypes in Danish purebred and two-way crossbred pigs using low-density panels #MMPMID26122927 Xiang T; Ma P; Ostersen T; Legarra A; Christensen OF Genet Sel Evol 2015[]; 47 (1): ä PMID26122927show ga Background: Genotype imputation is commonly used as an initial step in genomic selection since the accuracy of genomic selection does not decline if accurately imputed genotypes are used instead of actual genotypes but for a lower cost. Performance of imputation has rarely been investigated in crossbred animals and, in particular, in pigs. The extent and pattern of linkage disequilibrium differ in crossbred versus purebred animals, which may impact the performance of imputation. In this study, first we compared different scenarios of imputation from 5 K to 8 K single nucleotide polymorphisms (SNPs) in genotyped Danish Landrace and Yorkshire and crossbred Landrace-Yorkshire datasets and, second, we compared imputation from 8 K to 60 K SNPs in genotyped purebred and simulated crossbred datasets. All imputations were done using software Beagle version 3.3.2. Then, we investigated the reasons that could explain the differences observed. Results: Genotype imputation performs as well in crossbred animals as in purebred animals when both parental breeds are included in the reference population. When the size of the reference population is very large, it is not necessary to use a reference population that combines the two breeds to impute the genotypes of purebred animals because a within-breed reference population can provide a very high level of imputation accuracy (correct rate???0.99, correlation???0.95). However, to ensure that similar imputation accuracies are obtained for crossbred animals, a reference population that combines both parental purebred animals is required. Imputation accuracies are higher when a larger proportion of haplotypes are shared between the reference population and the validation (imputed) populations. Conclusions: The results from both real data and pedigree-based simulated data demonstrate that genotype imputation from low-density panels to medium-density panels is highly accurate in both purebred and crossbred pigs. In crossbred pigs, combining the parental purebred animals in the reference population is necessary to obtain high imputation accuracy. Electronic supplementary material: The online version of this article (doi:10.1186/s12711-015-0134-4) contains supplementary material, which is available to authorized users. äImputation of genotypes in Danish purebred and two-way crossbred pigs (epmc).pdf DeepDyve Pubget Overpricing