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Imputation of genotypes from different single nucleotide polymorphism panels in dairy cattle

Druet, T. ; Schrooten, C. ; de Roos, A.P.W.

Journal of dairy science, 2010-11, Vol.93 (11), p.5443-5454 [Periódico revisado por pares]

New York, NY: Elsevier Inc

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Título:
Imputation of genotypes from different single nucleotide polymorphism panels in dairy cattle
Autor: Druet, T. ; Schrooten, C. ; de Roos, A.P.W.
Assuntos: accuracy ; alleles ; Animal productions ; Animals ; Biological and medical sciences ; Cattle - genetics ; dairy cattle ; Dairying - methods ; Databases, Genetic ; Feasibility Studies ; Food industries ; Fundamental and applied biological sciences. Psychology ; Genetic Markers ; genetic techniques and protocols ; Genetics & genetic processes ; Genome-Wide Association Study - methods ; Genome-Wide Association Study - veterinary ; Genome-Wide Association Study/methods/veterinary ; Genotype ; genotyping ; Génétique & processus génétiques ; Holstein ; imputation ; Life sciences ; Male ; Milk and cheese industries. Ice creams ; Polymorphism, Single Nucleotide - genetics ; precision ; reference chips ; reference standards ; Sciences du vivant ; single nucleotide polymorphism ; Terrestrial animal productions ; Vertebrates
É parte de: Journal of dairy science, 2010-11, Vol.93 (11), p.5443-5454
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
scopus-id:2-s2.0-78649372542
Descrição: Imputation of missing genotypes is important to join data from animals genotyped on different single nucleotide polymorphism (SNP) panels. Because of the evolution of available technologies, economical reasons, or coexistence of several products from competing organizations, animals might be genotyped for different SNP chips. Combined analysis of all the data increases accuracy of genomic selection or fine-mapping precision. In the present study, real data from 4,738 Dutch Holstein animals genotyped with custom-made 60K Illumina panels (Illumina, San Diego, CA) were used to mimic imputation of genotypes between 2 SNP panels of approximately 27,500 markers each and with 9,265 SNP markers in common. Imputation efficiency increased with number of reference animals (genotyped for both chips), when animals genotyped on a single chip were included in the training data, with regional higher marker densities, with greater distance to chromosome ends, and with a closer relationship between imputed and reference animals. With 0 to 2,000 animals genotyped for both chips, the mean imputation error rate ranged from 2.774 to 0.415% and accuracy ranged from 0.81 to 0.96. Then, imputation was applied in the Dutch Holstein population to predict alleles from markers of the Illumina Bovine SNP50 chip with markers from a custom-made 60K Illumina panel. A cross-validation study performed on 102 bulls indicated that the mean error rate per bull was approximately equal to 1.0%. This study showed the feasibility to impute markers in dairy cattle with the current marker panels and with error rates below 1%.
Editor: New York, NY: Elsevier Inc
Idioma: Inglês;Russo

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Imputation of genotypes from different single nucleotide polymorphism panels in dairy cattle

Druet, T. ; Schrooten, C. ; de Roos, A.P.W.

New York, NY: Elsevier Inc

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