title: Practical capability and cost effectiveness of a DNA pool-based genome-wide association study using BovineSNP50 array in a cattle population.
abstract: Genome-wide association mapping for complex traits in cattle populations is a powerful, but expensive, selection tool. The DNA pooling technique can potentially reduce the cost of genome-wide association studies. However, in DNA pooling design, the additional variance generated by pooling-specific errors must be taken into account. Therefore, this study aimed to investigate factors such as: (i) the accuracy of allele frequency estimation; (ii) the magnitude of errors in pooling construction and in the array; and (iii) the effect of the number of replicate arrays on P-values estimated by a genome-wide association study. Results showed that the Illumina correction method is the most effective method to correct the allele frequency estimation; pooling errors, especially array variance, should be taken into account in DNA pooling design; and the risk of a type I error can be reduced by using at least two replicate arrays. These results indicate the practical capability and cost-effectiveness of pool-based genome-wide association studies using the BovineSNP50 array in a cattle population.
authors.affiliation: National Livestock Breeding Center, Nishigo, Fukushima, Japan. y0uemoto@nlbc.go.jp
authors.forename: Yoshinobu
authors.initials: Y
authors.lastname: Uemoto
authors.forename: Nanae
authors.initials: N
authors.lastname: Sasago
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Abe
authors.forename: Hideki
authors.initials: H
authors.lastname: Okada
authors.forename: Hitomi
authors.initials: H
authors.lastname: Maruoka
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Nakajima
authors.forename: Noriaki
authors.initials: N
authors.lastname: Shoji
authors.forename: Shin
authors.initials: S
authors.lastname: Maruyama
authors.forename: Naohiko
authors.initials: N
authors.lastname: Kobayashi
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Mannen
authors.forename: Eiji
authors.initials: E
authors.lastname: Kobayashi
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D003362:Cost-Benefit Analysis; D004247:DNA / Q000235:genetics*; D005787:Gene Frequency; D005788:Gene Pool; D055106:Genome-Wide Association Study / Q000191:economics* / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
chemical_list: D004247:DNA