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KMID : 0613820180280111255
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Journal of Life Science
2018 Volume.28 No. 11 p.1255 ~ p.1261
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Imputation Accuracy from 770K SNP Chips to Next Generation Sequencing Data in a Hanwoo (Korean Native Cattle) Population using Minimac3 and Beagle
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An Na-Rae
Son Ju-Hwan
Park Jong-Eun
Chai Han-Ha
Jang Gul-Won
Lim Da-Jeong
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Abstract
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Whole genome analysis have been made possible with the development of DNA sequencing technologies and discovery of many single nucleotide polymorphisms (SNPs). Large number of SNP can be analyzed with SNP chips, since SNPs of human as well as livestock genomes are available. Among the various missing nucleotide imputation programs, Minimac3 software is suggested to be highly accurate, with a simplified workflow and relatively fast. In the present study, we used Minimac3 program to perform genomic missing value substitution 1,226 animals 770K SNP chip and imputing missing SNPs with next generation sequencing data from 311 animals. The accuracy on each chromosome was about 94~96%, and individual sample accuracy was about 92~98%. After imputation of the genotypes, SNPs with R Square (R2) values for three conditions were 0.4, 0.6, and 0.8 and the percentage of SNPs were 91%, 84%, and 70% respectively. The differences in the Minor Allele Frequency gave R2 values corresponding to seven intervals (0, 0.025), (0.025, 0.05), (0.05, 0.1), (0.1, 0.2), (0.2, 0.3). (0.3, 0.4) and (0.4, 0.5) of 64~88%. The total analysis time was about 12 hr. In future SNP chip studies, as the size and complexity of the genomic datasets increase, we expect that genomic imputation using Minimac3 can improve the reliability of chip data for Hanwoo discrimination.
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KEYWORD
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Hanwoo, imputation, Minimac3, Next Generation Sequencing (NGS), SNP chip
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