Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples.

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成果类型：

期刊论文

作者：

Wu, X-L*;Xu, J.;Li, H.;Ferretti, R.;He, J.;...

通讯作者：

Wu, X-L

作者机构：

[Ferretti, R.; Tait, R. G., Jr.; Michell, T.; Wu, X-L; Xu, J.; Bauck, S.; Li, H.; Simpson, B.] Neogen GeneSeek, Bioinformat & Biostat, Lincoln, NE 68504 USA.

[Wu, X-L; Li, H.] Univ Wisconsin, Dept Anim Sci, Madison, WI 53706 USA.

[Xu, J.; Kachman, S. D.] Univ Nebraska, Dept Stat, Lincoln, NE 68583 USA.

[He, J.] Hunan Agr Univ, Coll Anim Sci & Technol, Changsha 410128, Hunan, Peoples R China.

[Xiao, Q.; Qiu, J.] Neogen GeneSeek, Qual Assurance, Lincoln, NE 68504 USA.

通讯机构：

[Wu, X-L] N

Neogen GeneSeek, Bioinformat & Biostat, Lincoln, NE 68504 USA.

语种：

英文

关键词：

bovine SNP chips;genotyping errors;mendelian errors;quality assurance

期刊：

ANIMAL GENETICS

ISSN：

0268-9146

年：

2019

卷：

期：

页码：

367-371

DOI：

10.1111/age.12800

基金类别：

We thank Dr. Mike Heaton for providing the 96 DNA samples that were used as QA type II samples in the present study. JX and JH were financially supported by Neogen GeneSeek. JH was also supported by the Bairen Plan of Hunan Province, China (XZ2016-08-07) and Hunan Co-Innovation center of Animal Production Safety, China. Joy J Wu is acknowledged for proof-reading this manuscript. The two anonymous reviewers are acknowledged for their valuable comments and suggestions.

机构署名：

本校为其他机构

院系归属：

动物科学技术学院

摘要：

SNP arrays are widely used in genetic research and agricultural genomics applications, and the quality of SNP genotyping data is of paramount importance. In the present study, SNP genotyping concordance and discordance were evaluated for commercial bovine SNP arrays based on two types of quality assurance (QA) samples provided by Neogen GeneSeek. The genotyping discordance rates (GDRs) between chips were on average between 0.06% and 0.37% based on the QA type I data and between 0.05% and 0.15% based on the QA type II data. The average genotypin...

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Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples.

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