Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array

CORC > 昆明动物研究所 > 昆明动物研究所 > 遗传资源与进化国家重点实验室 > 分子进化基因组学

	Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array
	Otecko NO 1,2; Peng MS 1,2; Yang HC 1; Zhang YP 1,2,3; Wang GD[*]1,2
刊名	Zoological Research
	2016
卷号	37 期号:6 页码:356-360
关键词	SNP array Dog Mitochondrial Y chromosomal Autosomal
通讯作者	wanggd@mail.kiz.ac.cn
英文摘要	Quality deficiencies in single nucleotide polymorphism (SNP) analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochondrial, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall, the individual missingness rate for mitochondrial SNPs was ~43.8%, with 980 (18.1%) individuals completely missing mitochondrial SNP genotyping (missingness rate=1). In males, the genotype missingness rate was ~28.8% for Y chromosomal SNPs, with 374 males recording rates above 0.96. These 374 males also exhibited completely failed mitochondrial SNPs genotyping, indicative of a batch effect. Individual missingness rates for autosomal markers were greater than zero, but less than 0.5. Neither mitochondrial nor Y chromosomal SNPs achieved complete genotyping (locus missingness rate=0), whereas 5.9% of autosomal SNPs had a locus missingness rate=1. The high missingness rates and possible batch effect show that caution and rigorous measures are vital when genotyping and analyzing SNP array data for domestic animals. Further improvements of these arrays will be helpful to future studies.
收录类别	其他
资助信息	This work was supported by grants from the NSFC (91531303) and the 973 programs (2013CB835200; 2013CB835202)
语种	英语
内容类型	期刊论文
源URL	[http://159.226.149.26:8080/handle/152453/10822]
专题	昆明动物研究所_分子进化基因组学昆明动物研究所_遗传资源与进化国家重点实验室
作者单位	1.State Key Laboratory of Genetic Resources and Evolution, Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 2.Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China 3.State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China
推荐引用方式 GB/T 7714	Otecko NO,Peng MS,Yang HC,et al. Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array[J]. Zoological Research,2016,37(6):356-360.
APA	Otecko NO,Peng MS,Yang HC,Zhang YP,&Wang GD[*].(2016).Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array.Zoological Research,37(6),356-360.
MLA	Otecko NO,et al."Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array".Zoological Research 37.6(2016):356-360.