title: Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array.
abstract: 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.
authors.affiliation: 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; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.
authors.forename: Newton
authors.initials: N
authors.lastname: O Otecko
authors.affiliation: 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; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.
authors.forename: Min-Sheng
authors.initials: MS
authors.lastname: Peng
authors.affiliation: 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.
authors.forename: He-Chuan
authors.initials: HC
authors.lastname: Yang
authors.affiliation: 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; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Zhang
authors.affiliation: 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; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China. wanggd@mail.kiz.ac.cn.
authors.forename: Guo-Dong
authors.initials: GD
authors.lastname: Wang
mesh_terms: D000818:Animals; D004285:Dogs; D005838:Genotype; D008928:Mitochondria / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D014998:Y Chromosome / Q000235:genetics*
keywords: Autosomal; Dog; Mitochondrial; SNP array; Y chromosomal