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Zoological Research
Kunming Institute of Zoology, Chinese Academy of Sciences
ISSN: 2095-8137
Vol. 37, No. 6, 2016, pp. 358-362
Bioline Code: zr16052
Full paper language: English
Document type: Report
Document available free of charge

Zoological Research, Vol. 37, No. 6, 2016, pp. 358-362

 en Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array
OTECKO, Newton O.; PENG, Min-Sheng; YANG, He-Chuan; ZHANG, Ya-Ping & WANG, Guo-Dong


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.

SNP array; Dog; Mitochondrial; Y chromosomal; Autosomal

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