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

Newton O. OTECKO; Min-Sheng PENG; He-Chuan YANG; Ya-Ping ZHANG; Guo-Dong WANG

doi:10.13918/j.issn.2095-8137.2016.6.356

Volume 37 Issue 6

Nov. 2016

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Article Navigation > Zoological Research > 2016 > 37(6): 356-360

Newton O. OTECKO, Min-Sheng PENG, He-Chuan YANG, Ya-Ping ZHANG, Guo-Dong WANG. Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array. Zoological Research, 2016, 37(6): 356-360. doi: 10.13918/j.issn.2095-8137.2016.6.356

Citation:

Newton O. OTECKO, Min-Sheng PENG, He-Chuan YANG, Ya-Ping ZHANG, Guo-Dong WANG. Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array. Zoological Research, 2016, 37(6): 356-360. doi: 10.13918/j.issn.2095-8137.2016.6.356

Citation:

Newton O. OTECKO, Min-Sheng PENG, He-Chuan YANG, Ya-Ping ZHANG, Guo-Dong WANG. Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array. Zoological Research, 2016, 37(6): 356-360. doi: 10.13918/j.issn.2095-8137.2016.6.356

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

doi: 10.13918/j.issn.2095-8137.2016.6.356

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

Funds: This work was supported by grants from the NSFC (91531303) and the 973 programs (2013CB835200; 2013CB835202)

More Information

Corresponding author: Guo-Dong WANG
Received Date: 2016-10-18
Rev Recd Date: 2016-11-04
Publish Date: 2016-11-18

Abstract

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.
- SNP array,
- Dog,
- Mitochondrial,
- Y chromosomal,
- Autosomal

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References(18)

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