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

Content Provider	Europe PMC
Author	OTECKO, Newton O. PENG, Min-Sheng YANG, He-Chuan ZHANG, Ya-Ping WANG, Guo-Dong
Copyright Year	2016
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.
Related Links	https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5359323&blobtype=pdf
ISSN	20958137
Journal	Zoological Research [Zool Res]
Volume Number	37
DOI	10.13918/j.issn.2095-8137.2016.6.356
PubMed Central reference number	PMC5359323
Issue Number	6
PubMed reference number	28105800
e-ISSN	20958137
Language	English
Publisher	Science Press
Publisher Date	2016-11-01
Publisher Place	16 Donghuangchenggen Beijie,Beijing 100717, China
Access Restriction	Open
Rights License	This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Subject Keyword	SNP array Dog Mitochondrial Y chromosomal Autosomal
Content Type	Text
Resource Type	Article
Subject	Ecology Animal Science and Zoology Ecology, Evolution, Behavior and Systematics Nature and Landscape Conservation

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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