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Newton O. OTECKO, 彭旻晟, 杨贺川, 张亚平, 王国栋. 2016: 重新评价家犬SNP芯片获得的线粒体、Y染色体和常染色体SNP数据质量. 动物学研究, 37(6): 356-360. DOI: 10.13918/j.issn.2095-8137.2016.6.356
引用本文: Newton O. OTECKO, 彭旻晟, 杨贺川, 张亚平, 王国栋. 2016: 重新评价家犬SNP芯片获得的线粒体、Y染色体和常染色体SNP数据质量. 动物学研究, 37(6): 356-360. DOI: 10.13918/j.issn.2095-8137.2016.6.356
Newton O. OTECKO, Min-Sheng PENG, He-Chuan YANG, Ya-Ping ZHANG, Guo-Dong WANG. 2016: Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array. Zoological Research, 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. 2016: Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array. Zoological Research, 37(6): 356-360. DOI: 10.13918/j.issn.2095-8137.2016.6.356

重新评价家犬SNP芯片获得的线粒体、Y染色体和常染色体SNP数据质量

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

  • 摘要: 单核苷酸多态位点(SNP)芯片数据的质量在分析中需重视。我们利用缺失比率衡量了最近发表的5392只狗和14只灰狼的Illumina SNP芯片数据,包含了424个线粒体SNPs,211个Y染色体SNPs,和160432个常染色体SNPs。分析结果表明,在线粒体SNPs中,缺失比率为43.8%,其中980个个体(18.1%)完全缺失;在雄性个体的Y染色体SNPs中,缺失比率为28.8%,其中374个个体的缺失率高达96%。此外,这374个个体的线粒体数据全部缺失,表明有批次效应的影响。在所有数据中,没有任何一个个体得到完整的线粒体或Y染色体SNP数据,有5.9%的常染色体SNPs的缺失率为1。高缺失率和可能存在的批次效应表明,在分析SNPS芯片数据时需非常小心和严格,在未来的研究中需要提高芯片的质量。

     

    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.

     

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