두 상업용 돼지 SNP 칩 간의 유전자형 일치율 및 데이터 호환성 평가

초록

In porcine genomic research, SNP chips from Affymetrix and Illumina are widely utilized, yet technical differences between platforms present challenges for data integration and comparative analysis. This study was conducted to directly compare the data compatibility between the Affymetrix Axiom Pig55K and Illumina PorcineSNP80v1 platforms and to provide practical guidelines for integrating and®utilizing data from both. Genotypes were generated by analyzing the same 127 pig samples on both platforms, followed by platform-specific quality control (QC). Common markers were identified by directly aligning Illumina probe sequences to the porcine reference genome (Sscrofa11.1), based on which the genotype concordance rate and Minor Allele Frequency (MAF) correlation were analyzed. Ultimately, 27,774 common markers were identified between the platforms, with an overall genotype concordance rate of 96.53%. This was, however, skewed by five outlier samples with extremely low concordance rates; the rate for the remaining 77 high-quality samples was very high, ranging from 98.88% to 99.88%. These results demonstrate that the quality of the analytical samples, rather than the technical differences between platforms, has a critical impact on data compatibility. If sample quality is assured, data from both platforms possess high reliability for interchangeable use, suggesting a viable foundation for large-scale data integration studies.

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