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Genotyping concordance tests included Coriell cell-line control DNA analyses checked against whole-genome sequencing data from 1000 Genomes and Complete Genomics, indicating a very high concordance rate of 99.8%.
We also recorded genotyping concordance as a genotyping quality metric.
Genotyping concordance rate was 99.996% based on study duplicates.
Genotyping concordance between Illumina Human610-Quad BeadChip and TaqMan SNP genotyping method was also checked on randomly selected samples, and the two methods showed complete concordance.
We have estimated the genotyping concordance between the results from the 48.48CS chip and the microtiter plates run on the Applied Biosystems 7900 HT system.
Genotyping concordance was perfect for the CYP2D6*4 and UGT1A8*2 variants (for both, weighted kappa = 1.00; 95% CI 1.00, 1.00).
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Ability to genotype and genotype concordance both reflect data quality.
Genotypic fidelity (SNP genotype concordance) between LCL and PBMC varied across sample pairs, with mismatch rates ranging from 0.175% to 0.664% (with no filtering).
The genotype concordance of directly genotyped common variants (irrespective of the genotype quality) showed an increased genotype concordance in 95% of the cases after imputation.
The fidelity of genotype concordance between paired cytology smears and surgical pathology specimens is unknown.
Based on genomic position, a total of 107,896 SNP were shared between the 2 platforms; however, based on genotype concordance, only 96,031 SNP had complete concordance at these loci.
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