Characteristic and influencing factors of Taqman genotyping calling error

Abstract

Background Taqman fluorescent probe was frequently applied in single nucleotide polymorphism (SNP) genotyping. However, the characteristic of calling error and the influencing factors remain unclear. Method Calling errors of Taqman genotyping was evaluated systematically based on Mendelian inheritance. Twenty‐two SNPs were genotyped by Taqman probe for 419 pedigrees. Mendelian genetic errors were counted for every SNP and pedigree. Cluster analysis was applied to investigate the compatibility between Taqman probes and DNA sample. Results On one hand, errors were found for all the SNPs. The error number ranged from 4 to 33 with median of 10.5. On the other hand, Mendelian genetic errors showed features of both randomness and cluster. Half of the pedigrees containing errors had only 1 Mendelian genetic error. But there was also a pedigree containing up to 10 Mendelian genetic errors. Furthermore, cluster analysis indicated that errors of different SNPs took place in different pedigree cluster. Conclusion It could be concluded that calling error is inevitable for Taqman genotyping of large samples. The quality of Taqman probe and DNA sample, as well as their compatibility, may account for the error incidence.

Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation

“…Our study demonstrates that practically, both HRM and TaqMan produce similar genotyping error rates, although these methods have been reported to differ in sensitivity to experimental conditions that may compromise them. For instance, HRM has large sensitivity of the melt curve shape to very small changes in environmental factors, including pH, ionic force, and cation concentration [ 28 ], and TaqMan is sensitive to the quality of the TaqMan probe [ 29 ].…”