Ruiz-Villalba, AdriánRuijter, Jan M.van den Hoff, Maurice J. B.2022-04-012022-04-012021-05-29Ruiz-Villalba A, Ruijter JM, van den Hoff MJB. Use and Misuse of Cq in qPCR Data Analysis and Reporting. Life. 2021 May 29;11(6):496http://hdl.handle.net/10668/3514In the analysis of quantitative PCR (qPCR) data, the quantification cycle (Cq) indicates the position of the amplification curve with respect to the cycle axis. Because Cq is directly related to the starting concentration of the target, and the difference in Cq values is related to the starting concentration ratio, the only results of qPCR analysis reported are often Cq, ΔCq or ΔΔCq values. However, reporting of Cq values ignores the fact that Cq values may differ between runs and machines, and, therefore, cannot be compared between laboratories. Moreover, Cq values are highly dependent on the PCR efficiency, which differs between assays and may differ between samples. Interpreting reported Cq values, assuming a 100% efficient PCR, may lead to assumed gene expression ratios that are 100-fold off. This review describes how differences in quantification threshold setting, PCR efficiency, starting material, PCR artefacts, pipetting errors and sampling variation are at the origin of differences and variability in Cq values and discusses the limits to the interpretation of observed Cq values. These issues can be avoided by calculating efficiency-corrected starting concentrations per reaction. The reporting of gene expression ratios and fold difference between treatments can then easily be based on these starting concentrations.enAtribución 4.0 Internacionalhttp://creativecommons.org/licenses/by/4.0/qPCR analysisCqQuantification cycleQuantification thresholdPCR efficiencyPoisson variationLODLOQArtefactosLaboratoriosExpresión génicaReacción en cadena en tiempo real de la polimerasaMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::ArtifactsMedical Subject Headings::Health Care::Health Care Facilities, Manpower, and Services::Health Facilities::LaboratoriesMedical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Processes::Gene ExpressionMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Nucleic Acid Amplification Techniques::Polymerase Chain Reaction::Real-Time Polymerase Chain Reactionreview article34072308Acceso abierto10.3390/life110604962075-1729PMC8229287