Limited effect of PCR ramp rate on qPCR Ct values: an exploratory study.

Ivan Zivotic, Ivana Kolic, Mariana Seke, Milan Stefanovic, Ljiljana Stojkovic, Aleksandra Stankovic, Maja Zivkovic

Abstract read

In one paragraph

Article in Molecular biology reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

7 authors.

Ivan ZivoticLaboratory for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia.

Ivana KolicLaboratory for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia. ivanak@vin.bg.ac.rs.

Mariana SekeLaboratory for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia.

Milan StefanovicLaboratory for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia.

Ljiljana StojkovicLaboratory for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia.

Aleksandra StankovicLaboratory for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia.

Maja ZivkovicLaboratory for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia.

Funding

the Ministry of Science, Technological Development and Innovation of the Republic of Serbia 451-03-33/2026-03/ 200017

6 · The paper itself

Abstract

backgroundQuantitative real-time PCR (qPCR) is highly sensitive to technical parameters, including thermal cycler ramp rate (RR). We systematically evaluated the effect of slow, intermediate and fast RR on cycle threshold (Ct) values using a commercial TaqMan™ SNP assay and two housekeeping genes, GAPDH and PPIA. METHODS AND

resultsEleven heterozygous DNA samples and three RNA samples were analyzed across two independent runs per RR. Across genotyping and gene expression assays, no consistent effect of qPCR RR on Ct values was observed. Intra-run analyses identified isolated statistically significant or borderline significant differences for the genotyping FAM-labeled probe and PPIA and GAPDH expression assays; however, these findings were not consistently reproduced across runs or pairwise comparisons. Overall, the observed effects appeared assay- and run-dependent rather than attributable to a consistent influence of RR.

conclusionsThese findings suggest that PCR RR does not have a consistent effect on Ct values across the evaluated genotyping and gene expression assays. The isolated differences observed between RRs were not consistently reproduced across runs. Larger studies involving more assays and samples are needed to determine whether PCR RR has a meaningful impact on qPCR performance and reproducibility under different experimental conditions.

Indexed as

Real-Time Polymerase Chain ReactionGenotypeHumansPolymorphism, Single NucleotideReproducibility of ResultsAmplification efficiencyCt variabilityProbe-based assaysQuantitative PCRThermal ramp rate

Identifiers

PMID42853298

DOI10.3390/medicina57121375

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.