Introducing the f

Calibration curve Curve analysis Delta CT Inflection cycle PCR efficiency Performance indicators Real-time PCR Variation between replicates

Journal

BMC bioinformatics

ISSN: 1471-2105

Titre abrégé: BMC Bioinformatics

Pays: England

ID NLM: 100965194

Informations de publication

Date de publication:
11 Jan 2024

Historique:

received: 01 11 2023

accepted: 02 01 2024

medline: 12 1 2024

pubmed: 12 1 2024

entrez: 11 1 2024

Statut: epublish

Résumé

qPCR is a widely used technique in scientific research as a basic tool in gene expression analysis. Classically, the quantitative endpoint of qPCR is the threshold cycle (C The performance of the new f We recommend using the f

Sections du résumé

BACKGROUND BACKGROUND

qPCR is a widely used technique in scientific research as a basic tool in gene expression analysis. Classically, the quantitative endpoint of qPCR is the threshold cycle (C

RESULTS RESULTS

The performance of the new f

CONCLUSIONS CONCLUSIONS

We recommend using the f

Identifiants

DOI: 10.1186/s12859-024-05630-y PMID: 38212692

pubmed: 38212692

doi: 10.1186/s12859-024-05630-y

pii: 10.1186/s12859-024-05630-y

doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

Pagination

Informations de copyright

Références

Navarro E, Serrano-Heras G, Castaño MJ, Solera J. Real-time PCR detection chemistry. Clin Chim Acta. 2015;439:231–50.

doi: 10.1016/j.cca.2014.10.017 pubmed: 25451956

VanGuilder HD, Vrana KE, Freeman WM. Twenty-five years of quantitative PCR for gene expression analysis. Biotechniques. 2008;44:619–26.

doi: 10.2144/000112776 pubmed: 18474036

Taylor SC, Nadeau K, Abbasi M, Lachance C, Nguyen M, Fenrich J. The ultimate qPCR experiment: producing publication quality, reproducible data the first time. Trends Biotechnol. 2019;37:761–74.

doi: 10.1016/j.tibtech.2018.12.002 pubmed: 30654913

Svec D, Tichopad A, Novosadova V, Pfaffl MW, Kubista M. How good is a PCR efficiency estimate: recommendations for precise and robust qPCR efficiency assessments. Biomol Detect Quantif. 2015;3:9–16.

doi: 10.1016/j.bdq.2015.01.005 pubmed: 27077029 pmcid: 4822216

Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative CT method. Nat Protoc. 2008;3:1101–8.

doi: 10.1038/nprot.2008.73 pubmed: 18546601

Hawke DC, Watson AJ, Betts DH. Selecting normalizers for microRNA RT-qPCR expression analysis in murine preimplantation embryos and the associated conditioned culture media. J Dev Biol. 2023;11:17.

doi: 10.3390/jdb11020017 pubmed: 37092479 pmcid: 10123758

Ruijter JM, Pfaffl MW, Zhao S, Spiess AN, Boggy G, Blom J, et al. Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications. Methods. 2013;59:32–46.

doi: 10.1016/j.ymeth.2012.08.011 pubmed: 22975077

Ruijter JM, Barnewall RJ, Marsh IB, Szentirmay AN, Quinn JC, van Houdt R, et al. Efficiency correction is required for accurate quantitative PCR analysis and reporting. Clin Chem. 2021;67:829–42.

doi: 10.1093/clinchem/hvab052 pubmed: 33890632

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55:611–22.

doi: 10.1373/clinchem.2008.112797 pubmed: 19246619

Nolan T, Hands RE, Bustin SA. Quantification of mRNA using real-time RT-PCR. Nat Protoc. 2006;1:1559–82.

doi: 10.1038/nprot.2006.236 pubmed: 17406449

Ruiz-Villalba A, Ruijter JM, van den Hoff MJB. Use and misuse of Cq in qPCR data analysis and reporting. Life. 2021;11:496.

doi: 10.3390/life11060496 pubmed: 34072308 pmcid: 8229287

Rutledge RG. Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications. Nucleic Acids Res. 2004;32:e178–e178.

doi: 10.1093/nar/gnh177 pubmed: 15601990 pmcid: 545475

Spiess A-N, Feig C, Ritz C. Highly accurate sigmoidal fitting of real-time PCR data by introducing a parameter for asymmetry. BMC Bioinform. 2008;9:221.

doi: 10.1186/1471-2105-9-221

Guescini M, Sisti D, Rocchi MBL, Stocchi L, Stocchi V. A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition. BMC Bioinform. 2008;9:326.

doi: 10.1186/1471-2105-9-326

Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB, et al. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 2009;37:e45–e45.

doi: 10.1093/nar/gkp045 pubmed: 19237396 pmcid: 2665230

Zhang L, Dong R, Wei S, Zhou H-C, Zhang M-X, Alagarsamy K. A novel data processing method CyC* for quantitative real time polymerase chain reaction minimizes cumulative error. PLoS ONE. 2019;14:e0218159.

doi: 10.1371/journal.pone.0218159 pubmed: 31185064 pmcid: 6559663

Zhang Y, Li H, Shang S, Meng S, Lin T, Zhang Y, et al. Evaluation validation of a qPCR curve analysis method and conventional approaches. BMC Genom. 2021;22:680.

doi: 10.1186/s12864-021-07986-4

Spiess A-N. Modelling and analysis of real-time PCR data—CRAN. 2018, p. 109.

Boggy GJ, Woolf PJ. A mechanistic model of PCR for accurate quantification of quantitative PCR data. PLoS ONE. 2010;5:e12355.

doi: 10.1371/journal.pone.0012355 pubmed: 20814578 pmcid: 2930010

Lievens A, Van Aelst S, Van den Bulcke M, Goetghebeur E. Enhanced analysis of real-time PCR data by using a variable efficiency model: FPK-PCR. Nucleic Acids Res. 2012;40:e10–e10.

doi: 10.1093/nar/gkr775 pubmed: 22102586

Vermeulen J, De Preter K, Naranjo A, Vercruysse L, Van Roy N, Hellemans J, et al. Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study. Lancet Oncol. 2009;10:663–71.

doi: 10.1016/S1470-2045(09)70154-8 pubmed: 19515614 pmcid: 3045079

Rao X, Huang X, Zhou Z, Lin X. An improvement of the 2ˆ(-delta delta CT) method for quantitative real-time polymerase chain reaction data analysis. Biostat Bioinform Biomath. 2013;3:71–85.

Posit team. RStudio: integrated development environment for R. 2023.

R Core Team. R: a language and environment for statistical computing. 2023.

Tellinghuisen J. Estimating real-time qPCR amplification efficiency from single-reaction data. Life. 2021;11:693.

doi: 10.3390/life11070693 pubmed: 34357065 pmcid: 8303528

Wang G, Becker E, Mesa C. Optimization of 6-carboxy-X-rhodamine concentration for real-time polymerase chain reaction using molecular beacon chemistry. Can J Microbiol. 2007;53:391–7.

doi: 10.1139/W06-145 pubmed: 17538648

Pödör Z, Manninger M, Jereb L. Advanced computational methods for knowledge engineering. Cham: Springer; 2014.