The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments
Open accessAbstract
Background: Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader’s ability to evaluate critically the quality of the results presented or to repeat the experiments. Content: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement. Summary: Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.
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Claims the paper makes
19 of 46 cited sources checked · 13 supported · 0 flagged · accuracy not yet measured
- Premisecitation
If multiple reactions are performed, accurate quantification of lower concentrations can be obtained via digital PCR.
“If multiple reactions are performed, however, accurate quantification of lower concentrations can be obtained via digital PCR (29,63,64 )”
Quote in the paperNot a substantial claim2 of 3 sources checked - Interpretationreasoning
Many molecular analyses still contain qPCR data that are poorly normalized.
“Consequently, many molecular analyses still contain qPCR data that are poorly normalized.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [70] 2008, Plant Biotechnol J source
- Premisecitation
The lack of concordance between mRNA and protein concentrations is particularly true for mRNAs specifying proteins that are part of multifunction protein complexes.
“which is particularly true for mRNAs that specify proteins that are part of multifunction protein complexes (37 ).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [37] 2007, Mol Syst Biol source
The Functional pathway analysis reports very low or negative protein–mRNA correlations for most multisubunit protein complexes, supporting the claim of poor concordance for their subunits. It does not establish that these complexes are multifunctional; that qualifier differs from the paper’s “multisubunit.” (LLM, conf=0.82)
Experimental — accuracy not yet measured
- Premisecitation
qPCR data-analysis methods differ substantially in performance.
“a systematic evaluation has revealed that qPCR data-analysis methods differ substantially in their performance (68 )”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [68] 2007, BMC Bioinformatics source
- Premisecitation
Splicing patterns vary across different tissues or developmental stages.
“with variation in splicing patterns reported in different tissues or at different developmental stages.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [31] 2007, BMC Bioinformatics source
The Utility section describes an exon occurring specifically in muscular, and possibly nervous, tissue; the Construction and content section also describes charts of tissue distribution for splicing events. These passages support variation across tissues, but our copy does not report variation across developmental stages (searched: developmental stages, developmentally regulated splicing). No page numbers are available in the indexed passages. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites [32] 2008, J Biol Chem source
- Premisecitation
Inhibitors copurified with DNA can distort results such as pathogen detection and quantification.
“no inhibitors copurified with the DNA will distort results, e.g., pathogen detection and their quantification (55 ).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [55] 2005, J Virol Methods source
- Premisecitation
Different PCR reactions may not be equally susceptible to inhibition by substances copurified in nucleic acid extracts.
“different PCR reactions may not be equally susceptible to inhibition by substances copurified in nucleic acid extracts (56,57 ).”
Quote in the paperSubstantial claim2 of 2 sources checked - Premisecitation
Variations in tissue-preparation procedures have a substantial effect on RNA yield and quality.
“variations in tissue-preparation procedures have a substantial effect on both RNA yield and quality (47 ).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [47] 2007, Biotechniques source
- Premisecitation
Autosomal nonimprinted genes with allelic imbalance in expression have been described.
“autosomal nonimprinted genes that display allelic imbalance in their expression have been described (33 ).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [33] 2008, Genome Res source
- Premisecitation
There is no consensus on the best methods for performing and interpreting qPCR experiments.
“Currently, a lack of consensus exists on how best to perform and interpret quantitative realtime PCR (qPCR) experiments.”
- Also stated in: § Abstract · plain
“This remarkable lack of consensus on how best to perform qPCR experiments has the adverse consequence of perpetuating a string of serious shortcomings that encumber its status as an independent yardstick (12 ).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [12] 2004, J Biomol Tech
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Also stated in: § Abstract · plain
- Premisecitation
Inappropriate data and statistical analyses can generate highly misleading qPCR results.
“inappropriate data and statistical analyses, generating results that can be highly misleading”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [12] 2004, J Biomol Tech
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
The theoretical minimum limit of detection for qPCR is 3 copies per PCR under assumptions of a Poisson distribution, a 95% chance of including at least one copy, and single-copy detection.
“The most sensitive LOD theoretically possible is 3 copies per PCR (28 ), assuming a Poisson distribution, a 95% chance of including at least 1 copy in the PCR, and single-copy detection.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [28] 2004, Molecular microbiology: diagnostic principles and practice
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Inadequate sample storage, preparation, and nucleic acid quality yield highly variable qPCR results.
“inadequate sample storage, preparation, and nucleic acid quality, yielding highly variable results”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [12] 2004, J Biomol Tech
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Poor choice of reverse-transcription primers and PCR primers or probes leads to inefficient and less robust qPCR assay performance.
“poor choice of reverse-transcription primers and primers and probes for the PCR, leading to inefficient and less-than-robust assay performance”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [12] 2004, J Biomol Tech
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationreasoning
LOD estimation in qPCR is complicated by the logarithmic nature of Cq because Cq is undefined when template concentration is zero.
“LOD estimates in qPCR analyses are complicated by the logarithmic nature of C q , because C q is undefined when the template concentration is zero.”
Quote in the paperNot a substantial claim - Interpretationcitation
The scientific literature is at risk of being corrupted by many publications reporting inadequate and conflicting qPCR results.
“there is the real danger of the scientific literature being corrupted with a multitude of publications reporting inadequate and conflicting results ( 13 ).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [13] 2009, Forthcoming
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
The reverse-transcription step introduces substantial variation into an RT-qPCR assay.
“The reverse-transcription step introduces substantial variation into an RT-qPCR assay (58,59 ).”
Quote in the paperSubstantial claim0 of 2 sources checked - Premisecitation
Different plastics exhibit substantial differences in fluorescence reflection and sensitivity.
“different plastics exhibit substantial differences in fluorescence reflection and sensitivity (60 ).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [60] 2008, Biotechnol Biotechnol Equip source
- Premisereasoning
Normalization is an essential component of a reliable qPCR assay because it controls for variations in extraction yield, reverse-transcription yield, and amplification efficiency, enabling comparisons of mRNA concentrations across samples.
“Normalization is an essential component of a reliable qPCR assay because this process controls for variations in extraction yield, reverse-transcription yield, and efficiency of amplification, thus enabling comparisons of mRNA concentrations across different samples.”
Quote in the paperSubstantial claim - Interpretationreasoning
When PCR efficiencies differ, the difference between target and reference Cq values does not remain constant as template amounts vary.
“differences between the C q values of the targets and the references will not remain constant as template amounts are varied”
Quote in the paperSubstantial claim - Premisecitation
mRNA and protein concentration data frequently lack concordance.
“there is frequently a lack of concordance between mRNA-and proteinconcentration data (36 ),”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [36] 1999, Mol Cell Biol source
- Interpretationreasoning
Relative differences in degradation of transcripts may produce incorrect target ratios.
“relative differences in the degradation of transcripts may produce incorrect target ratios.”
Quote in the paperSubstantial claim - Interpretationnone given
For ΔΔCq comparison to be accurate, the target and reference genes must be amplified with comparable efficiencies.
“The 2 genes must be amplified with comparable efficiencies for this com-parison to be accurate.”
Quote in the paperSubstantial claim- Rests on an assumption: PCR efficiency is particularly important when reporting mRNA concentrations for target genes relative to reference genes.
- Interpretationreasoning
An RT-qPCR assay targeting only one or at most two exons of an mRNA is insufficient to describe that gene's expression level.
“use of an RT-qPCR assay that simply targets one or at most 2 exons of an mRNA is no longer sufficient to describe the expression level of a particular gene.”
Quote in the paperSubstantial claim - Interpretationnone given
Differences in PCR efficiency produce calibration curves with different slopes.
“Differences in PCR efficiency will produce calibration curves with different slopes.”
Quote in the paperSubstantial claim - Interpretationreasoning
Sample acquisition is the first potential source of experimental variability, especially for RNA, because mRNA profiles are easily perturbed by sample-collection and processing methods.
“Sample acquisition constitutes the first potential source of experimental variability, especially for experiments targeting RNA, because mRNA profiles are easily perturbed by sample-collection and -processing methods.”
Quote in the paperSubstantial claim - Premisecitation
RNA degrades markedly in vivo due to natural regulation of mRNAs in response to environmental stimuli.
“RNA degrades markedly in vivo, owing to the natural regulation of mRNAs in response to environmental stimuli (49 ).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [49] 2007, Cell source
- Interpretationcitation
Universal reference DNA and RNA calibration materials, although helpful, will not be a universal panacea.
“the development of universal reference DNA and RNA calibration materials, although very helpful (39, 40 ), will not be a universal panacea (41,42 ).”
Quote in the paperSubstantial claim0 of 2 sources checked - Interpretationreasoning
LODs below 3 copies per PCR are not possible.
“Low-copy PCRs are stochastically limited, and LODs of Ͻ3 copies per PCR are not possible.”
Quote in the paperNot a substantial claim- Rests on an assumption: Low-copy PCRs are stochastically limited.
- Premisecitation
Cq values above 40 are suspect because they imply low amplification efficiency.
“C q values Ͼ40 are suspect because of the implied low efficiency and generally should not be reported”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [26] 2008, Eur Food Res Technol source
- Premisecitation
Reporting CVs for Cq values is inappropriate because Cq values are always lower than CVs calculated for copy numbers, making them potentially misleading.
“CVs should not be used with C q s (29 ) but can be used to express the variance in copy numbers or concentrations.”
- Also stated in: § 8. Data Analysis · plain
“reporting of CVs for C q s is inappropriate (29 ), because C q s will always be lower (and therefore potentially misleading) than CVs calculated for copy numbers.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [29] 2008, Nat Protoc source
- Also stated in: § 8. Data Analysis · plain
- Interpretationreasoning
Partial RNA degradation may reduce an assay's sensitivity for detecting a low-level transcript.
“the assay's sensitivity for detecting a low-level transcript may be reduced”
Quote in the paperSubstantial claim - Interpretationreasoning
Even high-quality RNA samples can show differential degradation of individual mRNAs.
“even high-quality RNA samples can show differential degradation of individual mRNAs.”
Quote in the paperNot a substantial claim - Interpretationreasoning
The A260/A280 ratio indicates RNA purity because DNA or residual phenol alters the ratio.
“The absorbance ratio does provide an indication of RNA purity, because the presence of DNA or residual phenol alters the ratio.”
Quote in the paperNot a substantial claim - Premisecitation
Poor annealing optimization has a large effect on assay quality.
“poor annealing optimization has a large effect on assay quality (51 ).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [51] 2006, Nat Protoc source
- Interpretationnone given
An accurate yes/no answer in qualitative PCR requires information about the low-end sensitivity of the assay.
“The problem with qualitative/quantitative stratification of PCR methods is that an accurate yes/no answer requires information about the low-end sensitivity of the PCR assay.”
Quote in the paperSubstantial claim
- May combine two claims. 12
- Classified as probably not a substantial claim. 6
May combine two claims.
PremisecitationOnly a few interlaboratory comparisons of qPCR diagnostic assays have been performed, and they emphasized the need for standardization.
“only a couple of interlaboratory comparisons have been performed, and both of these studies emphasized the need for standardization of qPCR diagnostic assays (44,45 ).”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [44] 2006, Clin Chem source
- cites [45] 2008, J Clin Microbiol source
The discussion (p. 4) describes this study as the first international evaluation of HIV-2 RNA quantification assays and says the collaboration is working toward standardization because results varied between laboratories. It does not establish that only a couple of interlaboratory comparisons of qPCR diagnostic assays had been performed generally. (LLM, conf=0.85)
Experimental — accuracy not yet measured
May combine two claims.
InterpretationcitationIn practice, qPCR is not a fixed gold standard; its standard is variable, and reporting results requires sophisticated analysis and interpretation.
“although qPCR has frequently been proclaimed a touchstone or a gold standard, in practice this “standard” is a variable one, and the reporting of results requires considerable sophistication of analysis and interpretation (43 ).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [43] 2005, J Mol Endocrinol source
- Rests on an assumption: A large part of the variance in reported RT-qPCR expression values comes from data-processing algorithm corrections rather than solely from protocol variation.
May combine two claims.
PremisecitationMost human genes and many genes in other multicellular organisms have alternatively spliced transcripts.
“The transcripts of most human genes and many genes in other multicellular organisms are alternatively spliced (31,32 ),”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [31] 2007, BMC Bioinformatics source
The Utility section reports that 61% of the human genes in the database were estimated to undergo alternative splicing, supporting the claim about most human genes. The passages found do not establish the claim about genes in other multicellular organisms; the paper’s analysis here concerns human genes. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [32] 2008, J Biol Chem source
May combine two claims.
PremisecitationThere is increased awareness of the importance of systematic validation and the potentially misleading effects of inappropriate reference genes are widely known, but these considerations are still widely disregarded.
“Unfortunately, although there is an increased awareness of the importance of systematic validation and although the potentially highly misleading effects of the use of inappropriate reference genes for normalization are widely known, these considerations also are still widely disregarded (70 ).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [70] 2008, Plant Biotechnol J source
The Introduction (page not provided) says that improperly validated reference genes remained widely used in plant RT-PCR and that their use may lead to misinterpretation; the paper also demonstrates a misleading normalization result. But it says the importance of earlier findings did not appear to have been recognized, rather than establishing increased awareness or that the risks were widely known. (LLM, conf=0.86)
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationAlternative, more generalized quantitative models have been developed to correct for differences in amplification efficiency and to allow the use of multiple reference genes.
“alternative, more generalized quantitative models have been developed to correct for differences in amplification efficiency (62 ) and to allow the use of multiple reference genes (30 ).”
Quote in the paperNot a substantial claim2 of 2 sources checkedClassified as probably not a substantial claim.
PremisecitationThe necessity for ensuring quality-assurance measures for qPCR and RT-qPCR assays is well recognized.
“The necessity for ensuring quality-assurance measures for qPCR and RT-qPCR assays is well recognized (25,44,(75)(76)(77)(78)(79)(80)(81)(82)(83)(84)(85)(86).”
Quote in the paperSubstantial claim1 of 3 sources checked- cites [25] 2006, BMC Biotechnol source
The Background (page unavailable) describes measures to improve the reliability of low-level DNA quantification by qPCR. The methods section headed “Reverse primer” (page unavailable) also reports contamination controls and checks on standard-curve quality. These support the need for quality assurance in qPCR, but the paper does not address reverse-transcription qPCR (RT-qPCR). (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [44] 2006, Clin Chem source
- cites [75] 2005, J Clin Microbiol source
May combine two claims.
PremisecitationArbitrary Cq cutoffs are not ideal because they may be too low, eliminating valid results, or too high, increasing false-positive results.
“however, the use of such arbitrary C q cutoffs is not ideal, because they may be either too low (eliminating valid results) or too high (increasing false-positive results) (26 )”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [26] 2008, Eur Food Res Technol source
Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).
PremisecitationKnowledge of the presence and function of specific microRNAs is as important to understanding gene expression as quantifying mRNA species.
“knowledge of the presence and function of specific microRNAs is as important to understanding gene expression as being able to quantify the mRNA species (38 ).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [38] 2008, Carcinogenesis
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
InterpretationreasoningWhen PCR efficiencies differ, calculations of relative concentrations are inaccurate and yield misleading results.
“calculations of relative concentrations will be inaccurate, yielding misleading results.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningSingle exon-based RT-qPCR assays may detect multiple splice variants, whereas intron-spanning primers may be more selective but can miss some splice variants.
“single exon-based RT-qPCR assays may detect a number of splice variants, whereas intron-spanning primers may be more selective but may miss some splice variants altogether.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationUse of a 3':5' integrity assay requires that the PCR efficiencies of both assays be virtually identical and not subject to differential inhibition.
“Use of a 3Ј:5Ј assay requires that the PCR efficiencies of both assays be virtually identical (51 ) and not be subject to differential inhibition.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [51] 2006, Nat Protoc source
Probably not a substantial claim: may not pass S3 (load-bearing).
InterpretationreasoningAlthough differences between biological replicates may be large, sufficient numbers may allow smaller experimental differences to be discerned.
“Although differences between biological replicates may be large, sufficient numbers may allow smaller experimental differences to be discerned.”
Quote in the paperNot a substantial claim- Rests on an assumption: The inherent variability of biological systems may rival or exceed experimental differences between groups.
May combine two claims.
InterpretationreasoningThe reference genes or materials used for standardization are critical, and assessing the validity of an RT-qPCR experiment must consider the appropriateness of the relative-quantification reference.
“Thus, the reference genes or materials used for standardization are critical, and any assessment of the validity of an RT-qPCR experiment must also consider the appropriateness of the relative-quantification reference.”
Quote in the paperSubstantial claim- Rests on an assumption: Most quantitative RNA measurements are relative, not absolute.
May combine two claims.
PremisecitationDifferent RNA quantification methods produce different results, making comparison of data obtained with different methods unwise.
“The methods produce different results, making it unwise to try to compare data obtained with the different methods (48 ).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [48] 2005, Expert Rev Mol Diagn source
Probably not a substantial claim: may not pass S3 (load-bearing).
InterpretationreasoningPower analysis is useful for determining the number of samples necessary for valid conclusions.
“Consequently, power analysis is useful for determining the number of samples necessary for valid conclusions.”
Quote in the paperNot a substantial claim- Rests on an assumption: Many factors contribute to experimental variation and influence the number of biological replicates necessary to achieve a given statistical power.
Classified as probably not a substantial claim.
InterpretationreasoningOne cannot assume that legacy PCR assays can translate directly into the qPCR format.
“This difference must be clearly recognized, and one cannot assume that legacy PCR assays can translate directly into the qPCR format.”
Quote in the paperSubstantial claim- Rests on an assumption: The main difference between qPCR and conventional PCR is the expectation that qPCR can quantify target nucleic acids accurately.
Probably not a substantial claim: may not pass S2 (checkable), S4 (based). May combine two claims.
InterpretationreasoningInvestigations that use this widely applied technology will produce data that are more uniform, more comparable, and ultimately more reliable.
“As a consequence, investigations that use this widely applied technology will produce data that are more uniform, more comparable, and, ultimately, more reliable.”
Quote in the paperNot a substantial claim
The paper relies on this without support.
Many qPCR publications lack enough experimental detail for readers to assess or repeat the work.
“The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader's ability to evaluate critically the quality of the results presented or to repeat the experiments.”
“The problem is exacerbated by the lack of information that characterizes most reports of studies that have used this technology, with many publications not providing sufficient experimental detail to permit the reader to critically evaluate the quality of the results presented or to repeat the experiments.”
The paper relies on this without support.
Presence of an mRNA does not establish that it is translated into protein or functional protein.
“detection of the presence of an mRNA provides no information on whether that mRNA will be translated into a protein or, indeed, whether a functional protein is translated at all.”
The paper relies on this without support.
Most quantitative RNA measurements are relative, not absolute.
“most quantitative RNA data are not absolute, but relative.”
The paper relies on this without support.
A large part of the variance in reported RT-qPCR expression values comes from data-processing algorithm corrections rather than solely from protocol variation.
“Much of the variance in reported expression values produced in RT-qPCR experiments is not simply due to variation in experimental protocols but is caused by corrections applied by various dataprocessing algorithms, each of which makes its own assumptions about the data.”
The paper relies on this without support.
PCR efficiency is highly dependent on the primers used.
“PCR efficiency is highly dependent on the primers used”
The paper relies on this without support.
The structure of the nucleic acid target has a substantial impact on the efficiency of reverse transcription and PCR.
“The structure of the nucleic acid target (e.g., stem and loop secondary RNA structure) has a substantial impact on the efficiency of reverse transcription and the PCR.”
The paper relies on this without support.
A marked presence of primer dimers produces lower PCR efficiency in probe-based assays and may generate false positives in SYBR Green I assays.
“A marked presence of primer dimers produces a lower PCR efficiency in probe-based assays and may generate false positives in assays based on SYBR Green I.”
The paper relies on this without support.
No-template controls detect PCR contamination when probes are used and can distinguish unintended amplification products from intended products in SYBR Green I reactions.
“NTCs detect PCR contamination when probes are used and can also distinguish unintended amplification products (e.g., primer dimers) from the intended PCR products in SYBR Green I reactions.”
The paper relies on this without support.
Robust and precise qPCR assays are usually correlated with high PCR efficiency.
“Robust and precise qPCR assays are usually correlated with high PCR efficiency.”
The paper relies on this without support.
PCR efficiency is particularly important when reporting mRNA concentrations for target genes relative to reference genes.
“PCR efficiency is particularly important when reporting mRNA concentrations for target genes relative to those of reference genes.”
The paper relies on this without support.
A260/A280 measurement is not sufficient for quantitative nucleic acid analysis, especially when measuring minor differences (<10-fold) in cellular mRNA concentrations.
“such measurement is not sufficient if the nucleic acid is to be used for quantitative analysis, especially when the aim is to measure minor differences (Ͻ10-fold) in cellular mRNA concentrations.”
The paper relies on this without support.
RNA integrity numbers relate to rRNA quality and cannot be expected to be an absolute measure of RNA quality.
“these numbers relate to rRNA quality and cannot be expected to be an absolute measure of quality.”
The paper relies on this without support.
The small amplicon size of qPCR assays helps minimize assay-related problems.
“The small amplicon size of qPCR assays helps to minimize assay-related problems”
The paper relies on this without support.
Lower limits of quantification are usually poorly defined.
“Because lower limits of quantification are usually poorly defined, the variation at the lowest concentration claimed to be within the linear interval should be determined.”
The paper relies on this without support.
Low-copy PCRs are stochastically limited.
“Low-copy PCRs are stochastically limited, and LODs of Ͻ3 copies per PCR are not possible.”
The paper relies on this without support.
Precision in qPCR typically varies with concentration, decreasing with copy number.
“Precision in qPCR typically varies with concentration, decreasing with the copy number.”
The paper relies on this without support.
Use of reference genes as internal controls is the most common method for normalizing cellular mRNA data.
“The use of reference genes as internal controls is the most common method for normalizing cellular mRNA data”
The paper relies on this without support.
The inherent variability of biological systems may rival or exceed experimental differences between groups.
“The inherent variability of biological systems may rival or exceed experimental differences between groups.”
The paper relies on this without support.
Many factors contribute to experimental variation and influence the number of biological replicates necessary to achieve a given statistical power.
“Many factors contribute to experimental variation and influence the number of biological replicates necessary to achieve a given statistical power.”
The paper relies on this without support.
The main difference between qPCR and conventional PCR is the expectation that qPCR can quantify target nucleic acids accurately.
“The main difference between qPCR and conventional (legacy) PCR assays is the expectation of the former's potential to quantify target nucleic acids accurately.”
The paper relies on this without support.
The concern about multiplexing accuracy is particularly important when targets of appreciably lower abundance are coamplified with highly abundant targets.
“This concern is of particular importance when targets of appreciably lower abundance are coamplified with highly abundant targets.”
The paper relies on this without support.
Reference gene utility must be experimentally validated for particular tissues or cell types and specific experimental designs.
“their utility must be experimentally validated for particular tissues or cell types and specific experimental designs”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Gene knockdown and PCR techniques rely upon the correct design and experimental use of RNA targeting reagents and PCR primers.
“Gene knockdown and PCR techniques rely upon the correct design and experimental use of RNA targeting reagents and PCR primers, respectively [17–19].”
From Semi-automated fact-checking of nucleotide sequence reagents in biomedical research publications: The Seek & Blastn tool (2019) · cites this paper as [18]
Section 7.2 (Specificity) supports the PCR-primer part: it says primer specificity must be validated experimentally and poor annealing optimization affects assay quality. The citation is attached to a sentence that also concerns RNA-targeting reagents for gene knockdown, which the cited passages do not address. (LLM, conf=0.85)
Experimental — accuracy not yet measuredEach published reagent descriptor is recommended to be accompanied by its corresponding nucleotide sequence.
“As the nucleotide sequences of these reagents define their identity and possible experimental use, each published reagent descriptor is recommended to be accompanied by its corresponding nucleotide sequence [18].”
From Semi-automated fact-checking of nucleotide sequence reagents in biomedical research publications: The Seek & Blastn tool (2019) · cites this paper as [18]
Section 7 (qPCR; page not provided) requires publication of the sequences of primers and other assay oligonucleotides, including probes. It does not extend that requirement to every published reagent descriptor; the claim is broader than the guideline. (LLM, conf=0.84)
Experimental — accuracy not yet measuredMIQE guidelines define a rigorous methodology for designing qPCR experiments that assures publication of reproducible and high quality data.
“The Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines and related articles published thereafter define a rigorous methodology for designing qPCR experiments that assures publication of reproducible and high quality data5–7.”
From Droplet Digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data (2017) · cites this paper as [5]
The Conclusions describe a checklist intended to help authors design and report qPCR experiments and enable others to reproduce them. The Abstract says following MIQE will encourage better practice and more reliable results; it does not guarantee that published data will be reproducible and high quality. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe qPCR method was optimized until the standard curve fitted qPCR standard guidelines (amplification efficiency 100 ± 10% and R2 > 0.95).
“The qPCR method was optimized until the characteristics of the standard curve fitted qPCR standard guidelines32 (amplification efficiency (E) = 100 ± 10% and the coefficient of correlation (R2) > 0.95).”
From An apicomplexan parasite drives the collapse of the bay scallop population in New York (2023) · cites this paper as [32]
Section 7.4.1 says PCR efficiency must be established from calibration curves and identifies 100% as the theoretical maximum. Section 7.4.2 requires reporting calibration-curve r² values. The copy does not specify 100 ± 10% efficiency or r² > 0.95 as guideline thresholds, so the cited paper supports the measures but not the stated cutoffs. (LLM, conf=0.88)
Experimental — accuracy not yet measuredFor qPCR to measure small fold changes, it is essential that some estimation of efficiency is made.
“it is also essential that some estimation of efficiency is made (25).”
From Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation (2012) · cites this paper as [25]
Real-time quantitative PCR was performed in accordance with the MIQE guidelines.
“Real-time quantitative PCR was performed in accordance with the MIQE guidelines (Supplementary Table S1 and Supplementary Figure S1) (25).”
From Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation (2012) · cites this paper as [25]
Quantitative RT-PCR was conducted following MIQE guidelines.
“Quantitative RT-PCR was conducted following the MIQE (minimum information for publication of quantitative real-time PCR experiments) guidelines38.”
From Neurotoxic reactive astrocytes are induced by activated microglia (2017) · cites this paper as [38]
At least two housekeeping genes should be used for RT-qPCR in line with MIQE.
“In line with the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments), we recommend using at least two housekeeping genes48,49.”
From Algorithmic assessment of cellular senescence in experimental and clinical specimens (2021) · cites this paper as [49]
Relative miRNA expression levels from eight independent experiments were calculated using the Cq method according to MIQE guidelines.
“Relative expression levels from eight independent experiments were calculated using the quantification cycle (Cq) method, according to MIQE guidelines24.”
From TNF-alpha-induced microglia activation requires miR-342: Impact on NF-kB signaling and neurotoxicity (2020) · cites this paper as [24]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Self-check results appear here once an independent check has confirmed them.
Cited works that were retracted
Works this paper cites that were later retracted, from the retraction notices publishers deposit. Major when the notice came out before this paper was published.
Cites a retracted work: 10.1126/science.1117768
MajorThe cited work was retracted on 2007-04-20 (notice 10.1126/science.316.5823.367b), before this paper was published (2009-04-01). Its authors could have known.
Cited work 10.1126/science.1117768 · retracted 2007-04-20 · notice 10.1126/science.316.5823.367b · this paper published 2009-04-01
“2005, Science, 309, 1694, 10.1126/science.1117768”
Cites a retracted work: 10.1126/science.316.5823.367b
InfoThe cited work was retracted; the date of the notice is not on record.
Cited work 10.1126/science.316.5823.367b · retraction date not known · this paper published 2009-04-01
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2 retracted
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A Thank You from Tulane University
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“From the definitions above it is evident that Cq values are instrumental readings, and must be recalculated to values with specific units, e.g., copies of organism, ng of DNA, various concentrations, etc., (Bustin et al., 2009; Johnson et al., 2013).”
BackgroundMethodInfluentialRole of TP53 mutations in the origin and evolution of therapy-related acute myeloid leukaemia
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Self-citationThe Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time
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How to do successful gene expression analysis using real-time PCR
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Self-citationA practical approach to RT-qPCR—Publishing data that conform to the MIQE guidelines
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“sers must be included in manuscripts, following the MIQE guidelines.[55] During the workshop, RNA spike-ins were discussed as a normalisation strategy, since these were recommended in the previous EV-RNA position paper.”
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Minimum information reporting in bio–nano experimental literature
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Self-citationClinical validation of the detection of KRAS and BRAF mutations from circulating tumor DNA
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Selection of reliable reference genes for gene expression studies in peach using real-time PCR
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Aquaporins: Highly Regulated Channels Controlling Plant Water Relations
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“Real-time PCR is based on PCR and measures the amount of PCR product after each round of amplification using a fluorescent readout [2].”
MethodTag jumps illuminated – reducing sequence‐to‐sample misidentifications in metabarcoding studies
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“(5) Primers that fail optimization using ddPCR technology should either be redesigned or the experimental design and samples should be re-assessed and undergo troubleshooting7.”
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Self-citationReporting the limits of detection and quantification for environmental DNA assays
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“…descriptions of assays include the sequence and form of the standard template, efficiency of the amplification, and the modeling function and software used to compute the concentra‐ tion values and report assay parameters (readers are directed to Bustin et al. (2009) and Goldberg et al. (2016)).”
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“This non-linear system of equations is solved by GenEx 6 [11], using a quasi-Newton method.”
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High Fragmentation Characterizes Tumour-Derived Circulating DNA
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“dPCR requires the same careful assay design considerations as those required for qPCR (53, 54).”
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First detection of SARS-CoV-2 RNA in wastewater in North America: A study in Louisiana, USA
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Recent advances in quantitative PCR (qPCR) applications in food microbiology
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Guidelines for validation of qualitative real-time PCR methods
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Reporting Guidelines to Increase the Reproducibility and Comparability of Research on Microplastics
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“Other fields, like molecular biology, 34 proteomics, 35 and transcriptomics, 36 already have highly successful examples of reporting guidelines that have been widely adopted by their field, and we hope this work serves a similar purpose in our field.”
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Real-time PCR detection chemistry
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“Real-time quantitative PCR was performed in accordance with the MIQE guidelines (Supplementary Table S1 and Supplementary Figure S1) (25).”
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Advances in multiplexed techniques for the detection and quantification of microRNAs
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LDPE microplastics affect soil microbial communities and nitrogen cycling
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“Reverse transcription quantitative PCR (RTPCR) technique is one of the most common techniques for measuring the mRNA abundance, however, it may be cumbersome since it requires the right design of experimental conditions such as specific and efficient primers [43].”
MethodPoritz, M. A., Blaschke, A. J., Byington, C. L., Allen, L. H., Nilsson, K., Jones, D. E., Thatcher, S. A., Robbins, T. C., Lingenfelter, B., Amiott, E. A., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026047 · Cited by 429 · see citing works
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Silica nanoparticles enhance disease resistance in Arabidopsis plants
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“…R1101-E 96-well plates BioRad HSP9601 Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, see Data S1 Bustin et al. (2009)55 Quantitative Real-Time PCR Experiments (MIQE) guidelines Digital Minimum Information for Publication of Quantitative Real-Time…”
Sterile protection against human malaria by chemoattenuated PfSPZ vaccine
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“This entails applying proper quality assurance and quality control measures [115, 116].”
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“CAPTURE METHOD: SX is equally effective as other tested eDNA capturing techniques in regard to DNA quantity and quality measured as the total extracted eDNA concentration [eDNAtot] and as Cq-values (quantification cycles, sensu Bustin et al. 2009) from two species-specific qPCR assays.”
MethodDisentangling metabolic functions of bacteria in the honey bee gut
Kesner, L., Mars, R. A. T., Ellegaard, K., Troilo, M., Sauer, U., & Engel, P. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2003467 · Cited by 402 · see citing works
“The MIQE guidelines (minimum information for publication of qPCR 576 experiments) were followed throughout the data analysis of the qPCR 577 experiments [77].”
Temporal neutrophil polarization following myocardial infarction
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The Acute bee paralysis virus–Kashmir bee virus–Israeli acute paralysis virus complex
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Why the need for qPCR publication guidelines?—The case for MIQE
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Understanding the role of the shrimp gut microbiome in health and disease
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Environmental DNA analysis for estimating the abundance and biomass of stream fish
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Soybean photosynthesis and crop yield are improved by accelerating recovery from photoprotection
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The Impact of Hemolysis on Cell-Free microRNA Biomarkers
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Evaluation of digital PCR for absolute DNA quantification
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“The simplified quantification is obtained through quantification cycles (Cqs) which are determined by fluorescence threshold or maximum second derivative [118] .”
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Accurate and objective copy number profiling using real-time quantitative PCR
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Self-citationMicroRNA-125b induces tau hyperphosphorylation and cognitive deficits in Alzheimer’s disease
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Five Freely Circulating miRNAs and Bone Tissue miRNAs Are Associated With Osteoporotic Fractures
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Standard methods for virus research in Apis mellifera
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Effects of Temperature and Trophic State on Degradation of Environmental DNA in Lake Water
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Gut microbiota structure differs between honeybees in winter and summer
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“the Cq values (quantification cycle [33]) obtained from the dilutions containing 10(2)–10(7) plasmid copies.”
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- Authors
- Bustin, S. A., Benes, V., Garson, J. A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M. W., Shipley, G. L., Vandesompele, J., & Wittwer, C. T.
- Affiliations
- Queen Mary University of London (GB)
- Genomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
- University College London Hospitals NHS Foundation Trust (GB)
- Ghent University Hospital (BE)
- University College London (GB)
- Czech Academy of Sciences, Institute of Biotechnology (CZ)
- Sequenom (United States) (US)
- Sigma–Aldrich, Haverhill, UK
- Technical University of Munich (DE)
- The University of Texas Health Science Center at Houston (US)
- University of Utah (US)
- Corresponding author
- Bustin, Stephen A
- ORCID
- Venue
- Clinical Chemistry
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-04-01
- Volume
- 55
- Issue
- 4
- Pages
- 611-622
- ISSN
- 0009-9147 (ISSN-L)
- 1530-8561
- OpenAlex
- W2168420558
- Cited by
- 16,303
- References
- 92
- Citations by year
- 2026: 1198 · 2025: 1087 · 2024: 1107 · 2023: 1118 · 2022: 1157 · 2021: 1339 · 2020: 1264 · 2019: 1139 · 2018: 1082 · 2017: 1067 · 2016: 991 · 2015: 944 · 2014: 832 · 2013: 704 · 2012: 556
- FWCI
- 168.11
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Clinical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion, other-oa)
- Funders
- Bowel and Cancer Research (1119105)
- ARUP Institute for Clinical and Experimental Pathology
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Social Sciences › Decision Sciences › Statistics, Probability and Uncertainty › Meta-analysis and systematic reviews
- Social Sciences › Arts and Humanities › History and Philosophy of Science › Academic Writing and Publishing
- Keywords
- MIQE guidelines, quantitative real-time PCR, reporting guidelines, reproducibility, scientific integrity
- MeSH terms
- Humans, Terminology as Topic, Nucleic Acids, Publishing, Time Factors, Polymerase Chain Reaction, Molecular Diagnostic Techniques, Reverse Transcription
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-07.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-07.
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