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M.Tevfik Dorak


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Absolute quantification: The absolute quantitation assay is used to quantitate unknown samples by interpolating their quantity from a standard curve (as in determination of viral copy number). (Absolute Quantification Page by Pfaffl).

Allelic discrimination assay: Assays designed to type for gene variants. Either differentially labeled (TaqMan®) probes (one for each variant) or a single probe and melting curve analysis can be used for this purpose. Alternative methods include dsDNA-binding dyes (in combination with melting curve analysis). TaqMan®-based allelic discrimination assays are analyzed by differences in threshold cycles or by endpoint fluorescence value for each allele. The results are plotted by fluorescence intensity or by Ct values for each allele at X and Y axes (see Osgood-McWeeney, 2000 and Figures 3-5 in Hu & Chen for examples). For increased specificity, MGB or LNA probes can be used (Kutyavin, 2000; Letertre, 2003; Johnson, 2004; Ugozzoli, 2004; Gibson NJ, 2006; Shen, 2009; Schleinitz, 2011). See ABI Allelic Discrimination with TaqMan® Probes and Getting Started Guides for ABI 7000 & 7900HT, LightScanner® and Amplifluor® SNPs Genotyping System. See SNPman (User Guide) for analysis of TaqMan allelic discrimination assay genotype calling for the ABI7300, LC480 and Bio-Rad CFX platforms (Konopac, 2011).

Amplicon: The amplified sequence of DNA in the PCR process. Also called PCR product.

Amplification plot: The plot of cycle number versus fluorescence signal which correlates with the initial amount of target nucleic acid during the exponential phase of PCR.

Anchor & reporter probes: Two partnering LightCycler (hybridizing) probes that hybridize on the target sequence in close proximity. The anchor probe (donor) emits fluorescence to excite the reporter probe (acceptor) to initiate FRET (see FRET probes). In allelic discrimination assays, it is important that the reporter probe spans the mutation and has a lower Tm than the anchor probe.

Baseline: The initial cycles of PCR during which there is little change in fluorescence signal (usually cycles 3 to 15).

Baseline range: The horizontal (flat) part of the baseline activity that is used for the baseline start and end cycles in baseline settings. Manually, it is best determined in the log-view (as it amplifies the background activity changes). Some instruments use cycles 3 to 15 as default baseline range and some employs adaptive baseline adjustment (a unique setting for each well or tube). Most occurrences of unexpected amplification curve distortions (tilted baseline or irregular shapes) are due to incorrect baseline settings and require manual handling (which may need to be done separately for each well). The baseline start cycle should be after the initial tailing of background noise and the end cycle should be before the signal shift due to amplification. The range does not have to be too large; around five cycles is sufficient but more is better. If baseline adjustment does not correct the irregularities in amplification curves, the lamp of the instrument may need replacing (a requirement after more than 2000 hours of use for most instruments). See ABI: Setting Baselines and Thresholds.

Baseline value: During PCR, changing reaction conditions and environment can influence fluorescence. In general, the level of fluorescence in any one well corresponds to the amount of target present. Fluorescence levels may fluctuate due to changes in the reaction medium creating a background signal. The background signal is most evident during the initial cycles of PCR prior to significant accumulation of the target amplicon. During these early PCR cycles, the background signal in all wells is used to determine the ‘baseline fluorescence’ across the entire reaction plate. The goal of data analysis is to determine when target amplification is sufficiently above the background signal, facilitating more accurate measurement of fluorescence.

Calibrator: A single reference sample used as the basis for relative-fold increase in expression studies (assuming constant reaction efficiency). This calibrator should be included in each assay.

Coefficient of variation (CV): Used as a measure of experimental variation. It is important that a linear value (e.g., copy numbers) is used to calculate the CV (but not Ct values which are logarithmic). Intra-assay CV quantifies the amount of error seen within the same assay (in duplicates) and inter-assay CV quantifies the error between separate assays.

Ct (threshold cycle): Threshold cycle reflects the cycle number at which the fluorescence generated within a reaction crosses the threshold. It is inversely correlated to the logarithm of the initial copy number. The Ct value assigned to a particular well thus reflects the point during the reaction at which a sufficient number of amplicons have accumulated. Also called crossing point (Cp) in LightCycler terminology. See ABI Publication: Understanding Ct Value.

Dark quencher: Quenchers with no native fluorescence that have replaced TAMRA (which fluoresces) as a quencher. They are also called non-fluorescent quenchers (NFQ). The prototype was DABCYL which has been eclipsed by black hole quencher (BHQ) dyes. BHQ dyes offer greater spectral overlap with reporter dye emission profiles than DABCYL (the original quencher TAMRA is not a dark quencher). In fact, the BHQ dyes have the best spectral overlap over the entire range of currently used reporter dyes. Dark quenchers allow flexibility in the design of multiplex assays by enabling the choice of spectrally well-resolved fluorophores with little or no spectral crosstalk (overlap). BHQ dyes can be used in any chemistry that requires a quencher (TaqMan, beacons, scorpions etc). See the Black Hole Quencher Dyes page and Brochure (Biosearch Technologies).

Derivative curve: This curve is used in Tm analysis. It has the temperature in the x axis and the negative derivative of fluorescence (F) with respect to temperature (T), shown as dF/dT, on the y axis. The reproducibility of a derivative melting curve is high with a standard deviation of only 0.1 oC between runs.

dsDNA-binding agent: A molecule that emits fluorescence when bound to dsDNA. The prototype is SYBR® Green I. In real-time PCR, the fluorescence intensity increases proportionally to dsDNA (amplicon) concentration. The problem with DNA-binding agents is that they bind to all dsDNA products: specific amplicon or non-specific products (misprimed targets and primer-dimers included). For this reason, analysis using DNA-binding agents is usually coupled with melting analysis. 

Dynamic range: The range of initial template concentrations over which accurate Ct values are obtained. If endogenous control is used for DDCt quantitation method, dynamic ranges of target and control should be comparable. In absolute quantitation, interpolation within this range is accurate but extrapolation beyond the dynamic range should be avoided. The larger the dynamic range, the greater the ability to detect samples with high and low copy number in the same run. See also ABI Publication: Understanding Ct Value for the effect on dynamic range on efficiency calculation.

Dye and dye selection: Misleadingly used for fluorophores (fluorescent dyes) that label probes and quenchers. See list of dyes and dye selection chart (Biosearch Technologies). Consideration of excitation, emission and absorption spectral relationships between acceptor and donor fluorophores (LightCycler probes), reporter and quencher flurorophores (TaqMan probes) and multiplexing is important and discussed in BHQ Brochure (Biosearch Technologies), Marras SA, 2006, and Singer & Johnson (Promega).

Efficiency of the reaction: The efficiency of the reaction can be calculated by the following equation:  E = 10(-1/slope) –1. The efficiency of the PCR should be 90-110% meaning doubling of the amplicon at each cycle. This corresponds to a slope of -3.1 to -3.6 in the Ct vs log-template amount standard curve (see Agilent Efficiency Calculator from the Slope). In order to obtain accurate and reproducible results, reactions should have efficiency as close to 100% as possible (e.g., two-fold increase of amplicon at each cycle), and in any case, efficiency should be similar for both target and reference (normalizer, calibrator, endogenous control, internal control). A number of variables can affect the efficiency of the PCR. These factors can include length of the amplicon, presence of inhibitors, secondary structure and primer design. Although valid data can be obtained that fall outside of the efficiency range, if it is < 0.90, the quantitative real-time PCR should be further optimized or alternative amplicons designed. If efficiency is found > 110%, try running a standard curve experiment with a minimum of 3 replicates and a minimum of 5 logs of template concentration and repeat the calculation. Efficiency of your reaction can be calculated using the online program CAmpER (Calculation of Amplification Efficiencies for RT-PCR). See Efficiency Determination and Standard Curve for more on efficiency.

End-point analysis: As opposed to quantitative analysis using the data collected during exponential phase of PCR, real-time applications can also be used to collect end-point data for qualitative assays. These are either allelic discrimination assays (genotyping) or absence/presence (minus/plus) assays (pathogen detection). For most reliable end-point assay results, there should be no non-specific amplification and the specificity of the assay should be high (i.e., one nucleotide mismatch should not result in any amplification -this can be best achieved by using MGB or LNA probes).

Endogenous control: This is an RNA or DNA that is naturally present in each experimental sample. By using an invariant endogenous control as an active 'reference', quantitation of a messenger RNA (mRNA) target can be normalized for differences in the amount of total RNA added to each reaction and correct for sample-to-sample variations in reverse transcriptase PCR efficiency. See ABI TaqMan Human Endogenous Control Plate; TATAA Biocenter Endogenous Control Gene Panel; geNorm kit; Ambion: 18S RNA as an Internal Control; Ambion: GAPDH, b-actin, cyclophilin, 18S RNA as internal controls; EXPOLDB: The most constantly expressed housekeeping genes; algorithms to select the best endogenous controls: geNORM (Vandesompele, 2002), NormFinder (Andersen, 2004), and qBasePlus (Hellemans, 2007).

Exogenous control: This is a characterized RNA or DNA spiked into each sample at a known concentration. An exogenous active reference is usually an in vitro construct that can be used as an internal positive control (IPC) to distinguish true target negatives from PCR inhibition. An exogenous reference can also be used to normalize for differences in efficiency of sample extraction or complementary DNA (cDNA) synthesis by reverse transcriptase. Whether or not an active reference is used, it is important to use a passive reference dye (usually ROX) in order to normalize for non-PCR-related fluctuations in fluorescence signal.

Extension step: Traditional PCR cycles include denaturation, annealing and extension steps but in real-time PCR, annealing and extension are merged into one step resulting in two steps per cycle. This is because of short (typically 75-150 bp) amplicon length and the power of Taq polymerase used in real-time PCR. Long (>400 bp) amplicons or primers with annealing temperatures <60°C may still require a separate extension step (3-step protocol) for optimum polymerase performance.

FAM: 6-carboxy fluorescein. Most commonly used reporter dye at the 5' end of a TaqMan® probe. In allelic discrimination assay the two probes are usually labeled by FAM (the more abundant wildtype allele-specific probe) and VIC (the variant allele-specific probe) for best spectral non-overlapping combination.

Fast PCR: A modified PCR protocol that allows shortening of overall reaction time to less than the typical 90 minutes (usually 40 minutes or less) thanks to recent developments in amplicon design, reagent chemistry, thermocycling conditions as well as the PCR machines with fast ramping rates. See Biocompare Tutorials > Fast PCR (text).

Fluorescence resonance energy transfer (FRET): The interaction between the electronic excited states of two dye molecules. The excitation is transferred from one (the donor) dye molecule to the other (the acceptor) dye molecule. FRET is distance-dependent and occurs when the donor and the acceptor dye are in close proximity (6 to 10 nucleotides). This is why chemistries that allow for shorter probes (like MGB or LNA probes) increase the detection sensitivity of the target.

FRET Probes (hybridization probes, HyProbe, adjacent probes, anchor & reporter probes, donor-acceptor probes or kissing probes): A pair of fluorescent probes placed in close proximity as in LightCycler (hybridizing) probes. Maximum fluorescence occurs with a one base separation between probes. The emission spectrum of one fluorophore overlaps significantly with the excitation spectrum of the other fluorophore. During FRET, the donor fluorophore is excited by a light source from the real-time PCR instrument, and transfers its energy to an acceptor fluorophore when positioned in the direct vicinity of the former. The acceptor fluorophore emits light of a longer wavelength, which is detected in specific channels by the instrument. The light source cannot excite the acceptor dye. The donor probe is labeled with fluorophore at the 3' end and the acceptor probe at 5' end (its 3'-end blocked to prevent extension). See an overview by Premier Biosoft, a presentation by BioChem, and a report on genotyping on LightCycler with FRET probes.

High resolution melting (HRM) curve analysis: See Melting curve (dissociation) analysis.

Housekeeping gene: Genes that are widely expressed in abundance and are usually used as reference genes for normalization in real-time PCR with the assumption of 'constant expression'. Also called maintenance genes. The current trend is first to check which housekeeping genes are suitable for the target cell or tissue and then to use more than one of them in normalization in qPCR assays. See for EXPOLDB: The most constantly expressed housekeeping genes housekeeping genes showing the least inter-individual difference in their expression levels. Note that not all housekeeping genes are ideal normalizers, and not all normalizers are housekeeping genes. See Dheda, 2004.

Hybridization probe: One of the main fluorescence-monitoring systems for DNA amplification. LightCycler probes are hybridization probes and are not hydrolyzed by Taq Polymerase. For this reason, melting curve analysis is possible with hybridization probes. See Wittwer, 1997 and Hybridization Probe Chemistry for details.

Hydrolysis probe: One of the main fluorescence-monitoring systems for DNA amplification. TaqMan® probes are an example. These kinds of probes are hydrolyzed by the 5' endonuclease activity of Taq Polymerase during PCR. See Wittwer, 1997 for details.

Internal positive control (IPC): An exogenous IPC can be added to a multiplex assay or run on its own to monitor the presence of inhibitors in the template. Most commonly the IPC is added to the PCR master mix to determine whether inhibitory substances are present in the mix. Alternatively, it can be added at the point of specimen collection or prior to nucleic acid extraction to monitor sample stability and extraction efficiency, respectively.

LATE (Linear After The Exponential)-PCR: A form of asymmetric PCR that uses primer pairs deliberately designed for use at unequal concentrations (Pierce, 2003; Sanchez, 2004). Unlike typical asymmetric PCR, LATE-PCR, amplification is efficient due to improved primer design (Pierce, 2005). LATE-PCR begins with an exponential phase in which amplification efficiency is similar to that of symmetric PCR. Once the limiting primer is depleted, the reaction abruptly switches to linear amplification, and the single-stranded product is made for many additional thermal cycles. LATE-PCR consistently generates strong signals because the absence of product strand reannealing permits unhindered hybridization of the molecular beacon to its target strand and continued accumulation of that strand beyond the cycle at which symmetric reactions typically plateau. By eliminating the exponential phase, LATE-PCR generates less error scatter among replicates. When used in conjunction with molecular beacons, LATE-PCR results in increased signal intensity and reduced sample variation. These features are particularly useful for real-time PCR initiated with single cells. LATE-PCR has been used to directly amplify ssDNA for pyrosequencing (Salk, 2006). See also Bonetta, 2005.

Light-up probe: The light-up probe is a peptide nucleic acid (PNA) oligomer to which an asymmetric cyanine dye thiazole orange (a single reporter dye) is tethered. Upon hybridization the thiazole orange moiety interacts with the nucleic acid bases and the probe becomes brightly (up to 50-fold) fluorescent (Svanvik, 2000a; 2000b & 2001;Isacsson, 2000; Wolffs, 2001). Being based on an uncharged analog (PNA), the light-up probe hybridizes faster and binds target DNA much stronger than oligonucleotide-based probes. See also LightUp Technologies.

Linear View: Amplification plot view displayed using exact DRn values on the Y-axis. The alternative is the log-view, which expands the initiation of exponential amplification phase (and also the baseline period activity). Either can be used for threshold setting. For baseline setting, log-view provides a more detailed display of background noise for more accurate determination of the baseline range (horizontal interval) to be used.

LinReg PCR: Linear regression on the Log(fluorescence) per cycle number data is an assumption-free method to calculate starting concentrations of mRNAs and PCR efficiencies for each sample (Ramakers, 2003). LinReg PCR identifies the exponential phase of the reaction by plotting the fluorescence on a log scale after which a linear regression is performed, leading to the estimation of the efficiency of each PCR reaction for each target. For an example, see Karlen, 2007.

Locked Nucleic Acid (LNA®) Probes: A new generation of sequence-specific probes designed using LNA (a novel nucleic acid analogue), which enhances hybridization performance and biological stability (Koch, 2003; Tolstrup, 2003; Johnson, 2004). Besides increased specificity and stability, by allowing shorter probes, LNA increases quenching efficiency and reduces signal-to-noise ratio. LNA probes perform similar to MGB probes (Letertre, 2003; Johnson, 2004). LNA is also used in primers to increase sensitivity (Latorra, 2003). See web brochures by Exiqon; Thermo; Eurogentec; IDT; Gene Link; PCR: Replicating Success (Moore, 2005) and Simplifying the Probe Set (Mouritzen, 2005).

Log-dilution: Serial dilutions in powers of 10 (10, 100, 1000 etc). In a standard curve experiment, ideally 5 to 7 log-dilutions of the templates (in triplicates) should be used.

Log-view: See Linear View.

LUXTM (Light Upon eXtension) primers: Created by Invitrogen, LUXTM primer sets include a self-quenched fluorogenic primer and a corresponding unlabeled primer. The labeled primer has a short sequence tail of 4–6 nucleotides on the 5′ end that is complementary to the 3′ end of the primer. The resulting hairpin secondary structure provides optimal quenching of the fluorophore. When the primer is incorporated into double-stranded DNA during PCR, the fluorophore is dequenched and the signal increases by up to ten-fold. By eliminating the need for a quencher dye, the LUXTM primers reduce the cost (LUXTM vs TaqMan®).

Melting curve (dissociation) analysis: Every piece of dsDNA has a melting point (Tm) at which temperature 50% of the DNA is single stranded. The temperature depends on the length of the DNA, sequence order, G:C content and Watson-Crick pairing. When DNA-binding dyes are used, as the fragment is heated, a sudden decrease in fluorescence is detected when Tm is reached (due to dissociation of DNA strands and release of the dye). This point is determined from the inflection point of the melting curve or the melting peak of the derivative plot (what is meant by derivative plot is the negative first-derivative of the melting curve). The same analysis can be performed when hybridization probes are used as they are still intact after PCR. As hydrolysis probes (e.g., TaqMan®) are cleaved during the PCR reaction, no melting curve analysis possible if they are used (because of their specificity, there is no need either). Mismatch between a hybridization probe and the target results in a lower Tm. Melting curve analysis can be used in known and unknown (new) mutation analysis as a new mutation will create an additional peak or change the peak area. See Ririe, 1997 & an overview by PremierBiosoft for details of melting curve analysis. High-resolution melting curve analysis can be achieved on most real-time PCR instruments (for example CFX96 or Corbett’s Rotor-Gene 6000) or on dedicated instruments like Idaho Technology's LightScanner®. See Human Mutation Special Issue (June 2009) on HRM.

Minor groove binders (MGBs): These dsDNA-binding agents are attached to the 3’ end of TaqMan® probes to increase the Tm value (by stabilization of hybridization) and to design shorter probes. Longer probes reduce design flexibility and are less sensitive to mismatch discrimination. Shorter probes make it easier to use short conserved or unique sequences for hybridization. MGBs also reduce background fluorescence and increase dynamic range due to increased efficiency of reporter quenching due to shorter distances between the reporter and quencher and the use of non-fluorescent (dark) quenchers (NFQ) at the 3’ end instead of fluorescence dyes like TAMRA. By allowing the use of shorter probes with higher Tm values, MGBs enhances mismatch discrimination in genotyping assays and also gene dosage discrimination. Thus, advantages of MGB probes are (i) increased duplex stability which reduces non-specific probe hybridization and results in low background fluorescence during the 5' nuclease PCR assay, (ii) shorter probes for hybridization-based assays (a 12mer MGB probe has the same Tm as a no-MGB 27mer probe) (Kutyavin, 2000), (iii) increased sequence specificity for better mismatch recognition due to larger differences between Tm values of matched and mismatched probes (Yao, 2006) and (iv) better signal-to-noise ratio due to having a NFQ at the 3’ end. An alternative to MGB probes which also shortens probe length is LNA (Letertre, 2003; Johnson, 2004) and BHQplusTM. See ABI Allelic Discrimination with TaqMan® Probes and MGB Primer & Probe Design on Primer Express.

Minus reverse transcriptase control (_ RTC): A quantitative real-time PCR control sample that contains the starting RNA and all other components for one-step reaction but no reverse transcriptase. Any amplification suggests genomic DNA contamination.

MIQE (Minimum Information for Publication of qPCR Experiments): An initiative by the International Real-time PCR Data Markup Language (RDML) Consortium to generate a structured and universal data standard for exchanging quantitative real-time PCR experiment data. This effort resulted in standard guidelines for reporting qPCR data (publication checklist: XLS, PDF). See also Bustin, 2009.

Molecular beacons: These hairpin probes consist of a sequence-specific loop region flanked by two inverted repeats. Reporter and quencher dyes are attached to each end of the molecule and remain in close contact unless sequence-specific binding occurs and reporter emission (FRET) occurs. See Marras, 1999; Didenko, 2001 and How it Works.

Monte Carlo effect: Problems with reproducible quantification of low abundance targets (<1000 copies) by qPCR. It is a limitation of PCR amplification from small amounts of any complex template due to differences in amplification efficiency between individual templates in an amplifying cDNA population. The Monte Carlo effect is dependent upon template concentration; the lower the abundance of any template, the less likely its true abundance will be reflected in the amplified product. Originally described by Karrer, 1995; see Bustin & Nolan, 2004 for details.

Multiplexing: Simultaneous analysis of more than one target in the same reaction. Specific quantification of multiple targets that are amplified within a reaction can be performed using a differentially labeled primer or probes. Amplicon or probe melting curve analysis allows multiplexing in allelic discrimination if a dsDNA-binding dye is used as the detection chemistry.

Normalization: A control gene that is expressed at a constant level is used to normalize the gene expression results for variable template amount or template quality. If RNA quantitation can be done accurately, normalization might be done using total RNA amount used in the reaction. The use of multiple housekeeping genes that are most appropriate for the target cell or tissue is the most optimal means for normalization. This normalization is performed by the experimenter and should not be mixed up with the normalization of fluorescence signal using the passive reference dye (usually ROX) performed by the equipment. See Normalization Methods for qPCR; Dheda, 2004.

Nucleic acid sequence based amplification (NASBA): NASBA is an isothermal nucleic acid amplification procedure based on target-specific primers and probes, and the coordinated activity of THREE enzymes: AMV reverse transcriptase, RNase H and T7 RNA polymerase. NASBA allows direct detection of viral RNA by nucleic acid amplification. For examples, see Loens, 2003; Guichon, 2004.

No amplification controls (NAC, a minus enzyme control): In mRNA analysis, NAC is a mock reverse transcription containing all the RT-PCR reagents, except the reverse transcriptase. If cDNA or genomic DNA is used as a template, a reaction mixture lacking Taq polymerase can be included in the assay as NAC. No product should be synthesized in the NTC or NAC. If the absolute fluorescence of the NAC is greater than that of the NTC after PCR, fluorescent contaminants may be present in the sample or in the heating block of the thermal cycler.

No template controls (NTC, a minus sample control): NTC includes all of the RT-PCR reagents except the RNA template. No product should be synthesized in the NTC or NAC; if a product is amplified, this indicates contamination (fluorescent or PCR products) or presence of genomic DNA in the RNA sample. NTC is not equivalent to H2O controls and H2O controls are not used in qPCR experiments.

Normalized amount of target: A unitless number that can be used to compare the relative amount of target in different samples.

Nucleic acid target: (also called “target template”) - DNA or RNA sequence that is going to be amplified.

Passive reference (reference dye): A fluorescence dye that provides an internal reference to which the reporter dye signal can be normalized during data analysis by the software. This type of normalization is necessary to correct for fluctuations from well to well caused by changes in concentration or volume. ROX is the most commonly used passive reference dye. After the run, in the multicomponent view, the passive reference dye (if used) should have lower fluorescence than the reporter dyes. Although its signal level should remain constant throughout the experiment, a dip in the ROX signal levels in late cycles (>35 cycles) is nothing to worry about. Not all instruments require the use of a passive reference dye in reaction setup. In those that do not require passive reference dye (like Stratagene and Bio-Rad), the master mix should not contain too much ROX (around 30nM final concentration is allowed). For the effect of ROX concentration on threshold, see ABI Publication: Understanding Ct Value.

Peltier element: The element used for heating and cooling in a qPCR machine. Peltier coolers (in ABI machines) use electron flow between semiconductor couples to heat or cool one side of a plate depending on the direction of current. Other systems use liquid or air flow or mechanical transition between blocks of different temperatures to cycle the samples.

Platform: Refers to hardware that performs real-time PCR. For a current list of available machines, see Michael Pfaffl’s page & Biocompare.

PNA (peptide nucleic acid oligomer): See light-up probe.

Primer Express® Software: A primer design algorithm by ABI. It designs TaqMan® primer and probe sets to be used at standard conditions of ABI real-time PCR equipment. See ABI Taqman Primer/Probe Design using Primer Express and Primer Express v.3 - Getting Started Guide.

Quencher: The molecule that absorbs the emission of fluorescent reporter when in close vicinity (6 to 10 nucleotides). Commonly used quenchers include TAMRA (fluorescent), and non-fluorescent ones DABCYL and black hole quencher (BHQ) dyes. The quenchers are usually at the 3’ end of a dual-labeled fluorescent probe. Quencher dye is also called acceptor. A quencher’s efficiency increases as the spectral overlap of the reporter dye emission profile and quencher absorption profile increases (highest for BHQ).

R: In illustrations of real-time PCR principles, 'R' represents fluorescent Reporter (fluorochrome). 

r coefficient: Correlation coefficient, which is used to analyze a standard curve (ten-fold dilutions plotted against Ct values) obtained by linear regression analysis. It should be ≥ 0.99 for gene quantitation analysis. It takes values between zero and -1 for negative correlation and between zero and +1 for positive correlations.

r2 coefficient: Usually mixed up with 'r' but this is r-squared (also called coefficient of determination). This coefficient only takes values between zero and +1. R2 / r2 is used to assess the fit of the standard curve to the data points plotted. The closer the value to 1, the better the fit (yet another coefficient is the coefficient of variation (CV) which is the standard deviation divided by mean, and the smaller the value the less the spread of the data. In real-time PCR, CV is used to assess the accuracy of the results obtained in triplicate experiments). See also GraphPad Guide to Correlation Parameters and Interpretation of r.

Rapid-cycle PCR: A powerful fast PCR technique for nucleic acid amplification and analysis that is completed in less than half an hour. Samples amplified by rapid-cycle PCR are immediately analyzed by melting curve analysis in the same instrument. In the presence of fluorescent hybridization probes, melting curves provide ‘dynamic dot blots’ for fine sequence analysis, including SNPs. Leading instruments that perform rapid-cycle PCR are RapidCycler2 (Idaho Technology) and LightCycler (Roche).

Real-time PCR: The continuous collection of fluorescent signal from polymerase chain reaction throughout cycles.

Reference: A passive or active signal used to normalize experimental results. Endogenous and exogenous controls are examples of active references. Active reference means the signal is generated as the result of PCR amplification.

Reference dye: Used in all reactions to obtain normalized reporter signal (Rn) adjusted for well-to-well variations by the analysis software. The most common passive reference dye is ROX and is usually included in the master mix. Not all instruments require the use of a reference dye (see Table 1 in Real-Time PCR by Qiagen).

Reporter dye (fluorophore): The fluorescent dye used to monitor amplicon accumulation. This can be attached to a specific probe or can be a dsDNA-binding agent (see for example SYBR® Green I). For specifications of common reporters, see Table 1 and Figure 1 in Real-Time PCR by Qiagen and for the recommended reporter and quencher combinations, follow this link.

Relative quantitation: A relative quantification assay is used to analyze changes in gene expression in a given sample relative to another reference sample (such as relative increase or decrease -compared to the baseline level- in gene expression in response to a treatment or in time etc). Includes comparative Ct (DDCt) and relative-fold methods. (Relative Quantification Page by Pfaffl).

Ribosomal RNA (rRNA): Commonly used as a normalizer in quantitative real-time RNA. It is not considered ideal due to its expression levels, transcription by a different RNA polymerase and possible imbalances in relative rRNA-to-mRNA content in different cell types.

Rn (normalized reporter signal): The fluorescence emission intensity of the reporter dye divided by the fluorescence emission intensity of the passive reference dye. Rn+ is the Rn value of a reaction containing all components, including the template and Rn is the Rn value of an unreacted sample. The Rn value can be obtained from the early cycles of a real-time PCR run (those cycles prior to a significant increase in fluorescence), or a reaction that does not contain any template.

DRn (delta Rn, dRn): The magnitude of the fluorescence signal generated during the PCR at each time point. The DRn value is determined by the following formula: (Rn+) – (Rn–). 

ROX: 6-carboxy-X-rhodamine. Most commonly used passive reference dye for normalization of reporter signals in ABI instruments. The emission recorded from ROX during the baseline cycles (usually 3 to 15) is used to normalize the emission recorded from the reporter due to amplification in later cycles. The use of ROX improves the results by compensating for small fluorescent fluctuations such as bubbles and well-to-well variations that may occur in the plate. Not using ROX or not designating it as the passive reference dye in the analysis may cause trailing of the clusters in the allelic discrimination plot if the instrument (like the ABI) requires a passive reference. ROX or any other internal reference dye is not required by all machines (see the list in Table 1 in Qiagen Publication: Checklist for Multiplex Real-time PCR). If in a ROX requiring instrument, a master mix with lower than required ROX concentration is used, the SD will be large and may be reduced by using an appropriate master mix.

R project for statistical computing: R is a language and environment for statistical computing and graphics which can be seen as a different implementation of the S language. R and a comprehensive set of programs written for a variety of statistical analysis are all available as Free Software. See the R Project Website & List of Contributed R Packages (including qpcR for Modeling and Analysis of Real-time PCR Data (Ritz & Spiess, 2008)).

Scorpion: A fluorescence detection system consists of a detection probe with a reporter dye at the 5' end (the tail), followed by a structure containing the complementary probe sequence (the stem) and the loop, quencher dye and a PCR primer at the 3' end (the primer). Between the primer and its tail (the probe), a blocking agent (DNA spacer/PCR stopper, hexaethylene glycol ‘HEG’) is placed. This structure makes the sequence-specific priming and probing a unimolecular event that creates enough specificity for allelic discrimination assays. When not annealed to the target (downstream of the primer) the reporter dye fluorescence is quenched, when the extension occurs, the probe end of the scorpion binds to the target and the reporter and quencher separate resulting in fluorescence emission. Scorpion primer and probe hybridize to the same strand and thus the detection is faster than those achieved by hybridization or hydrolysis probes (Didenko, 2001). The scorpion chemistry can be used for genotyping (with or without ARMS principle) or qPCR. See How it Works and Scorpion Technology.

Slope: Mathematically calculated slope of standard curve, e.g., the plot of Ct values against logarithm of ten-fold dilutions of target nucleic acid. This slope is used for efficiency calculation. Ideally, the slope should be 3.32 (3.1 to 3.6), which corresponds to 100% efficiency (precisely 1.0092) or two-fold (precisely, 2.0092) amplification at each cycle. Also called gradient.

SPUD assay: A universal system for rapid quality control of nucleic acid templates before qPCR. The assay is designed to detect the presence of inhibitors in the template (Nolan, 2006).

Standard: A sample of known concentration used to construct a standard curve. By running standards of varying concentrations, a standard curve is created from which the quantity of an unknown sample can be calculated.

Standard curve: Obtained by plotting Ct values against log-transformed concentrations of serial ten-fold (log) dilutions of the target nucleic acid. Standard curve is obtained for quantitative PCR and the range of concentrations included should cover the expected unknown concentrations range. It is used to find out the dynamic range of the target (and/or normalizer), to calculate the slope (therefore, efficiency), r and R2 coefficients, precision (standard deviation), sensitivity (y-intercept) and also to help with quantitation. Ideally, the slope of a standard curve should be -3.32, R2 > 0.99 and the y-intercept around 40 (Ct). For proper evaluation of PCR efficiency, a minimum of 3 points (ideally 5 - 7) in triplicates over 5 to 7 logs (1/10 dilutions) of template concentration is necessary. Otherwise, even when the efficiency is 100%, mathematical manipulation is influenced by standard deviations and efficiency calculation may result in a value between 70% and 170%. A poor standard curve is usually due to pipetting errors (including calibration issues) or the presence of inhibitors in the reaction. If not, the primers/probes may need to be redesigned. See the ABI Guide for Standard Curve Experiments and ABI Publication: Understanding Ct Value.

Standard deviation (SD): Precision of the real-time PCR values (Ct) are assessed by the standard deviation of the Ct values obtained from the replicates. If SD is >0.25, the power to discriminate between a two-fold dilution is less than 95%. If in a ROX requiring instrument, a master mix with lower than required ROX concentration is used, the SD will be large and may be reduced by using an appropriate master mix. See ABI Publication: Understanding Ct Value for more on SD.

SunriseTM primers: Originally created by Oncor, sunriseTM primers are similar to molecular beacons. They are self-complementary primers that dissociate through the synthesis of the complementary strand and produce fluorescence signals. See also LUX primers.

SYBR® Green I: A fluorogenic minor groove binding dye that emits little fluorescence when in solution but emits a strong fluorescent signal upon binding to double-stranded DNA. It is used as a cheaper alternative in real-time PCR applications. It does not bind to ssDNA but because of the lack of sequence specificity it binds to any dsDNA product. Its use usually requires melting curve analysis to assure specificity of the results (and if multiplexing is attempted). Similar dsDNA-binding fluorescent dyes developed for high-resolution melting analysis include EvaGreen and LCGreen (see HRM Overview). See also Morrison, 1998 and How it Works.

TAMRA: 6-carboxy-terta-methyl-rhodamine. TAMRA used to be the most commonly used quencher at the 3' end of a TaqMan® probe before the advent of dark quenchers.

TaqMan® probe: A dual-labeled specific hydrolysis probe designed to bind to a target sequence with a fluorescent reporter dye at one end (5’) and a quencher at the other (3’). Assays using Taqman probes are also called 5' nuclease assays. If being multiplexed, TaqMan reporter dyes should have distinct emission maximums. See Didenko, 2001 and How it Works.

Template: The nucleic acid sample used to amplify the target sequence is called template. In a typical qPCR, the cDNA sample included in the reaction is the template. Assessment of template integrity/quality is one of the MIQE requirements.

Threshold: Usually 10X the standard deviation of Rn for the early PCR cycles (background activity). The threshold should be set in the region associated with an exponential growth of PCR product (which may be easier in the log-view of the amplification plot is used) and not as high as the linear or plateau sections of the curve. It should be above the highest baseline signal level. It is assigned for each run to calculate the Ct (or Cp) value for each amplification. It may be necessary to have separate different Ct thresholds for each dye used in the reaction.

Unknown: A sample containing an unknown quantity of template. This is the sample of interest (experimental sample as opposed to positive controls or standards) whose quantity is being determined. 

y-intercept: In the standard curve, the value of y (Ct) where the curve crosses the y-axis at x = 1 copy or 3.08 picogram DNA equivalent template. The y-intercept value corresponds to the Ct value for a single copy of the target molecule. The value around 40 indicates good sensitivity of the assay. Ct values greater than 40 are encountered if PCR efficiency is lower than 100%.


M.Tevfik Dorak, MD, PhD


Last updated on 1 July 2013


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