- Software
- Open Access

# FCI: an R-based algorithm for evaluating uncertainty of absolute real-time PCR quantification

- Paolo Verderio
^{1}, - Sara Pizzamiglio
^{1}, - Fabio Gallo
^{1}and - Simon C Ramsden
^{2}Email author

**9**:13

https://doi.org/10.1186/1471-2105-9-13

© Verderio et al; licensee BioMed Central Ltd. 2008

**Received: **04 October 2007

**Accepted: **10 January 2008

**Published: **10 January 2008

## Abstract

### Background

FCI is an R code for analyzing data from real-time PCR experiments. This algorithm estimates standard curve features as well as nucleic acid concentrations and confidence intervals according to Fieller's theorem.

### Results

In order to describe the features of FCI four situations were selected from real data collected during an international external quality assessment program for quantitative assays based on real-time PCR. The code generates a diagnostic figure suitable for assessing the quality of the quantification process.

### Conclusion

We have provided a freeware programme using this algorithm specifically designed to increase the information content of the real-time PCR assay.

## Keywords

## Background

Real-time PCR is widely used for the quantification of nucleic acids in a wide range of clinical and research applications including the measurement of gene dosage, detection of residual disease in haematological malignancies and detection of bacterial and viral infection.

Real-time PCR typically employs fluorescent probes which generate a signal that accumulates during PCR cycling in a manner proportional to the concentration of amplification products. Absolute quantification of a nucleic acid target can be achieved using a standard curve, which is generated by amplifying known amounts of the target DNA. The standard curve is typically generated using a series of 10-fold dilutions of a control template. For each dilution, replicated determinations of the cycle threshold (ct) are performed and a straight line is fitted to the data by plotting the ct averages as a function of the logarithm of the starting concentration of the standards. By applying a technique known as "inverse regression," the straight line is used as a "calibrator" to estimate the unknown starting DNA concentration in the sample under examination.

As in any titration, evaluating the uncertainty in the estimated concentration of the unknown sample is critical for interpreting the data and optimizing experimental procedures. In addition to the point estimate it is important to calculate the confidence interval of the "true" value of the unknown concentration.

Commercial software specifically designed for generating standard curves and estimating nucleic acid concentrations is now available, however, there are currently no freeware tools available for calculating the uncertainty associated with the concentration estimates.

Several approaches have been proposed for constructing confidence intervals in inverse regression [1–5], but the most frequently used method is due to Fieller [6]. Fieller's theorem provides a general procedure for the construction of confidence limits for certain ratios of parameters, most often applied to ratios of linear combinations of parameters (e.g. inverse estimate from a linear regression model). In this note we propose a statistical tool, FCI (Fieller's Confidence Interval), to estimate the confidence interval (CI) of the "true" value of each unknown concentration according to Fieller's theorem.

## Implementation

FCI code has been tested on the WINDOWS platform with the R Software version 2.5.1 [7], an open-source statistical programming language. FCI implementation involves data import, FCI running and FCI output.

Before running the FCI code it is necessary to save the file in the new directory C:\DATA and install the 'car' package from the Packages menu of R.

Anova Table

Source | df | SS | MS | F.value |
---|---|---|---|---|

Regression | df | ${\text{SS}}_{\text{R}}={\displaystyle \sum _{\text{i}=\text{1}}^{\text{I}}{\text{J}}_{\text{i}}{\left({\widehat{\text{y}}}_{\text{i}}-\overline{\overline{\text{y}}}\right)}^{2}}$ | ${\text{MS}}_{\text{R}}=\frac{{\text{SS}}_{\text{R}}}{{\text{df}}_{\text{R}}}$ | $\frac{{\text{MS}}_{\text{R}}}{{\text{s}}_{\text{p}}^{\text{2}}}$ |

Error | ${\text{df}}_{\text{E}}=\left(\text{I}-\text{2}\right)+{\displaystyle \sum _{\text{i}=\text{1}}^{\text{I}}\left({\text{J}}_{\text{i}}-\text{1}\right)}$ | ${\text{SS}}_{\text{E}}={\displaystyle \sum _{\text{i}=\text{1}}^{\text{I}}{\displaystyle \sum _{\text{j}=1}^{{\text{J}}_{\text{i}}}{\left({\text{y}}_{\text{ij}}-{\widehat{\text{y}}}_{\text{i}}\right)}^{2}}}$ | ${\text{MS}}_{\text{E}}=\frac{{\text{SS}}_{\text{E}}}{{\text{df}}_{\text{E}}}$ | |

Lack of fit | df | ${\text{SS}}_{\text{L}}={\displaystyle \sum _{\text{i}=\text{1}}^{\text{I}}{\text{J}}_{\text{i}}}{\left({\widehat{\text{y}}}_{\text{i}}-{\overline{\text{y}}}_{\text{i}}\right)}^{\text{2}}$ | ${\text{MS}}_{\text{L}}=\frac{{\text{SS}}_{\text{L}}}{{\text{df}}_{\text{L}}}$ | $\frac{{\text{MS}}_{\text{L}}}{{\text{s}}_{\text{p}}^{\text{2}}}$ |

Pure error | ${\text{df}}_{\text{P}}={\displaystyle \sum _{\text{i}=\text{1}}^{\text{I}}\left({\text{J}}_{\text{i}}-\text{1}\right)}$ | ${\text{SS}}_{\text{P}}={\displaystyle \sum _{\text{i}=\text{1}}^{\text{I}}{\displaystyle \sum _{\text{j}=\text{1}}^{{\text{J}}_{\text{i}}}{\left({\text{y}}_{\text{ij}}-{\overline{\text{y}}}_{\text{i}}\right)}^{\text{2}}}}$ | ${\text{s}}_{\text{p}}^{\text{2}}=\frac{{\text{SS}}_{\text{p}}}{{\text{df}}_{\text{p}}}$ | |

Total corrected | ${\text{df}}_{\text{T}}=\left({\displaystyle \sum _{\text{i}=\text{1}}^{\text{I}}{\text{J}}_{\text{i}}}\right)-1$ | ${\text{SS}}_{\text{T}}={\displaystyle \sum _{\text{i}=\text{1}}^{\text{I}}{\displaystyle \sum _{\text{j}=\text{1}}^{{\text{J}}_{\text{i}}}{\left({\text{y}}_{\text{ij}}-\overline{\overline{y}}\right)}^{\text{2}}}}$ |

The code performs a "Lack of fit" test on the fitted calibration model, the computation of 95% confidence interval for regression coefficients and, where appropriate, provides messages to assist in the interpretation of the results. In addition it generates a diagnostic plot enabling both an assessment of PCR assay quality and also a visual representation of the Fieller's CI graphical derivation [9].

## Results and Discussion

In order to illustrate the functionality of FCI, we considered the data provided by four participants (laboratories A-D) in an international external quality assessment program (EQUAL-quant) for quantitative assays based on real-time PCR [10]. In this program laboratories received primers, labelled probe master mixture, plasmid standards (containing 10, 10^{2}, 10^{3}, 10^{4}, 10^{5} copies/5 μL), and three samples of unknown concentration (test samples). Participants were required to measure the target copy number in all test samples and provide all ct values in triplicate. For the purposes of this illustration we consider only performance in the analysis of the test sample corresponding to the lowest target copy number (56.21 copies/5 μl calculated as median value of copy number from a total of 92 laboratories).

For laboratory B the ct mean of the unknown sample (y0) lies outside the range of the standard dilutions used to fit the standard curve. In this situation (i.e. extrapolation) we cannot assume that the linear model on which the calibration is based will hold true outside the range of the standard dilutions. In this case the FCI code will not provide the Fieller's CI in the output (Figure 2, panel B), and the warning message "Out of standards range" appears in the legend of the corresponding figure (Figure 3, panel B).

For laboratory C the 95% CI of the true value of the slope includes the theoretical expected slope value (-3.32193) corresponding to 100% amplification efficiency. In such a situation the message "Optimal efficiency" appears in the output (Figure 2, panel C). This message appears only when no warning messages have been displayed. Figure 3, panel C reports the pertinent graph.

Laboratory D illustrates the situation in which no messages, either in the output or in the figure, are displayed (Figure 2, panel D; Figure 3, panel D).

When the 95% confidence interval of the true value of the slope includes zero (an unlikely eventuality in a real-time PCR experiment) the warning message "Not real confidence interval" appears in the FCI output. In this situation, not observed in our real data, the resulting Fieller's confidence interval is infinite in extent and the data have to be considered as valueless for estimating the unknown concentration.

## Conclusion

We have described an algorithm for the computation of CIs based on Fieller's theorem in the context of real-time PCR quantification. While the algorithm is designed in this case for real-time PCR experiments, it is easily adapted to other assays based on inverse estimation from a straight line model (calibration). FCI estimates the standard curve, the unknown sample concentration and its uncertainty. Furthermore it provides an insightful diagnostic figure.

## Methods

The statistical model corresponding to the standard curve is :

y_{ij} = β_{0} + β_{1}x_{i} + ε_{ij} (1)

where y_{ij} specifies the value of ct measured for the j-th replication (j = 1, 2,...,J_{i}) at the i-th standard (i = 1, 2,...,I), x_{i} defines the logarithm of the starting DNA/cDNA concentration of the i-th standard and ε_{ij} is the random component assumed to be normally distributed with mean zero and constant error variance σ^{2}. The estimates b_{0} and b_{1} of β_{0} and β_{1} respectively are obtained by the Ordinary Least Squared method.

The uncertainty associated to linear regression model underlying the standard curve can be broken up according to the analysis of variance (Anova) as reported in Table 1[11].

_{0}) is usually estimated by resorting to the inverse regression, as:

where ${\overline{\text{y}}}_{\text{0}}$ is the mean of the K replicated values of ct [ct_{k} = y_{k}, (k = 1, 2,....K)] measured for the sample under examination.

As shown in Verderio *et al*. [8] the limits of 100(1-α)% confidence interval of x_{0} according to Fieller's theorem are obtained as roots of a second degree equation.

## Availability and requirements

For the current version of FCI code please see Additional file 2. The commands for importing data, running the code and displaying the output are provided in Additional file 3. Further development as well as extended version of FCI code will be available trough our website: http://www.istitutotumori.mi.it/INT/dipartimenti/UO/biometria. FCI code use R Software http://www.r-project.org, an open-source statistical programming language.

## Declarations

### Acknowledgements

EQUAL-quant has been supported by the EU Sixth Framework Program (Contract 504842). This note was supported by the "Sovvenzione Globale INGENIO" awarded by the "Fondo Sociale Europeo, Ministero del Lavoro e della Previdenza Sociale and Regione Lombardia".

## Authors’ Affiliations

## References

- Hoadley B: A Bayesian look at inverse linear regression.
*J Am Stat Assoc*1970, 65: 356–369. 10.2307/2283598View ArticleGoogle Scholar - Cox C: Fieller's theorem, the likelihood and the delta method.
*Biometrics*1990, 46: 709–718. 10.2307/2532090View ArticleGoogle Scholar - Krutchkoff RG: Classical and inverse regression methods of calibration.
*Technometrics*1967, 9: 425–439. 10.2307/1266511View ArticleGoogle Scholar - Grybill FA:
*Theory and applications of the linear model*. Massachussets USA: Duxbury press; 1976.Google Scholar - Wu CFJ: Jackknife, bootstrap and other resampling methods in regression analysis.
*Ann Statist*1986, 14: 1261–1295. 10.1214/aos/1176350142View ArticleGoogle Scholar - Fieller EC: The biological standardization of insulin. J R Stat Soc 1940, (Suppl 7):1–64.Google Scholar
- Ihaka R, Gentleman R: R: A language for data analysis and graphics.
*J Comp Graph Stat*1996, 5: 299–314. 10.2307/1390807Google Scholar - Verderio P, Orlando C, Casini Raggi C, Marubini E: Confidence interval estimation for DNA and mRNA. concentration by real-time PCR: A new environment for an old theorem.
*Int J Biol Markers*2004, 19: 76–9.PubMedGoogle Scholar - Pizzamiglio S, Verderio P, Orlando C, Marubini E: Confidence Interval for DNA/mRNA concentration by real-time PCR.
*Int J Biol Markers*2007, 22: 232–6.PubMedGoogle Scholar - Ramsden SC, Daly S, Geilenkeuser WJ, Duncan G, Hermitte F, Marubini E, Neumaier M, Orlando C, Palicka V, Paradiso A, Pazzagli M, Pizzamiglio S, Verderio P: EQUAL-quant: An International External Quality Assessment Scheme for Real-Time PCR.
*Clin Chem*2006, 52: 1584–91. 10.1373/clinchem.2005.066019View ArticlePubMedGoogle Scholar - Draper NR, Smith H:
*Applied Regression Analysis*. Third edition. New York: John Wiley & Sons; 1998.Google Scholar

## Copyright

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.