Good practice guide for the application of quantitative PCR (qPCR) Good practice guide for the application of quantitative PCR (qPCR) First Edition 2013 Co-authors Tania Nolan (1) Jim Huggett (2) Elena Sanchez (2) Contributors (1) Anders Bergkvist Malcolm Burns (2) Rebecca Sanders (2) Nicholas Redshaw (2) Tim Wilkes (2) (3) Acknowledgements Foreword by Michael Pfaffl With special thanks to Susan Pang(2) and Vicki Barwick(2) for their help in the production of this guide. Acknowledgement of an individual does not indicate their agreement with this Guide in its entirety. (1) Sigma-Aldrich Production of this Guide was in part funded (2) LGC, Teddington by the UK National Measurement System. (3) Technical University Of Munich This publication should be cited as: T Nolan, J Huggett, E Sanchez, Good practice guide for the application of quantitative PCR (qPCR), LGC (2013). Copyright © 2013 LGC i Foreword by Michael W Pfaffl The polymerase chain reaction (PCR) is a rapid, sensitive, and rather simple technique to amplify DNA, using oligonucleotide primers, dNTPs and a heat stable Taq polymerase. It was invented in 1983 by Kary B. Mullis and co-workers, who, ten years later, were awarded the ‘Nobel Prize for Chemistry’. With the introduction of real-time PCR in the late nineties, the PCR method overcame an important hurdle towards becoming ‘fully quantitative’ (and therefore known as quantitative PCR, or qPCR). Currently, qPCR is regarded as the ‘gold standard’ in the quantitative analysis of nucleic acids, be it DNA, RNA or micro-RNA molecules. The main reasons for its success are its high sensitivity, robustness, good reproducibility, broad dynamic quantification range, and very importantly, affordability. The assay and primer design can often be fully automated and handling in the lab is blindingly easy. Another big draw for the user is that, in most instances, the qPCR experiments produce results, or as we call them, Cq data points. However, the generation of Cq data points is not dependent on good laboratory practice or the precise application of guidelines such as MIQE. In other words, when researchers obtain a Cq data point, they need to prove that that particular amplification result is valid, reliable and meaningful. And exactly here lies the main challenge of qPCR! This method is ‘too easy’ to apply and generates results any time. It is up to the researcher to demonstrate that the data obtained are valid and if not, investigate where the error could come from. Hence, it is essential to have a comprehensive understanding of the underlying basic qPCR principles, sources of error, and general issues inherent to nucleic acid isolation and/or quantification in order to develop assays and workflows which meet high analytical requirements in concordance with the MIQE guidelines. Unfortunately, we are still far from having developed such optimal workflows, with the highest sensitivity or the best RNA integrity metrics, to obtain reproducible and authentic results. Thus, I can warmly recommend to the research community this Good Practice Guide for the Application of Quantitative PCR, with the aim to improve researchers’ experimental workflows, from sampling to qPCR data analysis, and eventually take us to valid and confident research results. Michael W Pfaffl Michael W. Pfaffl Physiology Weihenstephan Technische Universität München Weihenstephaner Berg 3 85354 Freising Germany [email protected] ii Good Practice Guide for the Application of Quantitative PCR (qPCR) Contents Objectives of this guide ....................................................................................................................... 2 Terminology .......................................................................................................................................... 3 Common abbreviations ........................................................................................................................ 7 Section A. Technical information ....................................................................................................... 8 A.1 PCR and qPCR ......................................................................................................................... 8 A.2 Sample purification and Quality Control (QC) .................................................................... 10 A.3 qPCR assay design ............................................................................................................... 21 A.4 Assay optimisation and validation ...................................................................................... 32 A.5 Normalisation ......................................................................................................................... 41 A.6 Data analysis .......................................................................................................................... 44 A.7 Troubleshooting .................................................................................................................... 50 Section B. Applications of qPCR ...................................................................................................... 53 B.1 Use of PCR and qPCR in food authenticity studies ........................................................... 53 B.2 Pathogen detection for clinical analysis ............................................................................. 59 B.3 MicroRNA expression profiling ............................................................................................ 61 Section C: Protocols .......................................................................................................................... 64 C.1 Basic qPCR protocol ............................................................................................................. 65 C.2 The SPUD assay for detection of assay inhibitors ............................................................ 68 C.3 3’/5’ Assay for analysis of template integrity ..................................................................... 70 C.4 Reverse transcription (one-step and two-step) protocols ................................................ 72 C.5 Primer optimisation ............................................................................................................... 78 C.6 qPCR reference gene selection protocol ............................................................................ 84 C.7 qPCR efficiency determination protocol ............................................................................. 87 C.8 qPCR gene expression analysis protocols......................................................................... 90 Section D: Further resources ............................................................................................................ 94 Section E: Further reading ................................................................................................................ 95 Section F: References ........................................................................................................................ 96 1 Objectives of this guide There is little doubt that PCR (Polymerase Chain Reaction) has transformed the fields of clinical and biological research, due to its robustness and simplicity. Subsequent developments, such as real-time quantitative PCR (qPCR) and reverse transcription qPCR (RT-qPCR), offer simple methods for analysis of DNA and RNA molecules. However, completing qPCR assays to a high standard of analytical quality can be challenging for a number of reasons, which are discussed in detail in this guide. qPCR has a large number of applications in a wide range of areas, including healthcare and food safety. It is therefore of paramount importance that the results obtained are reliable in themselves and comparable across different laboratories. This guide is aimed at individuals who are starting to use qPCR and realise that, while this method is easy to perform in the laboratory, numerous factors must be considered to ensure that the method will be applied correctly. These additional considerations include – but are not limited to – methods of sampling, sample storage, nucleic acid extraction, and nucleic acid storage, manipulation and preparation. In other words, all the steps prior to undertaking the quantification technique must also be controlled. At the other end of the analytical process, reporting technical results may be highly subjective. Since qPCR is a relative method, requiring the comparison of two or more samples to a standard curve or to each other, standardisation of results is very challenging. The primary qPCR metric, the 1 quantification cycle (Cq) , depends on many factors including where a threshold is set, the choice of reporter and day-to-day variation in measurement. In addition, since Cq exists on a logarithmic scale, there are specific statistical challenges that need to be addressed to analyse these data accurately. All these factors combine to make a technically simple technique, challenging to interpret with absolute confidence. This guide aims to assist those who are, or will be, using qPCR by discussing the issues that need consideration during experimental design. The guide entails “tried and tested” approaches, and troubleshoots common issues. 2 Terminology Absolute (or Standard Curve) Quantification Absolute quantification is used when performing qPCR to describe estimation of target copy numbers by reference to a standard curve of defined, absolute concentration.