Afif M. Abdel Nour

Minimum information necessary for quantitative real-time PCR experiments.

The MIQE (minimum information for the publication of quantitative real-time PCR) guidelines were published in 2009 with the twin aims of providing a blueprint for good real-time quantitative polymerase chain reaction (qPCR) assay design and encouraging the comprehensive reporting of qPCR protocols. It had become increasingly clear that variable pre-assay conditions, poor assay design, and incorrect data analysis were leading to the routine publication of data that were often inconsistent, inaccurate, and wrong. The problem was exacerbated by a lack of transparency of reporting, with the details of technical information inadequate for the purpose of assessing the validity of published qPCR data. This had, and continues to have serious implications for basic research, reducing the potential for translating findings into valuable applications and potentially devastating consequences for clinical practice. Today, the rationale underlying the MIQE guidelines has become widely accepted, with more than 2,200 citations by March 2014 and editorials in Nature and related publications acknowledging the enormity of the problem. However, the problem we now face is rather serious: thousands of publications that report suspect data are populating and corrupting the peer-reviewed scientific literature. It will be some time before the many contradictions apparent in every area of the life sciences are corrected.

Five Years MIQE Guidelines: The Case of the Arabian Countries

The quantitative real time polymerase chain reaction (qPCR) has become a key molecular enabling technology with an immense range of research, clinical, forensic as well as diagnostic applications. Its relatively moderate instrumentation and reagent requirements have led to its adoption by numerous laboratories, including those located in the Arabian world, where qPCR, which targets DNA, and reverse transcription qPCR (RT-qPCR), which targets RNA, are widely used for region-specific biotechnology, agricultural and human genetic studies. However, it has become increasingly apparent that there are significant problems with both the quality of qPCR-based data as well as the transparency of reporting. This realisation led to the publication of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines in 2009 and their more widespread adoption in the last couple of years. An analysis of the performance of biomedical research in the Arabian world between 2001–2005 suggests that the Arabian world is producing fewer biomedical publications of lower quality than other Middle Eastern countries. Hence we have analysed specifically the quality of RT-qPCR-based peer-reviewed papers published since 2009 from Arabian researchers using a bespoke iOS/Android app developed by one of the authors. Our results show that compliance with 15 essential MIQE criteria was low (median of 40%, range 0–93%) and few details on RNA quality controls (22% compliance), assays design (12%), RT strategies (32%), amplification efficiencies (30%) and the normalisation process (3%). These data indicate that one of the reasons for the poor performance of Arabian world biomedical research may be the low standard of any supporting qPCR experiments and identify which aspects of qPCR experiments require significant improvements.

“Stay in touch while on the bench” - how the MIQE applet can increase the quality of your qPCR and dPCR experiments

BackgroundHow to check the quality of your qPCR experiments orthe reliability of an international publication by an electro-nic device? From now on iOS based mobile devices, e.g.iPhone, iPad or iPod, will help you to increase the qualityof qPCR experiment or publication, by providing a ‘MIQE(The MIQE Guidelines - Minimum Information for publi-cation of Quantitative real-time PCR Experiments) qPCR’applet [1,2]. Three years ago we created the first interac-tive solution for scientific guidelines, based on the MIQEqPCR publication [3].Materials and methodsThis first applet was downloaded 7800 times from 89 dif-ferent countries, and recently Biotechniques journal hasselected the APP as one of the leading “methods-orientedapplets” and recommended it by the“websites every lifescientist should try”.ResultsAfter this great success we are presenting today theMIQE applet for the digital PCR (Figure 1).The digital PCR MIQE guidelines were publishedrecently by a group of experts [4]. This new applicationcould be used by scientists to check whether their digitalPCR (dPCR) experiment or the used literature fulfills theMIQE requirement. The ‘MIQE Guidelines’ checklist pro-vides 83 parameters that dPCR studies should be requiredor recommended to meet before being considered forpublication. This checklist is based on the originalpublishedMIQEchecklistforthedPCRandwehopeitwill increase future publication quality and reliability.ConclusionsThere are much more wider seen goals of the‘MIQEguidelines’, all in all the goals might be summarized asfollow: 1) to increase reliability of results, 2) to helpinsuring the integrity of scientific work, with major focuson biological relevance. This is an easy to use applet thatcan help reviewers and authors to gain time in theremanuscript preparation. Recently by using this applet wemanaged to analyze and evaluate 461 scientific paperspublished by Arabian countries (paper accepted inPLOSOne).