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Andreas Untergasser1, Steve Lefever2, Jasper Anckaert2, Jan M Ruijter3, Jan Hellemans4, Jo Vandesompele2,4 1University of Heidelberg, Heidelberg, Germany; 2Ghent University, Ghent, Belgium; 3Academic Medical Center, Amsterdam, The Netherlands; 4Biogazelle, Zwijnaarde, Belgium |
Abstract
Quantitative PCR (qPCR) is the gold standard method for accurate and sensitive nucleic acid quantification. To improve the quality and transparency of experiment design, data-analysis and reporting of results, the MIQE guidelines were established in 2009 (Bustin et al., Clinical Chemistry). The Real-time PCR Data Markup Language (RDML) was designed to establish a vendor independent, freely available XML based file format to store and exchange qPCR data (Lefever et al., NAR). RDML stores the raw data acquired by the machine as well as the information required for its interpretation, such as sample annotation, primer and probe sequences and cycling protocol.
Today, several instrument manufacturers realized its potential and implemented functionality to export data in the RDML-format. Third party software (LinRegPCR and qbasePLUS) uses this information for advanced data analysis. Due to the flexibility of RDML, the majority of the current software uses only parts of the format. Furthermore, with different RDML versions available, the need to convert between versions became obvious. The open source editor RDML-Ninja was designed to edit RDML-files and convert between different versions (sourceforge.net/projects/qpcr-ninja/). It should serve as reference implementation of the RDML-format and assist researchers, reviewers as well as software developers by offering access to all data in an RDML-file.
Ultimately, RDML could be extended to store all information required by MIQE. Currently the information required by MIQE seems overwhelming to a researcher, but RDML offers an easy way out. All the information would be only entered once and stored in a basic RDML file. Researchers would not have to re-enter this information with every qPCR run, but will import from this RDML file only the parts needed for the current qPCR run. Furthermore integration of MIQE in RDML and RDML-Ninja would allow checking to which extend MIQE information is provided by calculating the checklist completeness based on a provided RDML-file. We would like to discuss this vision, its chances and its applicability.
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