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Andreas Untergasser1, Steve Lefever2, Jan M Ruijter3, Jan Hellemans4, Jo Vandesompele2,4 1University 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). One of the recommended items was making the raw qPCR data available under the form of a universal data format.
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. 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. When provided with publications, RDML-files should enable readers to re-evaluate the data and confirm the conclusions. The first version of RDML was published in 2009 and has already been cited 50 times. Furthermore, the RDML file format was supported by instrument manufacturers realizing its potential and today Bio-Rad (CFX96 and CFX384), Life Technologies (StepOne, ViiA7 and QuantStudio) and Roche (LC96) have enabled their instrument software to export data in the RDML-format. Additionally, third party software supporting RDML has started to emerge. The software solutions include primer design tools (primer3plus), assay databases (RTPrimerDB) and data analysis software (LinRegPCR and qbasePLUS). Even though more and more qPCR instruments are able to store data in the RDML format and RDML is being increasingly used in instrument independent data analysis, still too few publications make raw data available in the RDML format.
As qPCR continues to develop, so does RDML. The latter development is coordinated by the RDML consortium, a group of scientists, software developers and instrument manufacturers (http://www.rdml.org). The joined efforts resulted in an improved 1.1 version, and version 1.2 is currently being drafted. This consortium is not limited to its current members; it invites all interested parties to join the effort. [On behalf of the RDML consortium]
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