Management and Automation of qPCR Diagnostic Workflows

Matjaz Hren
BioSistemika, Slovenia

In the molecular diagnostics field, qPCR (Real-Time Polymerase Chain Reaction) is one of the leading methods because it allows detection and precise quantification of specific DNA / RNA sequences. The core advantages that ensure qPCR’s broad applicability are high sensitivity and specificity and a broad dynamic range. Sample preparation and data analysis are complex qPCR steps, mostly performed by high-level experts. There are several solutions available for automation of the so called “wet-lab” part of the workflow (which includes sample preparation, reagent & sample loading onto qPCR plates). However when it comes to the so called “dry-lab”, which covers experiment design, data analysis and interpretation, quality control and reporting, there are no simple solutions available. In addition to that there are no internationally accepted guidelines or standards for diagnostic use of qPCR such as MIQE for research qPCR community.
This problem can be solved by different approaches. One of the most common is in-house development of solutions by preparing a series of macro-based spreadsheet documents in combination with modifications of Laboratory Information Management Systems (LIMS) to automate as much of the qPCR workflow as possible. However users still have to use different program environments to design analyses, create templates for lab work (e.g. mastermix calculation) and finally to analyse and interpret results and to prepare reports. This approach is still quite tedious and includes some repetitive work, which is somewhat contradictory to the demand for obtaining fast results without compromising quality in qPCR diagnostics. So we see that these solutions only partially address the demand for automation, unification and simplification of the qPCR workflow in diagnostic environments. Therefore we designed easy to use software that manages complete diagnostic qPCR workflow. The software guides users from the initial experiment design, to the final reports utilizing powerful expert knowledge. This easy to use software unifies the entire qPCR workflow. It calculates reagent concentrations for selected analyses, prepares wet lab outputs, analyses raw data and interprets the results while taking into account the hierarchical positions among lab employees. It communicates with LIMS and qPCR thermal cyclers and is quality assurance compliant. It has been designed to turn complex and unconsolidated approach into one simple, controlled environment. Its basic purpose is easing the pressure on high-level scientists and to make qPCR diagnostics and efficient process.

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