Digital polymerase chain reaction (i.e., dPCR) is a refinement of conventional polymerase chain reaction methods that can be used to directly quantify and clonally amplify nucleic acids including DNA, cDNA or RNA. Differently to the traditional PCR, dPCR separates the sample into a large number of partitions (i.e., droplets) and the reaction is carried out in each partition individually. This separation allows a more reliable collection and sensitive measurement of nucleic acid amounts. The method has been demonstrated useful for studying variations in gene sequences (e.g., Copy Number Variation), quantify cancer biomarkers and study gene expressions. The Digital PCR module manages and tracks the samples analyzed using this technology. The following activities are available.
The user plans a set of aliquots for experiment using the Digital PCR technology from the Biobank module. During the experiment planning the user defines also a title and description (optional). Before performing the molecular experiment, the user should validate the scheduled aliquots and confirm the used quantity for each aliquot. The user should insert the barcode of each aliquot to perform the validation procedure.
All validated requests are visualized. After selecting an experiment, the user should define the instrument and the layout of the support used in the experiment. Once these parameters have been defined, the system shows the samples from the selected experiment and the layout of the support. The mutation targets used by the user in other experiments are shown in the “Targets” table. It is possible to add new targets by performing a search according to the gene symbol and the mutation syntax. The samples and the targets can be associated with the positions of the support by clicking on a single cell or the column/row header. The positions of the support will be updated with the sample label and/or target color. A position may contain only one sample and one target. Only the positions containing both a sample and a target will be saved into the system.
All experiments for which a layout has been defined are visualized. By selecting an experiment, the user can upload a file with the digital PCR results. A table with the measures is shown, according to the contents of the file. In addition to the measures, the user can also associate a set of files with an experiment.