Introduction to nanopore sensing
The GridION™ system
- GridION™ workflow
- Workflow versatility: no fixed run time
- Run until... sufficient data
- Sample scheduling and multiplexing
The MinION™ device: a miniaturised sensing system
Analytes and Applications: DNA, RNA, proteins
Fields of use
The GridION™ system is designed to enable users to run an experiment until sufficient data has been collected to reach a predetermined experimental endpoint. In contrast, other molecular analysis systems have a fixed analysis time, or ‘run time’ that delivers a surged batch of data at the end of that run. In such cases the user is forced to design the experiment to fit the machine that the analysis is performed on.
Conversely, by making use of the properties of nanopore sensing and rapid electronic measurement, users can instruct GridION nodes to monitor their own data output and look for key application-specific results. These results may be used to alter or optimise the behaviour of the nodes in real time, or simply stop them when the experiment is known to have been completed. For example, a node or a cluster of nodes can be instructed, through on-board software, to run until a certain datum has been seen a certain number of times at a specified confidence level. In this way, the experiment is defined by the user, not defined by the machine.
By using the 96-well plate-adapted cartridge, this further allows the system to process a series of experiments autonomously on different samples; the system simply runs one sample from the first well, and once completed, the node can automatically move onto the next sample to run another experiment.
A node or a cluster of nodes can be instructed to run until certain user-specified criteria have been met, for example:
• DNA sequencing: the GridION system may process the sample until they have seen a minimum of tenfold read coverage over specified regions of interest, until a specific mutation has been observed in a sample or until enough sequence data has been collected to reliably assemble a sample against a reference.
• Protein analysis: the GridION system may process the sample until the presence of a specific analyte has been determined to a certain confidence level, and process the sample further to determine its concentration.
• Small molecules: the GridION system may process the sample until it has determined that a specific analyte (for example a reactive molecule such as an explosive) was NOT present in the solution, to a pre-set confidence level.
During the experiment, data about the analyte is streamed in real time from the nodes. This can be supplied to software services on the user's system for real-time bioinformatic analyses during the experiment. These analyses can monitor for key success criteria. The system can then feed back, through the nodes or clusters API, to instruct the systems to stop when the application has been successful, or to adapt other settings in order to make it successful.
This has the added benefit that the user can monitor system performance and experimental progress in real time and use this information to make changes to the system during an experiment. It also means there is no wait at the end of run for a large data file to be processed by a bioinformatics pipeline.
The Run Until functionality is compatible with the Accelrys Pipeline Pilot® Next Generation Sequencing collection, which will be offered as the preferred and supported software solution with the GridION platform.