ION PROTON – new generation of sequencing

The Centre for Plant Biotechnology and Breeding of the Biotechnical Faculty recently obtained the new next generation sequencing system Ion Proton™. Together with a semi-automatic sample preparation system, the new sequencer enables fast, accurate and high-throughput DNA and RNA sequencing. Designed with users in mind, the Ion Proton™ System reduces the costs and complexity of sequencing in molecular and genetic laboratories.


The technology is based on a semiconductor chip, which contains millions of wells for sequence reactions of DNA and RNA (cDNA) molecules. Incorporation of a nucleotide in the sequencing reaction releases a hydrogen proton. The proton changes the pH of the sequencing solution in the well and an ion sensitive layer under the well transforms the change in pH to a change in voltage. The voltage change is detected by a sensor and the incorporation of the nucleotide is thus recorded.


Why sequence with the Ion Proton™ System?

1. The technology was user friendly designed, thus enabling large amounts of sequencing data to be obtained in the shortest possible time. The combination of semiconductor chips and biochemical changes in the sequence reaction directly transforms the chemical information of nucleotide incorporation into digital sequence data of the DNA or RNA molecule. The elimination of optic sensors and complex chemistry makes the Ion Proton™ Sequencing System affordable and easy to use.

2. Sequencing using one semiconductor chip suffices for obtaining 40 – 80 million sequence reads, which is enough for sequencing up to three human exomes and eight human transcriptomes in a single run. It is also possible to sequence multiple samples on one chip using barcode sequences ligated to the samples during the library construction process.

3. Library construction and sequence reaction preparation are fast, simple and clear, thus making the entire working process quick and effective:

1. Library construction

Using commercial kits compatible with the Ion Proton™ Sequencing System, a DNA or RNA (cDNA) library is designed. Given the application, as little as a few picograms up to a few nanograms of DNA or cDNA sample are needed for library preparation.

2. Template preparation

The sequence template is prepared in a couple of hours using the automatic IonOneTouch™ 2 System.

3. Run sequence

Torrent Suite™ Software provides a simple run setup using predesigned workflows and run monitoring in real-time. The run setup is followed by Ion Proton™ sequencer initialization and a sequence run lasting 2 to 4 hours.

4. Data analysis

Up to 80 M sequence reads are obtained in only four hours. Torrent Suite™ Software enables data to be exported in various formats (BAM, UBAM, FASTQ etc.) for further analysis using CLC Genomic Workbench software and others.


The Ion Proton™ System is an integrated system for obtaining sequences of biological molecules, enabling the user to execute the entire process from library construction to extracting sequence reads of high quality in only three days. The technology is applicable for Transcriptome Sequencing for gene expression analysis, Exome Sequencing for unraveling disease-related variants, Small RNA Sequencing for de novo identification of molecules, such as microRNAs, and for Targeted Sequencing of DNA and RNA molecules by using predesigned Ion AmpliSeq™ panels.


Further info from the manufacturer