Developed by Ion Torrent Systems in 2010, later acquired by Thermo Fisher Scientific. The Ion Torrent leverages semiconductor sequencing technology to enable fast and relatively inexpensive next generation sequencing. This platform distinguishes itself through bead-based amplification, resembling aspects of the Roche 454 Sequencing method. In the Ion Torrent workflow, each well in the sequencing chip serves as a pH sensor, contributing to real-time detection during the sequencing reaction.
- Ion Torrent uses semiconductor pH sensor technology
Library Preparation
Ion Torrent employs a bead-based amplification technique similar to Roche 454 Sequencing for preparing DNA fragments. This step sets the stage for subsequent sequencing processes.
- Ion torrent sequencing follows a bead-based amplification of DNA fragments like Roche 454 Sequencing method
Sequencing Reaction
The heart of Ion Torrent sequencing lies in the bead-embedded pH sensors within each well of the sequencing chip. During sequencing cycles, dNTPs are introduced one at a time. The pH changes resulting from nucleotide incorporation are detected in real-time, forming the basis for readout.
- Each well in the sequencing chip contains a pH sensor
- dNTPs are provided in cycles
- In each cycle, only one type of dNTP is provided
Advantages of Ion Torrent Sequencing
- Read length 400-700 bp
- Reasonably high accuracy (~99%)
- Economic with respect to the competition
- No expensive optical detection unit required
- No modified dNTP required
Drawbacks of Ion Torrent Sequencing
- Lower throughput compared to Illumina platform
- 100-130 million reads at most
- Depends on the sequencing chip used
- May not be suitable for large genome sequencing projects
- Higher error rate in homopolymeric stretches
- Beyond 8-10 bp, the signal intensity is not linearly proportional to the number of bases.
- unable to accurately determine the length of the homopolymeric stretch
- more indels
Ion Torrent Sequencers
- Ion GeneStudio S5: A key player in the Ion Torrent sequencer lineup, the GeneStudio S5 provides researchers with reliable and efficient sequencing capabilities.
- Ion Torrent Genexus: Another notable member of the Ion Torrent family, the Genexus model further advances the platform’s capabilities.
Ion Torrent PGM (Life Technologies) vs the MiSeq (Illumina)
Feature | Ion Torrent Sequencing | Illumina Sequencing |
Technology | Semiconductor pH sensor technology | Sequencing by Synthesis (SBS) technology |
Read Length | 400-700 bp | Varies (up to 2 x 250 bp for certain Illumina platforms) |
Accuracy | ~99% | Highly accurate (~99.9%) |
Throughput | Lower throughput compared to Illumina | High throughput, especially on HiSeq and NovaSeq platforms |
Homopolymeric Stretch Challenges | Higher error rate in homopolymeric stretches | Less pronounced issues with homopolymeric stretches |
Library Preparation | Bead-based amplification similar to Roche 454 Sequencing | Adapter ligation and bridge amplification |
Economic Efficiency | Economic with no need for expensive optical detection units | Generally cost-effective, but more expensive in some cases |
Applications | Suitable for various applications, especially cost-sensitive | Versatile, widely used across diverse genomic applications |
Instrument Examples | Ion GeneStudio S5, Ion Torrent Genexus | Illumina MiSeq, NextSeq, HiSeq, NovaSeq, etc. |
References
- Merriman B; Ion Torrent R&D Team; Rothberg JM. Progress in ion torrent semiconductor chip based sequencing. Electrophoresis. 2012 Dec; 33(23):3397-417
- Lahens, N.F., Ricciotti, E., Smirnova, O. et al. A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression. BMC Genomics 18, 602 (2017). https://doi.org/10.1186/s12864-017-4011-0
- Ion Torrent Next-Generation Sequencing Applications | Thermo Fisher Scientific – IN