Ion Torrent PGM System

PGM System is a sequencer released by Thermo Fisher Scientific in June 2010. It is based on Ion Torrent Semiconductor Sequencing.

Ion Torrent PGM System
Image of PGM: by ThermoFisher Scientific

PGM System is available in the following models:
  • PGM 314 Chip
  • PGM 316 Chip
  • PGM 318 Chip


Manufacturer Thermo Fisher Scientific
Technology Ion Torrent Semiconductor Sequencing
Release date June 2010
Price [2]
Type Benchtop
Weight 30 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ, SFF, BAM, and VCF
Read length Ion Torrent PGM 314 Chip: 200bp to 400bp
Ion Torrent PGM 316 Chip: 200bp to 400bp
Ion Torrent PGM 318 Chip: 200bp to 400bp
Run time Ion Torrent PGM 314 Chip: 2.3 to 3.7 hours
Ion Torrent PGM 316 Chip: 3 to 4.9 hours
Ion Torrent PGM 318 Chip: 4.4 to 7.3 hours
Reagent cost per Gb [1] Ion Torrent PGM 314 Chip: Unavailable
Ion Torrent PGM 316 Chip: Unavailable
Ion Torrent PGM 318 Chip: Unavailable
Data quality [3] Ion Torrent PGM 314 Chip: >99% aligned/measured accuracy
Ion Torrent PGM 316 Chip: >99% aligned/measured accuracy
Ion Torrent PGM 318 Chip: >99% aligned/measured accuracy
Maximum output per run (Gb)[4] Ion Torrent PGM 314 Chip: 0.10
Ion Torrent PGM 316 Chip: 1.00
Ion Torrent PGM 318 Chip: 2.00
Primary error type [5] Indels
Notes about the specifications

  1. Cost per Gb: The cost per Gb is calculated by dividing the costs of sequencing reagents by the manufacturer’s maximum output per run. For these runs, the manufacturer may have included their own controls and used specific library preparation kits. Actual performance may vary based on sample and library type and quality, loading concentration, and other experimental factors. The sequencing reagent costs used for calculations do not include any other costs associated with preparing the samples or running the instrument, including reagents used for extraction, quality control or library preparation, labor, electricity, lab consumables, storage, etc. Performance metrics and prices are subject to change.
  2. Price: The final price may be different depending on the supplier, the region and any discounts provided through bulk orders or negotiation. Other factors that may influence the final price are warranty options, maintenance contracts, possible trade-ins of older instruments, and any financing arrangements chosen.
  3. Data quality: This is the maximum data quality that the instrument can offer based on manufacturer’s specifications and optimizations. The quality of a specific run will depend on multiple factors, including sample quality, sample quantity, library prep protocol, run conditions, etc.
  4. Maximum output: This is the maximum output of a full instrument run. This number is based on manufacturer’s specifications and optimizations.
  5. Primary error type: This is the most common type of error that may occur due to sequencing. Other types of error may occur as well.

More about the PGM System

The Ion PGM System, launched by Thermo Fisher Scientific in 2010, was a member of the benchtop sequencer category of the next-generation sequencing (NGS) market. This segment caters to researchers who are new to NGS or have low-to-mediate throughput needs. It has since been discontinued and has been succeeded by the Ion Torrent S5 and Genexus Systems, which offer higher output.

Key Innovations

The PGM system boasted several key innovations:

  • Semiconductor chip technology: Unlike flow cells used in some NGS platforms, the PGM utilized semiconductor chips. This allows for miniaturization, leading to a smaller instrument footprint and faster run times (approximately 2 hours at the low end).
  • Bead-based amplification: Ion Torrent employs beads coated with adaptor complementary sequences. After DNA is fragmented, these templates are mixed with the small beads, PCR reagents and DNA polymerases. Amplification is then performed on the beads through emulsion PCR and the enriched beads are placed on Ion Chips.

Features and Technologies

  • Read length: Up to 400 base pairs (bp)
  • Average accuracy: >99% aligned/measured accuracy
  • Chip: The Ion 314, 316 and 318 Chips can be used

Intended Uses and Specific Applications

  • Targeted Sequencing: This application is ideal for researchers investigating specific sets of genes associated with diseases, phenotypes, or drug targets. Ion AmpliSeq panels are suitable here.
  • Virus Sequencing: Virus sequencing allows researchers to study the genomes of specific viruses-of-interest, which is especially useful for infectious disease research. Using the Ion AmpliSeq Designer to configured a panel specific to a virus would work here.
  • Small RNA Sequencing: MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in gene regulation. The Ion Total RNA-Seq Kit v2 would be appropriate for this.

Comparison with Competing Instruments

  • Illumina iSeq 100: The iSeq 100 offers comparable output along with offering paired end reads as well as single read, but the run times and read lengths themselves are shorter than the Ion PGM System.
  • Complete Genomics DNBSEQ-E25: While the DNBSEQ-E25 boasts significantly higher throughput and paired end reads, it has slower run times, and shorter read lengths than the Ion PGM System. Additionally, the PGM system offers a simpler library preparation workflow.

Special Considerations

  • Discontinued Instrument: It's important to note that the Ion PGM System has been discontinued. While technical support and consumables might still be available for a time, researchers looking to invest in a new NGS platform should consider Thermo Fisher's successor, the Ion Torrent S5 system, or instruments from alternate manufacturers.
  • Ideal for Past Projects: The PGM might still be valuable for laboratories continuing projects initiated on the platform.
  • Advantages: Even with discontinuation in mind, the PGM system's cost-effectiveness, fast run times, and simple workflows remain significant advantages for smaller-scale projects in the targeted sequencing or small RNA analysis space.

Need sequencing done on a Ion Torrent PGM System or a specific instrument? Tell us about your project here, and we'll connect you with a qualified provider.

This information on this page is up-to-date as of May 9, 2024 and based on the spec sheets published by the manufacturer.