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Thermo Fisher Scientific, Ion Personal Genome Machine (PGM) System (RUO)

Thermo Fisher Scientific, Ion Personal Genome Machine (PGM) System (RUO)

Next-generation sequencing instruments, December 2017

Contact Information

Thermo Fisher Scientific
5791 Van Allen Way
Carlsbad, CA 92008

Name of instrument Ion Personal Genome Machine (PGM) System (RUO)
Name of model/Model has been upgraded 508-U001/yes
Country where designed/Manufactured/FDA cleared or approved U.S./U.S., Singapore/no
First year sold in U.S./Outside U.S./First year installed 2010/2010/2010
Dimensions in inches (H × W × D)/Footprint of all instrumentation and computing hardware 21 × 20 × 24/5 square feet
Equipment supplied with system/Automation for library preparation Dell Precision T7500 Server/yes
Necessary equipment not included with system and additional cost general laboratory supplies
Bioinformatics tools provided/For use by biologist or bioinformatician Ion Reporter, Torrent Suite software, Torrent Circuit/biologist
Supplied with UPS/Entire workflow can occur in same lab no/yes
Clean room requirements/Electrical connection no/standard voltage 100–240 VAC, 50–60 Hz, 9 VA
List price/Total list price for equipment needed to perform simplest and fastest workflow from amplification through variant calling (not typically found in lab) $37,500/$50,000
Purchase options purchase or lease (financing available)
Warranties offered 1 year included, extended warranty available
Training included/Total time for standard install and basic training yes/<2 days
Training location/Follow-up training available on and off site/yes, extra charge
Instrument core performance:
Maximum No. of libraries amplified in single amplification event 384 samples, by employing custom barcoding
Read length/Percent bases >Q30 200 bp, 400 bp/Manfred
Paired-end capability/Tag lengths/Spans
Fragment/Tag lengths/Spans yes/200 bp, 400 bp/100–400 bp
Mate-pair/Tag lengths/Spans yes/200 bp, 400 bp/100–400 bp
Single-end/Tag lengths/Spans yes/200 bp, 400 bp/100–400 bp
RNA sequencing/Tag lengths/Spans yes/200 bp, 400 bp/100–400 bp
ChIP sequencing/Tag lengths/Spans yes/200 bp, 400 bp/100–400 bp
Bisulfite sequencing/Tag lengths/Spans no/customer demonstrated/100–400 bp
Output per run 100 Mb (Ion 314 chip, 400 bp kit); 1Gb (Ion 316 chip, 400 bp kit); 2 Gb (Ion 318 chip, 400 bp kit)
Total time from library construction to variant calling to achieve output per run/Technical bench time/Bioinformatics time <1 day/<2 hours/20 minutes
Sample preparation:
Total time for generating standard gDNA library <2 hours
• Paired-end
• Fragment <2 hours
• Mate-pair 2.5 days
• Single-end <2 hours
• RNA sequencing <6 hours
• ChIP sequencing customer demonstrated
• Bisulfite sequencing customer demonstrated
Hands-on time each:
• Paired-end
• Fragment ~10 minutes (Ion AmpliSeq 2.0)
• Mate-pair ~6 hours
• Single-end ~10 minutes (Ion AmpliSeq 2.0)
• RNA sequencing ~40 minutes (whole transciptome library, small RNA library); ~55 minutes for small RNA library with enrichment
• ChIP sequencing customer demonstrated
• Bisulfite sequencing
Equipment required for library construction standard laboratory equipment
Reagents and controls:
Cost per run $349 (Ion 314 chip), $549 (Ion 316 chip), $749 (Ion 318 chip)
Cost per sample* 30x coverage, 200 bp: $88.06 (Ion 318 chip), $213.75 (Ion 316 chip), $750.83 (Ion 314 chip)
Reagent tracking method on instrument barcode reader
Information contained in tracking method external barcode reader for sample and reagent tracking information
Reagent shipping conditions/Storage conditions -20°C, 4°C, and ambient/-20°C, 4°C, and ambient
Shelf life of amplification and sequencing reagents 9 months
Controls introduced during creation of library/Sequencing control avail. yes/yes
Capable of complete walkaway automation for amplification, sequencing, and variant calling yes
Remote system monitoring yes
Instrument control software and devices to start run/for data analysis 10 minutes/20 minutes–4.5 hours (100 Mb–2 Gb)
Total time required for setup of amplification, sequencing, and variant calling steps <30 minutes
Maximum No. of libraries sequenced in a single run 384
Types of maintenance plans available AB Assurance, AB Complete, AB Maintenance Plus, AB Maintenance Service
No. of field apps scientists and engineers based in U.S.
Weekly maintenance required/Monthly/Pre-run weekly cleaning/—/instrument initialization
System offers secondary analysis software developed by instrument vendor yes
Variant report generated directly on instrument yes
Third-party analysis software available yes (AB Assurance, AB Complete, AB Maintenance Plus, AB Maintenance Service)
Ability of software to detect mutations substitutions, indels, copy number changes, fusion transcript**
Total No. of peer-reviewed publications for this platform >845 based on RUO platform
Published applications in pathology-related research >195 based on RUO platform
Fastest published turnaround time from sample to analyzed result <15 hours based on RUO platform
Lowest published variant sensitivity level .01 fresh frozen; .02 FFPE based on RUO platform
Distinguishing features of sequencer (supplied by company) affordable, accurate, and flexible sequencer meets a range of research applications, budgets, project sizes, and input DNA amounts (as low as 10 ng of FFPE-derived sample) by employing scalable semiconductor technology (no laser or camera) with the Ion 3 series chips, coupled with highly multiplexed amplicon generation using Ion AmpliSeq technology; delivers fast run times, enabling a single-day workflow from sample to annotated variants for gene-panel sequencing featuring Ion AmpliSeq; produces accurate long reads with more than 99% raw-read accuracy; majority of bases at ≥Q30
*inclusive of sample prep, for multiple configurations, using 1 Mb and 30x average coverage per sample **Ion Reporter
Note: a dash in lieu of an answer means company did not answer question or question is not applicable
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