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Thermo Fisher Scientific, Ion PGM Dx System

Thermo Fisher Scientific, Ion PGM Dx System

Next-generation sequencing instruments, December 2017

Contact Information

Thermo Fisher Scientific
5791 Van Allen Way
Carlsbad, CA 92008

Name of instrument Ion PGM Dx System
Name of model/Model has been upgraded —/no
Country where designed/Manufactured/FDA cleared or approved U.S./Singapore/listed
First year sold in U.S./Outside U.S./First year installed 2014/2014/2014
Dimensions in inches (H × W × D)/Footprint of all instrumentation and computing hardware 21 × 24 × 20/8 square feet
Equipment supplied with system/Automation for library preparation Ion PGM Dx Sequencer, Chip Minifuge, and Wireless Scanner; Ion OneTouch Dx Instrument and ES Dx Instrument; Ion Torrent Server with Ion PGM Dx Torrent Suite software/no
Necessary equipment not included with system and additional cost Veriti Dx Thermal Cycler (or equivalent)
Bioinformatics tools provided/For use by biologist or bioinformatician Ion PGM Dx Torrent Suite Software/—
Supplied with UPS/Entire workflow can occur in same lab no/yes
Clean room requirements/Electrical connection no/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) —/$115,000
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/~5 days
Training location/Follow-up training available on site/yes, extra charge
Instrument core performance:
Maximum No. of libraries amplified in single amplification event 16
Read length/Percent bases >Q30 up to 200 bp/—
Paired-end capability/Tag lengths/Spans
Fragment/Tag lengths/Spans yes/up to 200 bp/—
Mate-pair/Tag lengths/Spans
Single-end/Tag lengths/Spans yes/up to 200 bp/—
RNA sequencing/Tag lengths/Spans
ChIP sequencing/Tag lengths/Spans
Bisulfite sequencing/Tag lengths/Spans
Output per run up to 1Gb; 200 bp workflow on Ion 318 Dx chip
Total time from library construction to variant calling to achieve output per run/Technical bench time/Bioinformatics time <2 days/<4.5 hours/<6 hours
Sample preparation:
Total time for generating standard gDNA library <5 hours
• Paired-end
• Fragment <5 hours
• Mate-pair
• Single-end <5 hours
• RNA sequencing
• ChIP sequencing
• Bisulfite sequencing
Hands-on time each:
• Paired-end
• Fragment <2 hours
• Mate-pair
• Single-end <2 hours
• RNA sequencing
• ChIP sequencing
• Bisulfite sequencing
Equipment required for library construction Veriti Dx Thermal Cycler (or equivalent)
Reagents and controls:
Cost per run ~$2,250 on Ion 318 Dx chip for 16 samples
Cost per sample* ~$140
Reagent tracking method on instrument barcode reader
Information contained in tracking method external barcode reader for sample and reagent tracking and expiration date, lot, and part numbers
Reagent shipping conditions/Storage conditions -20°C, 4°C, and ambient/-20°C, 4°C, and ambient
Shelf life of amplification and sequencing reagents 1 year
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/automated
Total time required for setup of amplification, sequencing, and variant calling steps <4.5 hours
Maximum No. of libraries sequenced in a single run up to 16
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 yes/—/run initialization
System offers secondary analysis software developed by instrument vendor no
Variant report generated directly on instrument no
Third-party analysis software available no
Ability of software to detect mutations substitutions, indels
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) delivers highly reproducible and accurate genetic variant analysis with 10 ng of input DNA derived from whole blood coupled with highly multiplexed amplicon generation using Ion AmpliSeq technology (RUO); produces accurate long reads with more than 99% raw-read accuracy; provides the speed and simplicity of the Ion Torrent platform; affordable and flexible sequencer that meets a range of applications, budgets, and project sizes; provides rapid turnaround time from sample to variant analysis in <2 days; integrated secure software enables role-based workflows and supports tracking of samples to reagents management and variant analysis throughout each run; provides traceability and auditable run analysis—a necessary part of 21 CFR Part 11 compliance
*inclusive of sample prep, for multiple configurations, using 1 Mb and 30x average coverage per sample
Note: a dash in lieu of an answer means company did not answer question or question is not applicable
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