First year sold in U.S./First year installed in U.S.
System sold internationally
Dimensions of sequencer (H × W × D)/Footprint of sequencer
Accessory equipment supplied with sequencer at no cost/Total footprint with accessory equipment
Type of computer supplied with sequencer
Analysis options provided with sequencer
Where library preparation is performed
Bioinformatics tools provided with sequencer
Sequencer supplied with UPS (uninterruptible power supply)
Electrical connection required for sequencer
List price of entire sequencer and necessary components
Purchase options
Warranties offered
Training included/Total time for basic training per operator
Training location/Follow-up training available
Maximum No. of samples amplified in a single amplification event
Read length/Percent bases >Q30
Paired-end capability/Tag lengths/Spans
Fragment/Tag lengths/Spans
Mate pair/Tag lengths/Spans
Single end/Tag lengths/Spans
RNA sequencing/Tag lengths/Spans
ChIP sequencing/Tag lengths/Spans
Bisulfite sequencing/Tag lengths/Spans
Maximum No. of reads or fragments sequenced per single-end run
Maximum No. of reads or fragments sequenced per paired-end run
Total No. of nucleotides (bases) sequenced per run
Wet lab bench time for sequencing preparation
Sequencing run time
Total time for generating standard gDNA library
• Paired end
• Fragment
• Mate pair
• Single end
• RNA sequencing
• ChIP sequencing
• Bisulfite sequencing
Hands-on time for the following
• Paired end
• Fragment
• Mate pair
• Single end
• RNA sequencing
• ChIP sequencing
• Bisulfite sequencing
Cost of sequencing reagents
Reagent tracking method
• Type of reagent information tracked
Shipping conditions for amplification/sequencing reagents
Storage conditions for amplification/sequencing reagents
Shelf life of amplification/sequencing reagents
System requires a control sample on sequencing run
• Company offers a sequencing control
Sequencing system control software and devices to start run/for data analysis
Complete walkaway automation for amplification, sequencing, and variant calling
Remote system monitoring
Total time required for setup of amplification, sequencing, and variant calling steps
Maximum No. of libraries sequenced in a single run
System includes secondary data-analysis software developed by company
System includes post-sequencing data-analysis software
Mutations detectable via data-analysis software
System can generate a variant report
Types of maintenance plans available/mean time between failures
No. of field application scientists and engineers based in U.S.
Maintenance required
• Weekly
• Monthly
• Pre-run
Distinguishing features of NGS system (supplied by company)
Note: a dash in lieu of an answer means company did not answer question or question is not applicable
Details
1
Illumina
info@illumina.com
San Diego, CA
858-202-4500
www.illumina.com
iSeq 100
research use/not required
U.S./Singapore
2018/2018
yes
16.8 × 12 × 13 in./1.1 sq. ft.
system test cartridge/—
computer for analysis and operations combined
onboard, cloud based
wet bench
Local Run Manager, BaseSpace
no
90–264 VAC at 47–63 Hz
$19,900
purchase
first year included with purchase; extended warranty available
no (customer installable)/<1 day
at customer site/yes (extra charge)
384 samples (>384 samples with custom barcodes)
2 × 150 bp/80%
yes/2 × 150 bp/—
yes/2 × 150 bp/—
yes/2 × 150 bp/—
yes/1 × 300 bp/—
yes/2 × 150 bp/—
yes/2 × 150 bp/—
yes/2 × 150 bp/—
>4 million
>8 million
up to 1.2 Gb
10 minutes
<19 hours
<3.5 hours (with Illumina DNA Prep)
<3.5 hours (with Illumina DNA Prep)
<7 hours (with AmpliSeq for Illumina); <6.5 hours (with Illumina DNA Prep with Enrichment)
—
<1 day (with TruSeq Small RNA)
<9 hours
<1.5 days (with TruSeq ChIP)
—
<1.5 hours
<1.5 hours (with AmpliSeq for Illumina); <2 hours (with Illumina DNA Prep with Enrichment)
—
<4 hours
<3 hours
—
—
$569 (pricing based on iSeq 8-pack reagent kit)
RFID
serial number, expiration date, lot and part numbers, number of cycles
—/dry ice
—/cartridge: -15°– -25°C; flow cell: 2°– 8°C
—/guaranteed 3 months
optional
yes (additional charge)
iSeq Control Software/Local Run Manager, BaseSpace
yes
yes
5 minutes
384 samples (>384 samples with custom barcodes)
yes (Local Run Manager, BaseSpace)
yes (included with purchase: Local Run Manager)
substitutions, indels, copy number changes
no
Advanced Exchange Service Plan/—
>500
—
system check with provided cartridge
—
low capital cost to obtain highly accurate results with sequencing-by-synthesis technology; small instrument footprint, clustering and sequencing all in one, analysis onboard or in the cloud; 19-hour run time for overnight results; dry box–optics on the flow cell and fluidics in the cartridge; dry box–optics on the flow cell and fluidics in the cartridge
2
Illumina
info@illumina.com
San Diego, CA
858-202-4500
www.illumina.com
MiniSeq System
research use/not required
U.S./Singapore
2016/2016
yes
20.4 × 18 × 18.9 in./2.4 sq. ft.
system test cartridge/—
computer for analysis and operations combined
onboard, cloud based
wet bench
Local Run Manager, BaseSpace
no
100–240 VAC at 50–60 Hz
$49,500
purchase, lease, reagent rental
first year included with purchase; extended warranty available
yes/<1 day
at customer site/yes (extra charge)
384 samples (>384 samples with custom barcodes)
2 × 150 bp/80%
yes/2 × 150 bp/—
yes/2 × 150 bp/—
yes/2 × 150 bp/—
yes/1 × 300 bp/—
yes/2 × 150 bp/—
yes/2 × 150 bp/—
yes/2 × 150 bp/—
up to 25 million
up to 50 million
up to 7.5 Gb
10 minutes
~5–24 hours
<3.5 hours (with Illumina DNA Prep)
<3.5 hours (with Illumina DNA Prep)
<7 hours (with AmpliSeq for Illumina); <6.5 hours (with Illumina DNA Prep with Enrichment)
—
<1 day (with TruSeq Small RNA)
<9 hours
<1.5 days (with TruSeq ChIP)
—
<1.5 hours
<1.5 hours (with AmpliSeq for Illumina); <2 hours (with Illumina DNA Prep with Enrichment)
—
<4 hours
<3 hours
—
—
$717–$2,012
RFID
serial number, expiration date, lot and part numbers, number of cycles
—/dry ice
—/cartridge: -15°– -25°C; flow cell: 2°– 8°C
—/guaranteed 3 months
optional
yes (additional charge)
MiniSeq Control Software/Local Run Manager, BaseSpace
yes
yes
10 minutes
384 samples (>384 samples with custom barcodes)
yes (Local Run Manager, BaseSpace)
yes (included with purchase: BaseSpace)
substitutions, indels, copy number changes
no
parts only, bronze, silver, gold, dedicated on site/—
>500
—
system check with provided cartridge
—
affordable to acquire, cost-efficient to run, even with low numbers of samples; push-button operation and simple data analysis; push-button operation and simple data analysis
3
Illumina
info@illumina.com
San Diego, CA
858-202-4500
www.illumina.com
MiSeq System
research use/not required
U.S./Singapore
2011/2011
yes
20.6 × 27 × 22.2 in./4.2 sq. ft.
system test cartridge/—
computer for analysis and operations combined
onboard, cloud based
wet bench
Local Run Manager, MiSeq Reporter, BaseSpace
no
100–240 VAC at 50–60 Hz
$99,000
purchase, lease, reagent rental
first year included with purchase; extended warranty available
yes/<1 day
at customer site/yes (extra charge)
384 samples (>384 samples with custom barcodes)
2 × 300 bp/70%
yes/2 × 300 bp/—
yes/2 × 300 bp/—
yes/2 × 150 bp/—
yes/1 × 300 bp/—
yes/2 × 300 bp/—
yes/2 × 300 bp/—
yes/2 × 300 bp/—
up to 25 million
up to 50 million
up to 15 Gb
10 minutes
~5–56 hours
<3.5 hours (with Illumina DNA Prep)
<3.5 hours (with Illumina DNA Prep)
<7 hours (with AmpliSeq for Illumina); <6.5 hours (with Illumina DNA Prep with Enrichment)
—
<1 day (with TruSeq Small RNA)
<9 hours
<1.5 days (with TruSeq ChIP)
—
<1.5 hours
<1.5 hours (with AmpliSeq for Illumina); <2 hours (with Illumina DNA Prep with Enrichment)
—
<4 hours
<3 hours
—
—
$378–$1,989
RFID
serial number, expiration date, lot and part numbers, number of cycles
—/dry ice
—/cartridge: -15°– -25°C; flow cell: 2°– 8°C
—/guaranteed 3 months
optional
yes (additional charge)
MiSeq Control Software/Local Run Manager, MiSeq Reporter, BaseSpace
yes
yes
10 minutes
384 samples (>384 samples with custom barcodes)
yes (Local Run Manager, BaseSpace)
yes (included with purchase: BaseSpace)
substitutions, indels, copy number changes
no
parts only, bronze, silver, gold, dedicated on site/—
>500
—
system check with provided cartridge
—
quality scores with >70% of bases higher than Q30 at 2 × 300 bp and >85% bases higher than Q30 at 2 × 75 bp; simple, streamlined workflow with as little as 30 minutes hands-on time from sample to answer; simple, streamlined workflow with as little as 30 minutes hands-on time from sample to answer; simple, streamlined workflow with as little as 30 minutes hands-on time from sample to answer
4
Illumina
info@illumina.com
San Diego, CA
858-202-4500
www.illumina.com
MiSeqDx System
in vitro diagnostic and research use/yes
U.S./U.S.
2013/2013
yes
20.6 × 27 × 22.2 in./4.2 sq. ft.
—
computer for analysis and operations combined
onboard, cloud based
wet bench
Local Run Manager, MiSeq Reporter, BaseSpace
yes (extra charge)
100–240 VAC at 50–60 Hz, 10 A, 400 W
$125,000
purchase, lease, reagent rental
first year included with purchase; extended warranty available
yes/<1 day
at customer site/yes (extra charge)
384 samples (>384 samples with custom barcodes)
up to 2 × 300 bp/80% (for 2 × 150 bp)
yes/up to 2 × 300 bp/up to 550 bp
yes/up to 2 × 300 bp/up to 550 bp
yes/up to 2 × 150 bp/2–12 kb
yes/up to 1 × 300 bp/up to 300 bp
yes/up to 2 × 300 bp/up to 550 bp
yes/up to 2 × 300 bp/up to 550 bp
yes/up to 2 × 300 bp/up to 550 bp
>15 million
>30 million
up to 7.5 Gb
10 minutes
<28 hours
<3.5 hours (with Illumina DNA Prep)
<3.5 hours (with Illumina DNA Prep)
<7 hours (with AmpliSeq for Illumina); <6.5 hours (with Illumina DNA Prep with Enrichment)
—
<1 day (with TruSeq Small RNA)
<9 hours
<1.5 days (with TruSeq ChIP)
—
<1.5 hours (with Illumina DNA Prep)
<1.5 hours (with AmpliSeq for Illumina); <2 hours (with Illumina DNA Prep with Enrichment)
—
<4 hours (with TruSeq Small RNA)
<3 hours
—
—
$2,440
RFID
serial number, expiration date, lot and part numbers, number of cycles
—/box 1: dry ice; box 2: gel pack
—/box 1: -15°– -25°C; box 2: 2°– 8°C
—/guaranteed 6 months
optional
yes (additional charge)
MiSeq Control Software/Local Run Manager, MiSeq Reporter, BaseSpace
yes
yes
10 minutes
384 samples (>384 samples with custom barcodes)
yes (MiSeq Reporter, Local Run Manager, BaseSpace)
—
substitutions, indels, copy number changes
yes
parts only, bronze, silver, gold, Dx, dedicated on site/—
>500
none (manual wash if instrument idle for 7 days)
maintenance wash
none (post-run wash required after every run)
FDA-regulated NGS platform allows clinical diagnostics in Dx mode and clinical research applications in research mode; FDA-regulated content includes MiSeqDx cystic fibrosis 139-variant assay, MiSeqDx cystic fibrosis clinical sequencing assay; leverages proven MiSeq technology
5
Illumina
info@illumina.com
San Diego, CA
858-202-4500
www.illumina.com
NextSeq 550Dx System
in vitro diagnostic and research use/yes
U.S./Singapore
2017/2017
yes
23 × 21 × 25 in./3.6 sq. ft.
—
computer for analysis and operations combined
onboard, cloud based
wet bench
Local Run Manager, BaseSpace
no
100–120 VAC at 50–60 Hz
$347,000
purchase, lease, reagent rental
first year included with purchase; extended warranty available
yes/2 days
at customer site/yes (extra charge)
384 samples (>384 samples with custom barcodes)
up to 2 × 150 bp/75%
yes/up to 2 × 150 bp/up to 350 bp
yes/up to 2 × 150 bp/up to 350 bp
yes/up to 2 × 150 bp/2–12 kb
yes/up to 1 × 300 bp/up to 300 bp
yes/up to 2 × 150 bp/up to 350 bp
yes/up to 2 × 150 bp/up to 350 bp
yes/up to 2 × 150 bp/up to 350 bp
>300 million
>600 million
up to 120 Gb
10 minutes
<36 hours
<3.5 hours (with Illumina DNA Prep)
<3.5 hours (with Illumina DNA Prep)
<7 hours (with AmpliSeq for Illumina); <6.5 hours (with Illumina DNA Prep with Enrichment)
—
<1 day (with TruSeq Small RNA)
<9 hours
<1.5 days (with TruSeq ChIP)
—
<1.5 hours (with Illumina DNA Prep)
<1.5 hours (with AmpliSeq for Illumina); <2 hours (with Illumina DNA Prep with Enrichment)
—
<4 hours (with TruSeq Small RNA)
<3 hours
—
—
$2,370–$6,841
RFID
serial number, expiration date, lot and part numbers, number of cycles
—/dry ice, gel pack, ambient (variable based on product)
NextSeq 550Dx Control Software and Operating Software/Local Run Manager, BaseSpace
yes
yes
10 minutes
384 samples (>384 samples with custom barcodes)
yes (BaseSpace)
yes (included with purchase)
substitutions, indels, copy number changes
yes
parts only, bronze, silver, gold, Dx, dedicated on site/—
>500
none (manual wash if instrument idle for 2 weeks)
none
none (automatic wash completed after every run)
FDA-regulated NGS platform allows clinical diagnostics in Dx mode and clinical research applications in research mode; FDA-regulated content includes NextSeq 550Dx high-output reagent kit v2.5, Illumina DNA Prep with Enrichment Dx kit; flexible output for sample multiplexing and different research applications, from targeted panels to whole genome
Company
Email
City, State
Phone
Website
Name of system
System application/FDA cleared or approved
Country where designed/Manufactured
First year sold in U.S./First year installed in U.S.
System sold internationally
Dimensions of sequencer (H × W × D)/Footprint of sequencer
Accessory equipment supplied with sequencer at no cost/Total footprint with accessory equipment
Type of computer supplied with sequencer
Analysis options provided with sequencer
Where library preparation is performed
Bioinformatics tools provided with sequencer
Sequencer supplied with UPS (uninterruptible power supply)
Electrical connection required for sequencer
List price of entire sequencer and necessary components
Purchase options
Warranties offered
Training included/Total time for basic training per operator
Training location/Follow-up training available
Maximum No. of samples amplified in a single amplification event
Read length/Percent bases >Q30
Paired-end capability/Tag lengths/Spans
Fragment/Tag lengths/Spans
Mate pair/Tag lengths/Spans
Single end/Tag lengths/Spans
RNA sequencing/Tag lengths/Spans
ChIP sequencing/Tag lengths/Spans
Bisulfite sequencing/Tag lengths/Spans
Maximum No. of reads or fragments sequenced per single-end run
Maximum No. of reads or fragments sequenced per paired-end run
Total No. of nucleotides (bases) sequenced per run
Wet lab bench time for sequencing preparation
Sequencing run time
Total time for generating standard gDNA library
• Paired end
• Fragment
• Mate pair
• Single end
• RNA sequencing
• ChIP sequencing
• Bisulfite sequencing
Hands-on time for the following
• Paired end
• Fragment
• Mate pair
• Single end
• RNA sequencing
• ChIP sequencing
• Bisulfite sequencing
Cost of sequencing reagents
Reagent tracking method
• Type of reagent information tracked
Shipping conditions for amplification/sequencing reagents
Storage conditions for amplification/sequencing reagents
Shelf life of amplification/sequencing reagents
System requires a control sample on sequencing run
• Company offers a sequencing control
Sequencing system control software and devices to start run/for data analysis
Complete walkaway automation for amplification, sequencing, and variant calling
Remote system monitoring
Total time required for setup of amplification, sequencing, and variant calling steps
Maximum No. of libraries sequenced in a single run
System includes secondary data-analysis software developed by company
System includes post-sequencing data-analysis software
Mutations detectable via data-analysis software
System can generate a variant report
Types of maintenance plans available/mean time between failures
No. of field application scientists and engineers based in U.S.
Maintenance required
• Weekly
• Monthly
• Pre-run
Distinguishing features of NGS system (supplied by company)
Note: a dash in lieu of an answer means company did not answer question or question is not applicable
wdt_ID:
Company:
Email:
City, State:
Phone:
Website:
Name of system:
System application/FDA cleared or approved:
Country where designed/Manufactured:
First year sold in U.S./First year installed in U.S.:
System sold internationally:
Dimensions of sequencer (H × W × D)/Footprint of sequencer:
Accessory equipment supplied with sequencer at no cost/Total footprint with accessory equipment:
Type of computer supplied with sequencer:
Analysis options provided with sequencer:
Where library preparation is performed:
Bioinformatics tools provided with sequencer:
Sequencer supplied with UPS (uninterruptible power supply):
Electrical connection required for sequencer:
List price of entire sequencer and necessary components:
Purchase options:
Warranties offered:
Training included/Total time for basic training per operator:
Training location/Follow-up training available:
Maximum No. of samples amplified in a single amplification event:
Read length/Percent bases >Q30:
Paired-end capability/Tag lengths/Spans:
Fragment/Tag lengths/Spans:
Mate pair/Tag lengths/Spans:
Single end/Tag lengths/Spans:
RNA sequencing/Tag lengths/Spans:
ChIP sequencing/Tag lengths/Spans:
Bisulfite sequencing/Tag lengths/Spans:
Maximum No. of reads or fragments sequenced per single-end run:
Maximum No. of reads or fragments sequenced per paired-end run:
Total No. of nucleotides (bases) sequenced per run:
Wet lab bench time for sequencing preparation:
Sequencing run time:
Total time for generating standard gDNA library:
• Paired end:
• Fragment:
• Mate pair:
• Single end:
• RNA sequencing:
• ChIP sequencing:
• Bisulfite sequencing:
Hands-on time for the following:
• Paired end:
• Fragment:
• Mate pair:
• Single end:
• RNA sequencing:
• ChIP sequencing:
• Bisulfite sequencing:
Cost of sequencing reagents:
Reagent tracking method:
• Type of reagent information tracked:
Shipping conditions for amplification/sequencing reagents:
Storage conditions for amplification/sequencing reagents:
Shelf life of amplification/sequencing reagents:
System requires a control sample on sequencing run :
• Company offers a sequencing control:
Sequencing system control software and devices to start run/for data analysis:
Complete walkaway automation for amplification, sequencing, and variant calling:
Remote system monitoring:
Total time required for setup of amplification, sequencing, and variant calling steps:
Maximum No. of libraries sequenced in a single run:
System includes secondary data-analysis software developed by company:
System includes post-sequencing data-analysis software:
Mutations detectable via data-analysis software:
System can generate a variant report:
Types of maintenance plans available/mean time between failures:
No. of field application scientists and engineers based in U.S.:
Maintenance required:
• Weekly:
• Monthly:
• Pre-run:
Distinguishing features of NGS system (supplied by company):
Note: a dash in lieu of an answer means company did not answer question or question is not applicable:
Laboratory-developed testing as it relates to next-generation sequencing was up first in the NGS conversation led online by CAP TODAY publisher Bob McGonnagle on March 19. Other topics: in-house NGS testing, artificial intelligence, and bioinformatics. “There’s a reality now where bioinformatics is solid, stable, and reliable,” said José Luis Costa, PhD, of Thermo Fisher Scientific.
May 2024—Laboratory-developed tests are top of mind for many people in laboratories. People who use next-generation sequencing panels and machines are, in many cases, heavily involved in laboratory-developed tests, in addition to the panels that many companies offer. Larissa Furtado, talk to us about the role of laboratory-developed tests in the context of next-generation sequencing testing.
Larissa V. Furtado, MD, molecular pathologist, St. Jude Children’s Research Hospital: They’re essential. In our practice, all the oncology NGS tests we have in-house are laboratory-developed tests. We don’t have FDA-approved tests.
Next-generation sequencing is a technology that evolves quickly. You can test multiple genomic anomalies at different genes simultaneously and multiple samples at one time. The flexibility of LDTs gives laboratories the ability to develop their own tests and update them according to their needs. I am in a pediatric hospital where most of our patients are in clinical trials, so we have a comprehensive testing approach, which may be different from other centers or smaller laboratories that use more targeted testing. With the existing accreditation requirements and framework, pathologists are well positioned to bring in these tests and ensure quality.