Next-Generation Sequencing Systems Product Guide, 2023

Company Name:

Name of system:

wdt_ID	Company Name	Email Address	City, State	Phone Number	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	• Paired end	• Fragment	• Mate pair	• Single end	• RNA sequencing	• ChIP sequencing	• Bisulfite sequencing	Library preparation equipment offered or supplied	Cost of sequencing reagents per run	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.	• Weekly	• Monthly	• Pre-run	Distinguishing features of NGS system (supplied by company)
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)/	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); <2 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);	—	<4 hours	<3 hours	—	—	none (standard lab equipment)	$548 (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
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/	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); <2 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);	—	<4 hours	<3 hours	—	—	none (standard lab equipment)	$680–$1,909	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
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/	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); <2 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);	—	<4 hours	<3 hours	—	—	none (standard lab equipment)	$359–$1,887	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
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/	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		<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	—	—	none	$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		<3.5 hours (with Illumina DNA Prep)	<3.5 hours (with Illumina DNA Prep)	<7 hours (with AmpliSeq for Illumina);	—	<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); <6.5 hours (with Illumina DNA Prep with Enrichment)	—	<4 hours (with TruSeq Small RNA)	<3 hours	—	—	none (standard lab equipment)	$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)	—/reagent cartridge, HT1 buffer: -15°– -25°C; flow cell: 2°– 8°C; buffer cartridge: 15°– 30°C	—/guaranteed 6 months	yes	yes (additional charge)	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 Name					Name of system

The outlook for in-house next-generation sequencing

Bringing next-generation sequencing in-house was at the center of a March 27 roundtable led by CAP TODAY publisher Bob McGonnagle, with costs, reimbursement, equity, and the electronic health record part of the conversation. Jeremy Segal, MD, PhD, of the University of Chicago, explains why the Genomics Organization for Academic Laboratories was formed. “By lowering barriers and encouraging cooperation,” he said, “we’ve seen our labs increase the pace of development and the quality of the assays they’re bringing on.”

There’s increasing interest in bringing next-generation sequencing in-house as opposed to sending it to a reference laboratory. While there are costs associated with bringing it in-house, if you look at total cost of the test and turnaround time, it’s an even horse race or slightly preferable to bring it in-house. Luca Quagliata, would you agree with that?

Luca Quagliata, BCMAS, PhD, VP and global head of medical affairs, Thermo Fisher Scientific: I do agree. Cost is an important component of being able to bring these tests in-house. We often think cost is driven only by reagents, but it’s not the component that most impacts overall expenditure. Cost of personnel to perform the analysis is equally important. With solutions that are going toward fully automated or semiautomated systems, you can free hands, better utilize the lab workforce, and effectively maximize budget.

The other part of the equation is the cost of treatment. A long turnaround time to results usually means placing the patient on any available treatment, which is not necessarily the best option. If a suboptimal treatment decision is made and subsequently a treatment change needs to be forced, the patient will pay for it in terms of outcomes. The health care system will probably also bear additional costs because those patients usually experience more side effects, which means rehospitalization costs and a prolonged process.

Fiona Nohilly, can you comment on the movement to in-house and how you look at the total cost of performing the test for the benefit of patients?

Fiona Nohilly, senior manager, product marketing, Americas regional marketing, Illumina: We are thinking about the total cost of ownership from sample and library preparation through sequencing and analysis. Since we last met for this roundtable, we have launched three new platforms.