The last three years have been anything but static for next-generation sequencing (NGS) companies. Several competitors have launched new sequencing technologies that have taken direct, and often public, aim at the offerings of the longtime NGS leader Illumina—a company that is only a few months removed from an eventful 2023. Besides sustaining changes in its C-suite leadership and business operations, Illumina started reshaping its board.
In 2024, we will learn if sequencing customers are comfortable enough to switch from Illumina to competing companies. Illumina’s rivals include PacBio (which launched the Onso, a benchtop short-read sequencing platform, at a party featuring Maroon 5 in October 2022); Singular Genomics (which rolled out its G4 Sequencing Platform in late 2021); and Element Biosciences (which announced AVITI Sequencing in March 2022).
“[The newer companies] all have some finite chance of going out of business,” said Alex Dickinson, PhD, a former Illumina senior vice president who is now executive chair of Ryght.AI. “They all have incredible burn rates, and we live in an environment where funding is very scarce.” (This comment, and others, was contributed to a recent GEN roundup of what 2024 holds for NGS and genomics.)
As for Illumina, it continues to double down on the NovaSeq X sequencing system it unveiled in 2022 and commercially launched last year. Illumina says that it received 390 orders for NovaSeq systems in 2023 and shipped 352 to customers, including 79 during the fourth quarter.
“NovaSeq X has been the most successful high-throughput product launch in our history,” Illumina CEO Jacob Thaysen, PhD, declared to analysts February 8 on the company’s Q4 2023 earnings call.
Regardless of how Illumina and its rivals fare this year, NGS has only scratched the surface of its commercial potential, according to a report issued by Research and Markets on March 7. The market research firm projects that the NGS market will more than triple over the next seven years, from $10.63 billion this year to $34.19 billion in 2030—sustaining a compound annual growth rate of 18.16%.
This A-List article presents two lists of sequencing instrument providers. One list includes eight companies that provide NGS instruments. The other includes three companies that provide Sanger instruments. (Since one company, Thermo Fisher Scientific, appears in both lists, the total number of sequencing instrument providers is 10.) Each company is listed by name, followed by a short description of recent company activity, including financial activity from 2023 (either revenue—if it had been disclosed—or total capital raised). Because only some of the instrument providers disclose how much revenue they generate from NGS, they are listed alphabetically, not ranked. (The most recent ranking of NGS companies appeared in 2019.)
Besides companies that provide sequencing instruments, the sequencing industry includes companies that provide workflow solutions. Three workflow giants—Agilent Technologies, QIAGEN, and Roche—appear in their own section of this A-List article. (Again, these companies appear alphabetically because they do not specify what portion of their revenues comes from enabling sequencing.)
PROVIDERS OF NGS INSTRUMENTATION
Element Biosciences
Element Biosciences last month announced a series of partnerships focused on workflows for its AVITI System. With Volta Labs, Element will partner to optimize sequencing throughput by launching Volta’s Callisto Sample Prep System for AVITI. With Twist Bioscience, Element will develop the Twist for Element, Exome 2.0 plus Comprehensive Exome Spike-in Workflow for AVITI, an exome sequencing solution. And with Integrated DNA Technologies, Element has launched a suite of adapters, universal blockers, and library amplification primer mixes designed exclusively for AVITI. Element disclosed preliminary 2023 revenues of $25 million in January at the 42nd Annual J.P. Morgan Healthcare Conference.
Illumina
Through its new CEO, Jacob Thaysen, PhD, the longtime NGS giant has laid out its priorities for 2024, which include boosting its “topline” or revenues by increasing placements of all its instruments—especially the NovaSeq X sequencing system, unveiled in 2022—as well as enhancing its commercial processes and driving more sequencing activity. Thaysen’s appointment in September 2023 capped a turbulent year that saw predecessor Francis deSouza resign after a partially successful proxy campaign by Carl C. Icahn. Illumina finished 2023 with a $1.161 billion net loss, improved from 2022’s $4.404 billion net loss, while revenue slid 2% year-over-year to $4.5 billion.
MGI Tech
MGI Tech—whose U.S. subsidiary is Complete Genomics—announced March 4 that Eurofins Genomics has ordered the DNBSEQ-T20×2 (T20) ultra-high throughput sequencer, along with the genomics data center ZTRON Appliance and numerous MGI lab automation products and systems. Launched in February 2023, the T20 is powered by MGI’s DNBSEQ technology and designed to significantly reduce sequencing costs to below $100 per genome when running 50,000 whole genome sequences per year. The T20 aims to address high-throughput processing needs for various types of sequencing technologies. These include whole genome, whole genome bisulfite, single-tube long fragment read, and single-cell sequencing technologies. The same is true for spatiotemporal omics technologies, such as MGI Tech’s Stereo-seq. China’s sluggish economy has affected MGI, which finished last year with a net loss of RMB 597.1 million (about $83 million), compared with net income of RMB 2.03 billion ($282 million) in 2022.
Oxford Nanopore Technologies
Oxford Nanopore Technologies on March 7 announced the early access launch of the PromethION 2 Integrated (P2i), its all-in-one desktop sequencing device. P2i is designed to facilitate real-time base calling and post run analysis directly within the device, eliminating dependency on external computing resources. In December, Oxford Nanopore promoted improvements in DNA sequencing accuracy powered by machine learning–guided enzyme engineering and improved models. The company reached a record of Q28 (99.8 %) in median simplex single molecule accuracy. Oxford Nanopore finished 2023 with a net loss of £154.5 million ($197.4 million) on revenue of £169.7 million ($216.8 million). However, excluding COVID-19 sequencing and the company’s largest customer, The Emirati Genome Program, “underlying” revenue jumped 39% to £149.7 million ($191.5 million).
PacBio
PacBio launched two new high-throughput library preparation kits and workflows optimized for its Revio sequencing system in February. HiFi Prep Kit 96 and HiFi Plex Prep Kit 96 allow users to automate long-read sequencing workflow steps and streamline preparing, pooling, and loading of samples, which according to PacBio will reduce costs 40% and cut workflow time 60%. HiFi Plex Prep Kit 96 customers can run 1,536 samples in a single Revio run. Delivery of the kits is planned for early in the second quarter. PacBio’s net loss dipped 2% in 2023, to $306.735 million, on revenue that soared 56% year-over-year to $200.521 million.
Singular Genomics
Singular Genomics has unveiled an upgrade to its G4 Sequencing Platform—the G4X™ Spatial Sequencer, a high-throughput in situ spatial sequencing platform designed for simultaneous direct RNA sequencing, targeted transcriptomics, proteomics, and fluorescent hematoxylin and eosin stain analysis from formalin-fixed, paraffin-embedded tissues. G4X is expected to be available by the end of 2024. Singular also announced upgrades to G4 that include a higher-throughput F4 Flow Cell estimated to produce 600 million–800 million paired reads per flow cell, potentially doubling the G4 sequencer run output to 3.2 billion reads. F4 is expected to be released in the second half of 2024.
Thermo Fisher Scientific
Thermo Fisher Scientific’s NGS technology carries the Ion Torrent name. Last year, Thermo Fisher launched two new NGS-based research tools for preimplantation genetic testing-aneuploidy (PGT-A). (This type of testing is used for in vitro fertilization and intracytoplasmic sperm injection.) The Ion ReproSeq PGT-A Kit and the Ion AmpliSeq Polyploidy Kit are the first research-use reproductive health assays available on the company’s Ion Torrent Genexus Integrated Sequencer, and they are designed to deliver complete workflows from sample to aneuploidy analysis result. Also last year, Thermo Fisher began partnering with Pfizer to expand access to NGS-based cancer testing for patients in 30-plus countries across Latin America, Africa, the Middle East, and Asia. Thermo Fisher’s sequencing business is within the Genetic Sciences business of its Life Sciences Solutions segment, which generated 23% ($9.977 billion) of the company’s $42.86 billion in 2023 revenue.
Ultima Genomics
Ultima Genomics last month launched the UG 100 system, which has an ultra-high-throughput sequencing architecture that features an open silicon wafer instead of multiple traditional flow cells. This architecture, Ultima says, will reach and even break through the barrier known as the $100 genome. The UG 100 includes full 24/7 run automation, flexibility for smaller and significantly faster runs, high accuracy for germline applications, and an extreme accuracy mode for somatic applications and rare event detection. According to Ultima, the UG 100’s new ppmSeq technology provides industry-leading raw read accuracy for calling single nucleotide variants for rare event detection applications such as detecting low-level circulating tumor DNA. Privately held Ultima emerged from stealth in 2022 after raising approximately $600 million.
PROVIDERS OF SANGER SEQUENCING INSTRUMENTATION
Hitachi High-Tech
Hitachi High-Tech last month joined Sysmex to announce that the companies agreed to partner on developing genetic testing systems based on capillary electrophoresis (CE) sequencers. Sysmex and Hitachi High-Tech aim to develop more efficient genetic testing systems at a lower cost, and to expand and optimize genetic testing for individual diseases. Hitachi High-Tech will pursue approval for CE sequencers as medical devices while Sysmex will seek development and regulatory approval for testing reagents for use with such devices, plus develop analysis software. Hitachi markets the Compact CE Sequencer DS3000, which applies CE technology developed by Hitachi High-Tech over several decades in a compact system designed to facilitate sequencing analysis and fragment analysis.
Promega
Promega markets the Spectrum Compact CE system, a benchtop
instrument designed for Sanger sequencing analysis. Spectrum Compact supports Sanger sequencing applications for verification of NGS base calls. It is designed to confirm successful genome edits in transformed cultures and to screen secondary clones for successful CRISPR-Cas9 edits. Spectrum Compact CE is designed for use with existing sequencing chemistries using fluorescently labeled dideoxynucleotide triphosphates and 4-, 5-, and 6-dye short tandem repeat kits from Promega, and other commercially available kits. Spectrum Compact CE can also be used for DNA fragment analysis for forensic labs.
Thermo Fisher Scientific
In addition to its NGS tools and technology, Thermo Fisher Scientific markets genetic analyzers and workflow tools for Sanger sequencing under the Applied Biosystems brand. Applied Biosystems’ SeqStudio Series systems are designed to analyze nucleic acids using CE with Sanger sequencing or fragment analysis and to enable applications that range from simple, targeted sequencing to identification of SARS variants of concern. The most recent instrument in the series, Applied Biosystems’ SeqStudio Flex Series Genetic Analyzer, was introduced in 2022. Thermo Fisher’s sequencing business is within the Genetic Sciences business of its Life Sciences Solutions segment, which generated 23% ($9.977 billion) of the company’s $42.86 billion in 2023 revenue.
PROVIDERS OF WORKFLOW SOLUTIONS
Agilent Technologies
Speaking with analysts last November, CEO Mike McMullen quantified Agilent’s genomics business at $500 million—part of the Diagnostics and Genomics Group, which generated $1.409 billion last year, up 1% from 2022. Roughly half of the genomics business relates to sample preparation chemistries, such as Agilent’s SureSelect. The other half enables quality assurance and quality control of NGS samples to validate quality prior to sequencing.
QIAGEN
QIAGEN credits growth in its portfolios of universal NGS solutions for use with third-party NGS systems with a 6% boost in sales (to $239 million) of the company’s Genomics/NGS business in 2023.
Roche
Sequencing investment was among “significant areas of spending,” Roche stated in its Finance Report 2023, without furnishing figures. Roche Sequencing Solutions is within Roche’s Diagnostics Division, which last year generated CHF 14.1 billion ($16.1 billion) in revenue, down 20.5% from 2022 due to lower sales of COVID-19-related tests.
