Top 5 Genetic Sequencing Startups Shaking Up the Industry

Genetic sequencing has changed out of all recognition since the Human Genome Project was officially completed in 2003. The technology is faster, cheaper and more accurate, but for a long time the market has been dominated by a few large companies. This is now starting to change and these five relative newcomers are bringing change and competition to the industry.

Between 80-90% of the sequencing market is dominated by one company, Illumina. The short-read sequencing specialists have had an annual turnover of $2.5-4.5 billion and produce a wide array of machines that are used by thousands of labs around the world. However, on the long-read side of things, Pacific Biosciences and Oxford Nanopore Technologies are arguably the most prominent companies.

In 2018, Illumina made an offer to buy PacBio to move into the long read space, but this deal was blocked by the Federal Trade Commission due to the large market share already owned by Illumina and was abandoned in 2019. Since then, PacBio has taken its first steps into the short-read sequencing market after acquiring Omniome and announcing the launch of its Onso short-read platform.

Short-read sequencing remains the most highly used type of sequencing. While prices are still going down, with Illumina announcing its new line of NovaSeq X machines in September that could allow genomes to be sequenced for as little as $200, in reality the technology still remains out of reach for many. For example, Illumina machines are expensive and in order to drive down prices many samples need to be sequenced. This can be difficult for small labs or those in developing countries with limited budgets.

Over the last decade a number of new sequencing companies have been founded, perhaps inspired by the expiration of some of Illumina’s key patents in 2020, with others due to expire soon. It is a competitive field, which is hard to succeed in, but these five companies bring their own innovative technology to the market and are competing to challenge the dominance of Illumina and other market leaders.

1. Element Biosciences: Founded: 2017
Headquarters: Greater San Diego Area, U.S.

Founded in 2017, by current CEO Molly He and two former colleagues from Illumina, Element has a focus on making sequencing more decentralized and democratized. The company has created a new and disruptive sequencing platform in less than 5 years. The scientific founders have applied their expertize in reagent design to ensure their machines can produce higher quality data at a lower price than Illumina.

The company achieved a $276M Series C Financing round last summer, with more than $400M raised in total. It began shipping its AVITI system machines to customers in June.

In accordance with the company’s mission to make sequencing more accessible and affordable, it is guaranteeing reagent prices will not go up during the life of the AVITI machines. It also says it has the lowest industry cost for single cell sequencing.

While Element machines are mostly focused on short read sequencing, the company recently announced the launch of LoopSeq long-read sequencing kits. The LoopSeq sequencing chemistry provides synthetic long-read capabilities (up to 5kb) on the AVITI short-read sequencer.

2. Ultima Genomics: Founded: 2016
Headquarters: California

Ultima Genomics was officially launched in 2016, but came out of stealth mode earlier this year when it announced it has developed a high-throughput, low-cost sequencing platform that could deliver a genome for only $100, something that has long been a target for Illumina and other players in the industry.

The company managed to raise $600M in funding, from investors such as Andreessen Horowitz, Peter Thiel’s Founders Fund and Khosla Ventures, while in stealth mode and is now using that money to further develop its platform.

The sequencing process used by Illumina has a number of different steps including splitting the DNA into single strands, breaking these into small fragments, loading these into a flow cell and placing that into the sequencing machine. Ultima has developed what it says is a faster and cheaper process that speeds up how reagents are added to the machine and also how the DNA is prepared and read while maintaining accuracy.

Since going public in May, Ultima announced several new partnerships and collaborations. For example, it will collaborate with Regeneron to develop and test Ultima’s second-generation sequencing platform, the follow-on from its first machine the UG100. It will also partner with cancer screening and diagnostics experts Exact Sciences to co-develop cheaper genetic testing and screening.

3. Singular Genomics: Founded: 2016
Headquarters: Greater San Diego Area, U.S.

Singular Genomics was founded in 2016 by Drew Spaventa, Eli Glezer, and David Barker. The company came out of stealth mode in May 2021 when it launched on the Nasdaq raising approximately $258M from an upsized IPO.

The company has developed the G4 benchtop sequencer and associated kits, aimed at the next generation sequencing market. It uses sequencing by synthesis and has the potential to output 4 whole genomes in 19 hours. Like the other companies on this list, it is aiming for fast, economic and accurate sequencing for its customers.

Singular has partnered with various companies to help prepare library prep and target enrichment kits for the G4 machine including New England Biolabs, Lexogen, Dovetail Genomics, Watchmaker Genomics and Twist Biosciences. In a recent statement, the company says it is on track to start shipping its G4 machines before the end of the year.

The IPO funds will also help develop Singular’s second machine, the PX, that will combine single cell analysis, spatial analysis, genomics and proteomics in one instrument and is estimated to launch in 2023.

4. 10X Genomics: Founded: 2012
Headquarters: Pleasanton, U.S.

One of the older and larger companies on the list, 10x Genomics was founded in 2012 by Serge Saxonov (founding R&D director at 23andMe), Ben Hindson and Kevin Ness and is headquartered in Pleasanton, California, although it also has several other offices in the U.S., EU and Asia.

10x has three main technologies, Chromium, Visium and Xenium. There are three Chromium machines that use different versions of the company’s single cell sequencing technology. The Xenium machine allows in-situ profiling of RNA targets and the Visium machine combines histology and genomics to allow spatial transcriptomics analysis.

In 2019 10x launched on the Nasdaq raising over $390M, significantly higher than the predicted $100M. The 2021 company revenue was $490.5M a significant increase on previous years turnover.

The 10x founders worked at Quantalife prior to its acquisition by Bio-Rad in 2011. In 2014, Bio-Rad launched a legal dispute against the three 10x founders stating they did not fulfill obligations owed to Bio-Rad after it acquired Quantalife, Bio-Rad also claimed patent infringement in a later case. This dispute continued until 2020, when 10x lost its appeal against a court order to pay Bio-Rad $24 million in damages and a 15% royalty on sales, and the two companies settled the dispute. A new patent dispute is now ongoing between 10x and NanoString over patents behind 10x’s Visium Spatial system.

5. MGI Tech: 2016
Headquarters: Founded: Shenzhen, China

MGI was founded in China in 2016 as a subsidiary of the BGI Group, formerly the Beijing Genomics Institute. Its focus is on producing high-throughput genetic sequencing and laboratory automation systems for the life sciences and healthcare industry.

In 2013, the BGI group acquired Complete Genomics, now based in San Jose, California, and in 2018 it became part of MGI. Complete Genomics developed its own DNA nanoball-based sequencing platform and sequenced its first genomes in 2009.

MGI also developed a low-cost sequencing machine based on similar DNA nanoball sequencing technology, which uses rolling circle replication to amplify small pieces of DNA into the so-called nanoballs. Complementary fluorescent nucleotides bind to the bases and are used to determine the sequence. Following the purchase of Complete Genomics, MGI were able to refine this process further by combining and refining the technologies from the two companies.

This year Complete Genomics launched a new sequencer in the U.S. in August DNBSEQ-G400* and has three more machines, designed for low to very high throughput labs, due to launch next year. In September, MGI launched on the Shanghai STAR Market with a $518M IPO.

Helen Albert is senior editor at Inside Precision Medicine and a freelance science journalist. Prior to going freelance, she was editor-in-chief at Labiotech, an English-language, digital publication based in Berlin focusing on the European biotech industry. Before moving to Germany, she worked at a range of different science and health-focused publications in London. She was editor of The Biochemist magazine and blog, but also worked as a senior reporter at Springer Nature’s medwireNews for a number of years, as well as freelancing for various international publications. She has written for New Scientist, Chemistry World, Biodesigned, The BMJ, Forbes, Science Business, Cosmos magazine, and GEN. Helen has academic degrees in genetics and anthropology, and also spent some time early in her career working at the Sanger Institute in Cambridge before deciding to move into journalism.

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