Illumina’s systems employ short-read sequencing techniques, which has been the predominant NGS technology for the last decade. The company has made huge advances in the NGS space and now markets a wide variety of sequencing machines, capable of generating between 1 gigabase and several terrabases per run.
Many of the available Illumina platforms are tailored for specific applications. Using technologies from a single company can be advantageous for institutions that require numerous NGS experiments. This is because researchers have the opportunity to deal with a single provider, enabling them to produce DNA sequences that can be analysed with one bioinformatic solution.
Currently, Illumina is comfortably the largest gene-sequencing company, with more than 13,000 of its newest NovaSeq 6000 machines installed worldwide. But how did Illumina manage to monopolise the gene-sequencing market, and what are the consequences of the lack of competition within the industry?
*This article was updated on 03/11/2022 to reflect key changes in the past year.
Join David Smith (Mayo Clinic), Shawn Baker (SanDiegOmics) and Tiffany Boughtwood (Australian Genomics) as they discuss how the upcoming shifts within the NGS market could affect genomics research in the future and what impact it may have on healthcare around the world: Exploring the Current Sequencing Landscape
The Illumina growth timeline
1998: The sequencing company Solexa was formed, with most of their early research and development being conducted in the Cambridge Chemistry Department in the first few years. Separately, Illumina was also founded this year.
2001: Solexa’s corporate facilities had been established and the team’s research progress attracted a £12 million series A funding.
2002: Illumina launched its first system, called the BeadLab, which used GoldenGate Genotyping technology.
2004: Solexa acquired molecular clustering technology from Manteia Predictive Medicine. This enabled the amplification of single DNA molecules in clusters, enhancing the accuracy of base calling and reducing the cost of system optics by generating stronger signals.
2005: The Solexa team sequenced the complete genome of bacteriophage Phi X-174. This genome was the same genome that Sanger sequencing first generated, but Solexa’s novel technology greatly increased the amount of sequence data (over 3 million bases were delivered per run).
2006: The first Solexa sequencer was launched, called the Genome Analyzer. This gave scientists the power to sequence 1 gigabase of data per run.
2007: Solexa was acquired by Illumina. At this time, the price of sequencing a human genome was estimated to be $1 million.
2009: Illumina announced the launch of their own personal full genome sequencing service for $48,000.
2010: Illumina’s personal full genome sequencing service price dropped to $19,500. The company also achieved approval for its BeadXpress system to be used in clinical tests.
2011: Illumina acquired Epicentre Biotechnologies. Roche bid to buy the company for about $6.8 billion, but Illumina rejected the offer. At this time, the company also announced that their personal full genome sequencing service now cost $4,000.
2014: Illumina’s technology reportedly reduced the cost of sequencing a human genome to $1,000 using the HiSeq X Ten. By this time, the company already held 70% of the genome sequencing market and their machines accounted for over 90% of all DNA data being produced.
2015: Illumina spun off a company, called GRAIL, which focussed on blood testing for cancer tumours. Illumina maintained a 20% share in GRAIL even after receiving over $100 million during series A funding.
2016: Illumina filed a lawsuit against Oxford Nanopore Technologies due to their use of a biological nanopore, called M. smegmatis porinA. This was settled by Oxford Nanopore Technologies using the CsgG nanopore from E. coli instead.
2017: Illumina’s NovaSeq machine was launched. The advent of this technology allowed the prediction that the cost of sequencing a genome may soon drop to $100. Illumina’s sales are estimated to be $2.7 billion.
2018: Illumina proposed the acquisition of Pacific Biosciences for around $1.2 billion. Illumina’s sales are around $3.3 billion.
2019: The Federal Trade Commission sued to block Illumina acquiring Pacific Biosciences, and within a year, the proposed deal was abandoned, with Illumina paying Pacific Biosciences a $98 million termination fee. Illumina’s sales total around $3.8 billion.
2020: Illumina filed a patent infringement suit against BGI for their Cool-MPS sequencing products.
2021: Illumina owns around 80% share of the DNA sequencing market globally, and controls at least 90% of the UK sector. Nevertheless, the Federal Trade Commission blocks Illumina’s bid to acquire GRAIL for $7.1 billion.
2022: Ultima Genomics steps onto the scene, announcing the $100 genome just 8 years after Illumina’s HiSeq X Ten Sequencer breakthrough in 2014. Illumina immediately counters with the launch of its NovaSeq X Series, which promises to generate more than 20,000 whole genomes per year.
As Illumina’s patents begin to expire we could see even more competition from key players like MGI, but we are yet to see how this increased competition will impact the sequencing market.
Consequences of the domination
Despite the recent competition, Illumina still has a near-monopoly on the NGS space. The company has somehow managed to successfully eliminate most of their competition in the sequencing market. A single organisation having control of the hugely important high throughput sequencing sector does not benefit the scientific community, or have a positive impact on clinical practise.
Gail Levine, the Federal Trade Commission Bureau of Competition Deputy Director, explained about the potential Illumina and Pacific Biosciences merge: “When a monopolist buys a potential rival, it can harm competition. These deals help monopolists maintain power. That’s why we challenged this acquisition.”
Illumina acquiring various companies, including the attempt to purchase Pacific Biosciences, has the potential to further reduce the firm’s incentive to innovate and develop new products. This would allow Illumina’s domination of the sequencing market to last longer than it should. This is evidenced by the fact that Illumina did not make dramatic developments in sequence output after 2015, which in turn slowed the decline of the whole genome sequence pricing. The lack of real competition in the sequencing industry is almost certainly to blame, but there could be hope on the horizon. According to the journal Science, 2022 “is the year of the big shake-up” for DNA sequencing with increased competition coming in the form of players such as Ultima Genomics. Could we be standing on the verge of the next revolution in cancer genomics? We’ll have to wait and see.
For more information, download the latest edition of the Sequencing Buyer’s Guide here.
Image credit: Illumina