Illumina (company)

Illumina, Inc.

Type	Public
Traded as	NASDAQ: ILMN NASDAQ-100 Component S&P 500 Component
Industry	Biotechnology
Founded	1998
Founder	David Walt Larry Bock John Stuelpnagel Anthony Czarnik Mark Chee
Headquarters	San Diego, California, U.S.
Key people	Francis deSouza (President & CEO)
Website	www.illumina.com

Coordinates: 32°53′15″N 117°10′23″W / 32.8875924°N 117.1730577°W / 32.8875924; -117.1730577

Illumina, Inc. is an American company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. The company provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California.

Illumina's technology had purportedly by 2013 reduced the cost of sequencing a human genome to US$4,000, down from a price of US$1 million in 2007.^[1] Customers include genomic research centers, pharmaceutical companies, academic institutions, clinical research organizations and biotechnology companies.

History

Czarnik, Stuelpnagel and Chee at their Illumina office in the Summer of 1998.

Illumina was founded in April 1998 by David Walt, Larry Bock, John Stuelpnagel, Anthony Czarnik, and Mark Chee. While working with CW Group, a venture capital firm, Bock and Stuelpnagel uncovered what would become Illumina's BeadArray technology at Tufts University and negotiated an exclusive license to that technology. Illumina completed its initial public offering in July 2000.

Illumina began offering single nucleotide polymorphism (SNP) genotyping services in 2001 and launched its first system, the Illumina BeadLab, in 2002, using GoldenGate Genotyping technology. Illumina currently offers microarray-based products and services for an expanding range of genetic analysis sequencing, including SNP genotyping, gene expression, and protein analysis. Illumina's technologies are used by a broad range of academic, government, pharmaceutical, biotechnology, and other leading institutions around the globe.

On January 26, 2007, the Company completed the acquisition of Solexa, Inc. Solexa was founded in June 1998 by Shankar Balasubramanian, and David Klenerman to develop and commercialize genome sequencing technology invented by the founders at the University of Cambridge. Solexa INC was formed in 2005 when Solexa Ltd reversed into Lynx Therapeutics of Hayward.^[2] Illumina also uses the DNA colony sequencing technology, invented in 1997 by Pascal Mayer and Laurent Farinelli ^[3] and which was acquired by Solexa in 2004 from the company Manteia Predictive Medicine. It is being used to perform a range of analyses, including whole genome resequencing, gene expression analysis and small ribonucleic acid (RNA) analysis.

In June 2009, Illumina announced the launch of their own Personal Full Genome Sequencing Service at a depth of 30X for $48,000 per genome,^[4] and a year later dropped the price to $19,500.^[5] This is still too expensive for true commercialization but the price will most likely decrease substantially over the next few years as they realize economies of scale and given the competition with other companies such as Complete Genomics and Knome.^[6][7] As of May 2011, Illumina reduced the price to $4,000.^[8][9]

Up until 2010 Illumina sold only instruments that were labeled "for research use only"; in early 2010 Illumina obtained FDA approval for its BeadXpress system to be used in clinical tests.^[10][11] This was part of the company's strategy at the time to open its own CLIA lab and begin offering clinical genetic testing itself.^[12]

Illumina acquired Epicentre Biotechnologies, based in Madison, Wisconsin, on January 11, 2011.^[13] On January 25, 2012, Hoffmann-La Roche made an unsolicited bid to buy Illumina for $44.50 per share or about $5.7 billion.^[14][15] Roche tried other tactics, including raising its offer (to $51.00, for about $6.8 billion).^[16] Illumina rejected the offer,^[1][17] and Roche abandoned the offer in April.^[18] As of April 2013, the company's chief executive officer was Jay Flatley.^[1]

In 2014, the company announced a multimillion-dollar product, HiSeq X Ten, that it forecast would provide large-scale whole-genome sequencing for $1,000/genome. The company claimed that forty such machines would be able to sequence more genomes in one year than had been produced by all other sequencers to date.^[19] In January 2014, Illumina already held 70 percent of the market for genome-sequencing machines.^[20] Illumina machines accounted for more than 90 percent of all DNA data produced.^[21]

On July 5, 2016 Jay Flatley assumed the role of executive chairman of the board of directors. Francis deSouza took on the role of president and chief executive officer, and continues to serve on the Illumina board of directors.^[22][23]

In late 2015, Illumina spun off the company Grail, focused on blood testing for cancer tumors in the bloodstream. The company has plans in 2017 to raise $1 billion in its second round of financing, and has received funding from Bill Gates and Jeff Bezos investing $100 million in Series A funding, and with Illumina maintaining a 20% holding share in Grail.^[24] The company is working with a blood test trial with over 120,000 women during scheduled mammogram visits in the states of Minnesota and Wisconsin, as well as a partnership with the Mayo Clinic. The company Grail uses Illumina sequencing technology for tests.^[25] The company plans to roll out the tests by 2019, with a cost of $500 per individual.^[26]

Products

DNA Sequencing

Illumina sells a number of high-throughput DNA sequencing systems, also known as DNA sequencers, based on technology developed by Solexa. The technology features bridge amplification to generate clusters and reversible terminators for sequence determination.^[27][28] The technology behind these sequencing systems involves ligation of fragmented DNA to a chip, followed by primer addition and sequential fluorescent dNTP incorporation and detection.

Sequencing Systems 

MiniSeq: The MiniSeq System is a flexible benchtop sequencer that enables a broad range of DNA and RNA sequencing applications — from examining single genes to entire pathways — in a single run. MiniSeq was introduced in 2016.^[29]

MiSeq: The Illumina MiSeq System offers capabilities for small whole-genome sequencing, amplicon sequencing, gene expression profiling, small RNA analysis and 16s metagenomic sequencing in a compact instrument. Using a high throughput kit, MiSeq can produce as much as 15 Gb of output from 50 million paired end reads (at a read length of 300 bp). The system also features an intuitive touch screen interface, plug-and-play reagent cartridges with RFID tracking, on-screen video tutorials and step-by-step guides throughout each sequencing workflow. Illumina introduced MiSeq in 2011.^[30]

NextSeq: The NextSeq 500 System provides high-throughput performance on a desktop instrument. When launched in 2014, the sequencing system contained 20 new innovations, including a new flow cell design and surface chemistry and can sequence a whole-human genome and up to 16 exomes in a single day. It also is flexible enough to switch to lower throughput sequencing when needed.^[31]

HiSeq: Illumina launched the first HiSeq system, the HiSeq 2000, in 2010. There are currently 3 HiSeq models, the 2500, 3000 and 4000. All HiSeq sequencers features intuitive, touch-screen controls, and accompanying software with guided step-by-step workflow directions. In addition, real-time run statistics can be monitored locally or remotely. HiSeq systems utilize Illumina’s well-established sequencing by synthesis (SBS) method in which fluorescently labeled nucleotide bases are detected as they are incorporated into DNA template strands. All four reversible terminator-bound dNTPs are present in each sequencing cycle; this feature minimizes bias of incorporation and greatly reduces raw error rates.^[32][33]

The HiSeq 2500 System is a powerhouse of Illumina sequencers for high throughput applications such as small and large whole genome sequencing, exome sequencing, targeted sequencing, whole transcriptome, mRNA-seq and shotgun metagenomics. It has the capacity to produce 160 Gb of data per day (or 1 Tb per run) and the system can be configured to run 1 or 2 flow cells simultaneously. In high output mode, it can process up to 8 human genomes at 30x coverage with one genome being sequenced in 27 hours.^[34]

The Illumina HiSeq 3000 flow cell features a capacity of processing over 200 Gb per day or 750 Gb per run, with up to 2.5 billion single reads. In a single run it can sequence up to 6 whole human genomes (at 30x coverage), up to 48 exomes and up to 50 transcriptomes, assuming 50 million reads per sample.^[35]

The Illumina HiSeq 4000 uses a dual flow cell capable of processing over 400 Gb per day or 1.5 Tb per run, with up to 5 billion single reads. In a single run it can sequence up to 12 whole human genomes (at 30x coverage), up to 96 exomes and up to 100 transcriptomes, assuming 50 million reads per sample.^[36]

HiSeq X: The HiSeq X Ten Sequencing System was launched in 2014 as the first high-throughput system designed to process 20,000 genomes per year at a cost of $1,000 each.^[37] With HiSeq X Ten, Illumina introduced a new optical technology that utilizes a 2 dye system: adenine and cytosine bases are each represented by one dye, an absence of dye for guanine bases and both dyes for thymine. This allows Illumina to utilize lower resolution cameras with half the number of images. HiSeq X Ten also employs new patterned flow cells with larger clusters that use nanowells and are scanned bi-directionally, making optical scanning 6 times faster than a HiSeq 2500. The HiSeq X Ten was initially launched as a set of 10 instruments.^[31] In 2015, Illumina began to offer a scaled-down version of the system, the HiSeq X Five.^[38]

NovaSeq: Illumina launched the NovaSeq Series in January 2017. There are two configurations of the NovaSeq including the NovaSeq 5000 and the NovaSeq 6000. The NovaSeq 5000 has the capacity to run up to two flow cells at a time, with 2 flow cell options to choose from. The highest throughput flowcell (S2) can process up to 3.3 billion reads and generate up to 1000 Gb of data (with 150 bp read lengths). The NovaSeq 6000 can run four flow-cell formats, including S1, S2, S3 and S4. The S3 and S4 flow cells will generate up to 4 Tb and 6 Tb of data, respectively, in two and a half days. Read lengths for these outputs are 2x150 bases. The system is compatible with Illumina library preparation kits and can support virtually any sequencing application — whole genome sequencing, whole transcriptomes, whole exomes, metagenomics and more. Users can sequence any species using any application.^[39][40][41]

Specialty Sequencing Systems

MiSeqDx: The MiSeqDx System is the first FDA-cleared NGS platform for in vitro diagnostic (IVD) testing.^[42]

MiSeq FGx: The MiSeq FGx Forensic Genomics System is validated for forensic genomics applications.^[43]

Microarray Scanning Systems

NextSeq 550: The NextSeq 550 System offers sequencing and cytogenomic array scanning on one instrument.^[44]

iScan: The iScan System supports high-sample throughput and exceptional data quality.^[45]

Bioinformatics Platforms

Illumina offers BaseSpace Sequencing Hub, a cloud-enabled environment for sequencing data management and analysis, launched in 2011.^[46] The company also acquired the translational NextBio Software platform in 2013 ^[47], today available as BaseSpace Correlation Engine and BaseSpace Cohort Analyzer. In 2015, illumina acquired GenoLogics Life Sciences Software in 2015, a developer of laboratory information management systems (LIMS).^[48]

See also

• List of companies of the United States#I

References

External links

Wikimedia Commons has media related to Illumina (company).

• Illumina's Company Website
• DNAVision - Illumina official service provider.
• Gene Logic - performs research based on Illumina's Golden gate assay
• Illumina's Personal Full Sequencing Genome Service
• National Center for Genome Resources (NCGR) Sequencing Center - an Illumina Certified Service Provider.
• Genotypic Technology GENOMICS SIMPLIFIED - an Illumina Certified Service Provider.

• • Business data for Illumina: Google Finance
  • Yahoo! Finance
  • Reuters
  • SEC filings