A geographic coordinate system is a coordinate system that enables every location on Earth to be specified by a set of numbers, letters or symbols. The coordinates are often chosen such that one of the numbers represents a vertical position and two or three of the numbers represent a horizontal position; alternatively, a geographic position may be expressed in a combined three-dimensional Cartesian vector. A common choice of coordinates is latitude, longitude and elevation. To specify a location on a plane requires a map projection.
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.
In genetics and biochemistry, sequencing means to determine the primary structure of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succinctly summarizes much of the atomic-level structure of the sequenced molecule.
Genotyping is the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence. It reveals the alleles an individual has inherited from their parents. Traditionally genotyping is the use of DNA sequences to define biological populations by use of molecular tools. It does not usually involve defining the genes of an individual.
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA.
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.[2] Customers include genomic research centers, pharmaceutical companies, academic institutions, clinical research organizations and biotechnology companies.
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.
The human genome is the complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome, and the mitochondrial genome. Human genomes include both protein-coding DNA genes and noncoding DNA. Haploid human genomes, which are contained in germ cells consist of three billion DNA base pairs, while diploid genomes have twice the DNA content. While there are significant differences among the genomes of human individuals, these are considerably smaller than the differences between humans and their closest living relatives, the chimpanzees and bonobos.
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. In 1999 Illumina acquired Spyder Instruments (founded by Michal Lebl, Richard Houghten, and Jutta Eichler) for their technology of high throughput synthesis. Illumina completed its initial public offering in July 2000.
Lawrence A. "Larry" Bock was an American entrepreneur who has aided in starting or financing 50 early-stage growth companies, with a combined market value of more than $70 billion.
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.[3] Illumina also uses the DNA colony sequencing technology, invented in 1997 by Pascal Mayer and Laurent Farinelli [4] 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.
Sir Shankar Balasubramanian is an Indian-born British chemist and Herchel Smith Professor of Medicinal Chemistry in the Department of Chemistry at the University of Cambridge, Senior Group Leader at the Cancer Research UK Cambridge Institute and Fellow of Trinity College, Cambridge. He is recognised for his contributions in the field of nucleic acids. He is scientific founder of Solexa and Cambridge Epigenetix.
Sir David Klenerman is a British biophysical chemist and a professor of biophysical chemistry at the Department of Chemistry at the University of Cambridge and a Fellow of Christ's College, Cambridge. He is best known for his contribution in the field of next-generation sequencing of DNA, nanopipette-based scanning ion-conductance microscopy, and super-resolution microscopy.
Hayward is a city located in Alameda County, California in the East Bay subregion of the San Francisco Bay Area. With a 2014 population of 149,392, Hayward is the sixth largest city in the Bay Area and the third largest in Alameda County. Hayward was ranked as the 37th most populous municipality in California. It is included in the San Francisco–Oakland–Fremont Metropolitan Statistical Area by the US Census. It is located primarily between Castro Valley and Union City, and lies at the eastern terminus of the San Mateo–Hayward Bridge. The city was devastated early in its history by the 1868 Hayward earthquake. From the early 20th century until the beginning of the 1980s, Hayward's economy was dominated by its now defunct food canning and salt production industries.
In June 2009, Illumina announced the launch of their own PersonalFull Genome Sequencing Service at a depth of 30X for $48,000 per genome,[5] and a year later dropped the price to $19,500.[6][7]As of May2011[update], 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,[2][17] and Roche abandoned the offer in April.[18]
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, who had been CEO since 1999, 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]
In November 2018 the company acquired Pacific Biosciences for $8.00 per share or around $1.2 billion in total.[27][28]
Litigation
This section needs to be updated. Please update this article to reflect recent events or newly available information.(July 2018)
In 2010, Cornell University and Life Technologies filed a lawsuit against Illumina because its microarray products infringed eight patents held by the university and exclusively licensed to the start-up. In 2017, Cornell attempted to exit a settlement with Illumina based on fraudulence for "misrepresentations to Cornell and concealed a broader settlement agreement with Illumina to fraudulently induce Cornell to execute the settlement agreement."[29]
In February 2016, Illumina filed a lawsuit against Oxford Nanopore Technologies, which was the first company to commercialize nanopore sequencing. Illumina claimed that Oxford Nanopore infringed on its patents.[30][31]
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.[32][33] 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.
Related Research Articles
A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine). This is then reported as a text string, called a read. Some DNA sequencers can be also considered optical instruments as they analyze light signals originating from fluorochromes attached to nucleotides.
Affymetrix, Inc. was an American company that manufactured DNA microarrays; it was based in Santa Clara, California, United States. The company was acquired by Thermo Fisher Scientific in March 2016.
This is an example of a molecular biology core developed in an academic institution over the past 35 years. These molecular biology cores are now commonplace and necessary in that they provide NIH funded academic labs access to expensive instrumentation in a shared use setting.
454 Life Sciences was a biotechnology company based in Branford, Connecticut that specialized in high-throughput DNA sequencing. It was acquired by Roche in 2007 and shut down by Roche in 2013 when its technology became noncompetitive, although production continued until mid-2016.
Mostafa Ronaghi is an Iranian molecular biologist, specializing in DNA sequencing methodology. He earned his Ph.D. from the Royal Institute of Technology in Sweden in 1998.
23andMe is a privately held personal genomics and biotechnology company based in Mountain View, California. The company is named for the 23 pairs of chromosomes in a normal human cell.
Personal genomics or consumer genetics is the branch of genomics concerned with the sequencing, analysis and interpretation of the genome of an individual. The genotyping stage employs different techniques, including single-nucleotide polymorphism (SNP) analysis chips, or partial or full genome sequencing. Once the genotypes are known, the individual's variations can be compared with the published literature to determine likelihood of trait expression, ancestry inference and disease risk.
SOLiD is a next-generation DNA sequencing technology developed by Life Technologies and has been commercially available since 2006. This next generation technology generates hundreds of millions to billions of small sequence reads at one time.
Whole genome sequencing is ostensibly the process of determining the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. In practice, genome sequences that are nearly complete are also called whole genome sequences.
Massive parallel signature sequencing (MPSS) is a procedure that is used to identify and quantify mRNA transcripts, resulting in data similar to serial analysis of gene expression (SAGE), although it employs a series of biochemical and sequencing steps that are substantially different.
Exome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding region of genes in a genome. It consists of two steps: the first step is to select only the subset of DNA that encodes proteins. These regions are known as exons – humans have about 180,000 exons, constituting about 1% of the human genome, or approximately 30 million base pairs. The second step is to sequence the exonic DNA using any high-throughput DNA sequencing technology.
Pacific Biosciences of California, Inc. is a biotechnology company founded in 2004 that develops and manufactures systems for gene sequencing and some novel real time biological observation. PacBio describes its platform as single molecule real time sequencing (SMRT), based on the properties of zero-mode waveguides. The company's first commercial product, the PacBio RS, was sold to a limited set of customers in 2010 and was commercially released in early 2011. A new version of the sequencer called the PacBio RS II was released in April 2013. On 25 September 2013 a partnership between Pacific Biosciences and Roche Diagnostics was announced for the development of in vitro diagnostic products using the technology, with Roche providing US$75,000,000 in the deal. In 2015, the company launched a new sequencing instrument called the Sequel System with approximately 7-fold greater capacity than the PacBio RS II.
Manteia Predictive Medicine S.A. was a start-up company created in November 2000 as a spin-off of Serono, a Swiss-based biotechnology company, now part of Merck-Serono, by private founders. Its aim was to provide preventive and curative treatment guidelines for common and complex diseases. These guidelines were envisaged as composed of two parts:
Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged in 1994-1998 and have been commercially available since 2005. These technologies use miniaturized and parallelized platforms for sequencing of 1 million to 43 billion short reads per instrument run.
The $1,000 genome refers to an era of predictive and personalized medicine during which the cost of fully sequencing an individual's genome (WGS) is roughly USD $1,000. It is also the title of a book by British science writer and founding editor of Nature Genetics, Kevin Davies. By late 2015, the cost to generate a high-quality 'draft' whole human genome sequence was just below $1,500.
Illumina dye sequencing is a technique used to determine the series of base pairs in DNA, also known as DNA sequencing. The reversible terminated chemistry concept was invented by Bruno Canard and Simon Sarfati at the Pasteur Institute in Paris. It was developed by Shankar Balasubramanian and David Klenerman of Cambridge University, who subsequently founded Solexa, a company later acquired by Illumina. This sequencing method is based on reversible dye-terminators that enable the identification of single bases as they are introduced into DNA strands. It can also be used for whole-genome and region sequencing, transcriptome analysis, metagenomics, small RNA discovery, methylation profiling, and genome-wide protein-nucleic acid interaction analysis.
Oxford Nanopore Technologies Limited is a U.K.-based company which is developing and selling nanopore sequencing products for the direct, electronic analysis of single molecules.
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