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Monday, March 9, 2020

Elsevier

From Wikipedia, the free encyclopedia
 
IndustryPublishing
Founded1880; 140 years ago
Headquarters
Revenue£2.54 billion (2018)
600,000,000 United States dollar[2] (2009) Edit this on Wikidata
Number of employees
6,900 (2008) Edit this on Wikidata
ParentRELX
Websitewww.elsevier.com

Elsevier (Dutch: [ˈɛlzəviːr]) is a Dutch publishing and analytics company specializing in scientific, technical, and medical content. It is a part of the RELX Group, known until 2015 as Reed Elsevier. Its products include journals such as The Lancet and Cell, the ScienceDirect collection of electronic journals, the Trends and Current Opinion series of journals, the online citation database Scopus, and the ClinicalKey search engine for clinicians. Elsevier's products also include digital tools for data-management, instruction, and assessment.

Elsevier publishes more than 470,000 articles annually in 2,500 journals. Its archives contain over 16 million documents and 30,000 e-books. Total yearly downloads amount to more than 1 billion.

Elsevier's high operating profit margins (37% in 2018) and 950 million pounds in profits, often on publicly funded research works and its copyright practices have subjected it to criticism by researchers.

History

The original seal of the Elsevier family, used by Elsevier company as logo until 2019.
 
Elsevier was founded in 1880 and adopted the name and logo from the Dutch publishing house Elzevir that was an inspiration but has no connection to the contemporary Elsevier.[6] The Elzevir family operated as booksellers and publishers in the Netherlands; the founder, Lodewijk Elzevir (1542–1617), lived in Leiden and established the business in 1580. As company logo, Elsevier used the Elzevir family's printer's mark, a tree entwined with a vine and the words Non Solus, which is Latin for "not alone." Elsevier suggests that this logo represents "the symbiotic relationship between publisher and scholar".

The expansion of Elsevier in the scientific field after 1945 was funded with the profits of the newsweekly Elsevier, which published its first issue on 27 October 1945. The weekly was an instant success and earned lots of money. The weekly was a continuation, as is stated in its first issue, of the monthly Elsevier, which was founded in 1891 to promote the name of the publishing house and had to stop publication in December 1940 because of the Nazi occupation of the Netherlands.

In 1947, Elsevier began publishing its first English-language journal, Biochimica et Biophysica Acta.

In 2013, Elsevier acquired Mendeley, a UK company making software for managing and sharing research papers. Mendeley, previously an open platform for sharing of research, was greatly criticized for the acquisition, which users saw as acceding to the "paywall" approach to research literature. Mendeley's previously open sharing system now allows exchange of paywalled resources only within private groups. The New Yorker described Elsevier's reasons for buying Mendeley as two-fold: to acquire its user data, and to "destroy or coöpt an open-science icon that threatens its business model".

In the first half of 2019, RELX reported the first slowdown in revenue growth for Elsevier in several years: 1% vs. an expectation of 2% and a typical growth of at least 4% in the previous 5 years.

Company statistics

During 2018, researchers submitted over 1.8 million research papers to Elsevier-based publications. Over 20,000 editors managed the peer review and selection of these papers, resulting in the publication of more than 470,000 articles in over 2,500 journals. Editors are generally unpaid volunteers who perform their duties alongside a full-time job in academic institutions, although exceptions have been reported. 

In 2013, the five editorial groups Elsevier, Springer, Wiley-Blackwell, Taylor & Francis, and SAGE Publications published more than half of all academic papers in the peer-reviewed literature. At that time, Elsevier accounted for 16% of the world market in science, technology, and medical publishing.

Elsevier breaks down its revenue sources by format and by geographic region. Approximately 44% of revenue by geography in 2018 derived from North America, 24% from Europe and the remaining 32% from the rest of the world. Approximately 83% of revenue by format came from electronic usage and 17% came from print.

Elsevier employs more than 7,800 people in over 70 offices across 24 countries. Following the integration of its Science & Technology and Health Sciences divisions in 2012, Elsevier has operated under a traditional business structure with a single chief executive officer (CEO). The CEO is Kumsal Bayazit, who was appointed on 15 February 2019. 

In 2018, Elsevier accounted for 34% of the revenues of RELX group (₤2.538 billion of ₤7.492 billion). In operating profits, it represented 40% (₤942 million of ₤2,346 million). Adjusted operating profits (with constant currency) rose by 2% from 2017 to 2018.

In 2018, Elsevier reported a mean 2017 gender pay gap of 29.1% for its UK workforce, while the median was 40.4%, more than twice the UK average and by far the worst figure recorded by any academic publisher in UK. Elsevier attributed the result to the under-representation of women in its senior ranks and the prevalence of men in its technical workforce.

Market model

Products and services

Products and services include electronic and print versions of journals, textbooks and reference works, and cover the health, life, physical and social sciences.

The target markets are academic and government research institutions, corporate research labs, booksellers, librarians, scientific researchers, authors, editors, physicians, nurses, allied health professionals, medical and nursing students and schools, medical researchers, pharmaceutical companies, hospitals, and research establishments. It publishes in 13 languages including English, German, French, Spanish, Italian, Portuguese, Polish, Japanese, Hindi, and Chinese.

Flagship products and services include VirtualE, ScienceDirect, Scopus, Scirus, EMBASE, Engineering Village, Compendex, Cell, SciVal, Pure, and Analytical Services, The Consult series (FirstCONSULT, PathCONSULT, NursingCONSULT, MDConsult, StudentCONSULT), Virtual Clinical Excursions, and major reference works such as Gray's Anatomy, Nelson Pediatrics, Dorland's Illustrated Medical Dictionary, Netter's Atlas of Human Anatomy, and online versions of many journals including The Lancet.

ScienceDirect is Elsevier's platform for online electronic access to its journals and over 6,000 e-books, reference works, book series, and handbooks. The articles are grouped in four main sections: Physical Sciences and Engineering, Life Sciences, Health Sciences, and Social Sciences and Humanities. For most articles on the website, abstracts are freely available; access to the full text of the article (in PDF, and also HTML for newer publications) often requires a subscription or pay-per-view purchase.

Research and information ecosystem

RELX Group has been active in mergers and acquisitions. Elsevier has been joined by businesses which were either complementing or competing in the field of research and publishing and which reinforce its market power, such as Mendeley (after the closure of 2collab), SSRN, bepress/Digital Commons, PlumX, Hivebench, Newsflo. These integrations are seen as a way to exert additional power on the research process. The group contains additional information and analytics companies, particularly LexisNexis and ThreatMetrix.

Conferences

Elsevier conducts conferences, exhibitions and workshops around the world, with over 50 conferences a year covering life sciences, physical sciences and engineering, social sciences, and health sciences.

Pricing

In the 21st century, the subscription rates charged by the company for its journals have been criticized; some very large journals (with more than 5,000 articles) charge subscription prices as high as £9,634, far above average, and many British universities pay more than a million pounds to Elsevier annually. The company has been criticized not only by advocates of a switch to the open-access publication model, but also by universities whose library budgets make it difficult for them to afford current journal prices.

For example, a resolution by Stanford University's senate singled out Elsevier's journals as being "disproportionately expensive compared to their educational and research value", which librarians should consider dropping, and encouraged its faculty "not to contribute articles or editorial or review efforts to publishers and journals that engage in exploitive or exorbitant pricing". Similar guidelines and criticism of Elsevier's pricing policies have been passed by the University of California, Harvard University, and Duke University.

In July 2015, the Association of Universities in the Netherlands (VSNU) announced a plan to start boycotting Elsevier, which refused to negotiate on any Open Access policy for Dutch universities. In December 2016, Nature Publishing Group reported that academics in Germany, Peru and Taiwan are to lose access to Elsevier journals as negotiations had broken down with the publisher.

A complaint about Elsevier/RELX was made to the UK Competition and Markets Authority in December 2016. In October 2018, a competition complaint against Elsevier was filed with the European Commission, alleging anti-competitive practices stemming from Elsevier's confidential subscription agreements and market dominance.

Shill review offer

According to the BBC, "the firm [Elsevier] offered a £17.25 Amazon voucher to academics who contributed to the textbook Clinical Psychology if they would go on Amazon.com and Barnes & Noble (a large US books retailer) and give it five stars." Elsevier said that "encouraging interested parties to post book reviews isn't outside the norm in scholarly publishing, nor is it wrong to offer to nominally compensate people for their time. But in all instances the request should be unbiased, with no incentives for a positive review, and that's where this particular e-mail went too far", and that it was a mistake by a marketing employee.

Blocking text mining research

Elsevier seeks to regulate text and data mining with private licenses, claiming that reading requires extra permission if automated and that the publisher holds copyright on output of automated processes. The conflict on research and copyright policy has often resulted in researchers being blocked from their work.

In November 2015, Elsevier blocked a scientist from performing text mining research at scale on Elsevier papers, even though his institution already pays for access to Elsevier journal content. The data were collected via parsing of downloaded PDF and HTML files, although Elsevier claimed that the method used was screenscraping.

Academic practices

"Who's Afraid of Peer Review"

One of Elsevier's journals was caught in the sting set up by John Bohannon, published in Science, called "Who's Afraid of Peer Review?" The journal Drug Invention Today accepted an obviously bogus paper made up by Bohannon that should have been rejected by any good peer review system. Instead, Drug Invention Today was among many open access journals that accepted the fake paper for publication. As of 2014, this journal had been transferred to a different publisher.

Fake journals

At a 2009 court case in Australia where Merck & Co. was being sued by a user of Vioxx, the plaintiff alleged that Merck had paid Elsevier to publish the Australasian Journal of Bone and Joint Medicine, which had the appearance of being a peer-reviewed academic journal but in fact contained only articles favourable to Merck drugs. Merck described the journal as a "complimentary publication," denied claims that articles within it were ghost written by Merck, and stated that the articles were all reprinted from peer-reviewed medical journals. In May 2009, Elsevier Health Sciences CEO Hansen released a statement regarding Australia-based sponsored journals, conceding that they were "sponsored article compilation publications, on behalf of pharmaceutical clients, that were made to look like journals and lacked the proper disclosures." The statement acknowledged that it "was an unacceptable practice." The Scientist reported that, according to an Elsevier spokesperson, six sponsored publications "were put out by their Australia office and bore the Excerpta Medica imprint from 2000 to 2005," namely the Australasian Journal of Bone and Joint Medicine (Australas. J. Bone Joint Med.), the Australasian Journal of General Practice (Australas. J. Gen. Pract.), the Australasian Journal of Neurology (Australas. J. Neurol.), the Australasian Journal of Cardiology (Australas. J. Cardiol.), the Australasian Journal of Clinical Pharmacy (Australas. J. Clin. Pharm.), and the Australasian Journal of Cardiovascular Medicine (Australas. J. Cardiovasc. Med.). Excerpta Medica was a "strategic medical communications agency" run by Elsevier, according to the imprint's web page. In October 2010, Excerpta Medica was acquired by Adelphi Worldwide.

Chaos, Solitons & Fractals

There was speculation that the editor-in-chief of Elsevier journal Chaos, Solitons & Fractals, Mohamed El Naschie, misused his power to publish his own work without appropriate peer review. The journal had published 322 papers with El Naschie as author since 1993. The last issue of December 2008 featured five of his papers. The controversy was covered extensively in blogs. The publisher announced in January 2009 that El Naschie had retired as editor-in-chief. As of November 2011 the co-Editors-in-Chief of the journal were Maurice Courbage and Paolo Grigolini. In June 2011, El Naschie sued the journal Nature for libel, claiming that his reputation had been damaged by their November 2008 article about his retirement, which included statements that Nature had been unable to verify his claimed affiliations with certain international institutions. The suit came to trial in November 2011 and was dismissed in July 2012, with the judge ruling that the article was "substantially true", contained "honest comment" and was "the product of responsible journalism". The judgement noted that El Naschie, who represented himself in court, had failed to provide any documentary evidence that his papers had been peer-reviewed. Judge Victoria Sharp also found "reasonable and serious grounds" for suspecting that El Naschie used a range of false names to defend his editorial practice in communications with Nature, and described this behavior as "curious" and "bizarre." 

Plagiarism

Some Elsevier journals automatically screen submissions for plagiarism, but not all.

In 2018, Elsevier journal Procedia was reported to have published plagiarism by an Albanian politician in 2012.

Control of journals

Resignation of editorial boards

In November 1999 the entire editorial board (50 persons) of the Journal of Logic Programming (founded in 1984 by Alan Robinson) collectively resigned after 16 months of unsuccessful negotiations with Elsevier Press about the price of library subscriptions. The personnel created a new journal, Theory and Practice of Logic Programming, with Cambridge University Press at a much lower price, while Elsevier continued publication with a new editorial board and a slightly different name (the Journal of Logic and Algebraic Programming).

In 2002, dissatisfaction at Elsevier's pricing policies caused the European Economic Association to terminate an agreement with Elsevier designating Elsevier's European Economic Review as the official journal of the association. The EEA launched a new journal, the Journal of the European Economic Association.

In 2003, the entire editorial board of the Journal of Algorithms resigned to start ACM Transactions on Algorithms with a different, lower-priced, not-for-profit publisher, at the suggestion of Journal of Algorithms founder Donald Knuth. The Journal of Algorithms continued under Elsevier with a new editorial board until October 2009, when it was discontinued.

The same happened in 2005 to the International Journal of Solids and Structures, whose editors resigned to start the Journal of Mechanics of Materials and Structures. However, a new editorial board was quickly established and the journal continues in apparently unaltered form with editors D.A. Hills (Oxford University) and Stelios Kyriakides (University of Texas at Austin).

In August 2006, the entire editorial board of the distinguished mathematical journal Topology handed in their resignation, again because of stalled negotiations with Elsevier to lower the subscription price. This board then launched the new Journal of Topology at a far lower price, under the auspices of the London Mathematical Society. After this mass resignation, Topology remained in circulation under a new editorial board until 2009, when the last issue was published.

The French École Normale Supérieure has stopped having Elsevier publish the journal Annales Scientifiques de l'École Normale Supérieure (as of 2008).

The elevated pricing of field journals in economics, most of which are published by Elsevier, was one of the motivations that moved the American Economic Association to launch the American Economic Journal in 2009.

In May 2015, Stephen Leeder was removed from his role as editor of the Medical Journal of Australia after its publisher decided to outsource the journal's production to Elsevier. As a consequence, all but one of the journal's editorial advisory committee members co-signed a letter of resignation.

In October 2015, the entire editorial staff of the general linguistics journal Lingua resigned in protest of Elsevier's unwillingness to agree to their terms of Fair Open Access. Editor in Chief Johan Rooryck also announced that the Lingua staff would establish a new journal, Glossa.

In January 2019, the entire editorial board of Elsevier's Journal of Informetrics resigned over the open-access policies of its publisher and founded open-access journal called Quantitative Science Studies.

"The Cost of Knowledge" boycott

In 2003 various university librarians began coordinating with each other to complain about Elsevier's "big deal" journal bundling packages, in which the company offered a group of journal subscriptions to libraries at a certain rate, but in which librarians claimed there was no economical option to subscribe to only the popular journals at a rate comparable to the bundled rate. Librarians continued to discuss the implications of the pricing schemes, many feeling pressured into buying the Elsevier packages without other options.

On 21 January 2012, mathematician Timothy Gowers publicly announced he would boycott Elsevier, noting that others in the field have been doing so privately. The three reasons for the boycott are high subscription prices for individual journals, bundling subscriptions to journals of different value and importance, and Elsevier's support for SOPA, PIPA, and the Research Works Act.

Following this, a petition advocating non-cooperation with Elsevier (that is, not submitting papers to Elsevier journals, not refereeing articles in Elsevier journals, and not participating in journal editorial boards), appeared on the site "The Cost of Knowledge". By February 2012 this petition had been signed by over 5,000 academics, growing to over 17,000 by November 2018.

Elsevier disputed the claims, claiming that their prices are below the industry average, and stating that bundling is only one of several different options available to buy access to Elsevier journals. The company also claimed that its profit margins are "simply a consequence of the firm's efficient operation". The academics replied that their work was funded by public money and thus should be freely available.

On 27 February 2012, Elsevier issued a statement on its website that declared that it has withdrawn support from the Research Works Act. Although the Cost of Knowledge movement was not mentioned, the statement indicated the hope that the move would "help create a less heated and more productive climate" for ongoing discussions with research funders. Hours after Elsevier's statement, the sponsors of the bill, US House Representatives Darrell Issa and Carolyn Maloney, issued a joint statement saying that they would not push the bill in Congress.

Plan S

The Plan S open-access initiative, which began in Europe and has since spread to some US research funding agencies would force researchers receiving some grants to publish in open access journals by 2020. A spokesman for Elsevier said "If you think that information should be free of charge, go to Wikipedia". In September 2018 UBS advised to sell Elsevier (RELX) stocks, noting that Plan S could affect 5-10% of scientific funding and may force Elsevier to reduce pricing.

Relationship with academic institutions

Finland

In 2015 Finnish research organizations paid a total of 27 million euros in subscription fees. Over one third of the total costs went to Elsevier. The information was revealed after successful court appeal following a denied request on the subscription fees, due to confidentiality clauses in contracts with the publishers. Establishing of this fact lead to creation of tiedonhinta.fi petition demanding more reasonable pricing and open access to content signed by more than 2800 members of the research community. While deals with other publishers have been made, this was not the case for Elsevier, leading to the nodealnoreview.org boycott of the publisher signed more than 600 times.

In January 2018, it was confirmed that a deal had been reached between those concerned.

France

The French Couperin consortium agreed in 2019 to a 4-year contract with Elsevier, despite criticism from the scientific community.

Germany

Almost no academic institution in Germany is subscribed to Elsevier.

Germany's DEAL project (Projekt DEAL) which includes over 60 major research institutions, has announced that all of its members are cancelling their contracts with Elsevier, effective 1 January 2017. The boycott is in response to Elsevier's refusal to adopt "transparent business models" to "make publications more openly accessible". Horst Hippler, spokesperson for the DEAL consortium states that "taxpayers have a right to read what they are paying for" and that "publishers must understand that the route to open-access publishing at an affordable price is irreversible". In July 2017, another 13 institutions announced that they would also be cancelling their subscriptions to Elsevier journals. In August 2017, at least 185 German institutions had cancelled their contracts with Elsevier. In 2018, whilst negotiations were ongoing, around 200 German universities who cancelled their subscriptions to Elsevier journals were granted complimentary open access to them until this ended in July of the year.

On 19 December 2018 the Max Planck Society (MPS) announced that the existing subscription agreement with Elsevier would not be renewed after the expiration date of 31 December 2018. The Max Planck Society counts 14.000 scientists in 84 research institutes, publishing 12.000 articles each year.

Hungary

In March 2018, the Hungarian Electronic Information Service National Programme entered negotiations on its 2019 Elsevier subscriptions, asking for a read-and-publish deal. Negotiations were ended by the Hungarian consortium in December 2018, and the subscription was not renewed.

Iran

In 2013, Elsevier changed its policies in response to sanctions announced by the US Office of Foreign Assets Control that year. This included a request that all Elsevier journals avoid publishing papers by Iranian nationals which are employed by the Iranian government. Elsevier executive Mark Seeley expressed regret on behalf of the company but did not announce an intention to challenge this interpretation of the law.

Italy

CRUI (association of Italian universities) sealed a 5-year-long deal for 2018-2022, despite protests from the scientific community, protests focused on aspects such as the lack of prevention of cost increases by means of the double dipping.

Netherlands

In 2015 a consortium of all of Netherlands' 14 universities threatened to boycott Elsevier if it could not agree that articles by Dutch authors would be made open access and settled with the compromise of 30% of its Dutch papers becoming open access by 2018. Gerard Meijer, president of Radboud University in Nijmegen and lead negotiator on the Dutch side notes that "it's not the 100% that I hoped for".

Norway

In March 2019, the Norwegian government on behalf of 44 institutions — universities, university colleges, research institutes and hospitals — decided to break negotiations on renewal of their subscription deal with Elsevier, because of disagreement regarding open access policy and Elsevier's unwillingness to reduce the cost of reading access.

South Korea

In 2017, over 70 university libraries confirmed a "contract boycott" movement involving three publishers including Elsevier. As of January 2018, whilst negotiations remain underway, a decision will be made as to whether or not continue the participating libraries will continue the boycott. It was subsequently confirmed that an agreement had been reached.

Sweden

In May 2018, the Bibsam Consortium, which negotiates license agreements on behalf of all Swedish universities and research institutes, decided not to renew their contract with Elsevier, alleging that the publisher does not meet the demands of transition towards a more open access model, and referring to the rapidly increasing costs for publishing. Swedish universities will still have access to articles published before 30 June 2018. Astrid Söderbergh Widding, Chairman of the Bibsam Consortium, said that "the current system for scholarly communication must change and our only option is to cancel deals when they don't meet our demands for a sustainable transition to open access".

Sweden has a goal of open access by 2026.

Taiwan

In Taiwan more than 75% of universities, including the region's top 11 institutions, have joined a collective boycott against Elsevier. On 7 December 2016, the Taiwanese consortium, CONCERT, which represents more than 140 institutions, announced it would not renew its contract with Elsevier.

United States

In March 2018, Florida State University's faculty elected to cancel its $2 million subscription to a bundle of several journals. Starting in 2019 it will instead buy access to titles à la carte.

In February 2019, the University of California said it would terminate subscriptions "in push for open access to publicly funded research." After months of negotiations over open access to research by UC researchers and prices for subscriptions to Elsevier journals, a press release by the UC Office of the President issued Thursday, 28 February 2019 stated "Under Elsevier’s proposed terms, the publisher would have charged UC authors large publishing fees on top of the university’s multi-million dollar subscription, resulting in much greater cost to the university and much higher profits for Elsevier." On July 10, 2019 Elsevier began restricting access to all new paywalled articles and approximately 5% of paywalled articles published before 2019.

Dissemination of research

Lobbying efforts against open access

Elsevier have been known to be involved in lobbying against open access. These have included the likes of:

Selling open access articles

In 2014, 2015, 2016 and 2017, Elsevier was found to be selling some articles which should have been open access, but had been put behind a paywall. A related case occurred in 2015, when Elsevier charged for downloading an open access article from a journal published by John Wiley & Sons. However, it was not clear whether Elsevier was in violation of the license under which the article was made available on their website.

Action against academics posting their own articles online

In 2013, Digimarc, a company representing Elsevier, told the University of Calgary to remove articles published by faculty authors on university web pages; although such self-archiving of academic articles may be legal under the fair dealing provisions in Canadian copyright law, the university complied. Harvard University and the University of California, Irvine also received takedown notices for self-archived academic articles, a first for Harvard, according to Peter Suber.

Months after its acquisition of Academia.edu rival Mendeley, Elsevier sent thousands of takedown notices to Academia.edu, a practice that has since ceased following widespread complaint by academics, according to Academia.edu founder and chief executive Richard Price.

After Elsevier acquired the repository SSRN in May 2016 academics started complaining that some of their work has been removed without notice. The action was explained as a technical error.

Sci-Hub and LibGen lawsuit

In 2015 Elsevier filed a lawsuit against the sites Sci-Hub and LibGen, which make copyright protected articles available for free. Elsevier also claimed illegal access to institutional accounts.

Rejection of the Initiative for Open Citations

Among the major academic publishers, Elsevier alone declined to join the Initiative for Open Citations. In the context of the resignation of the Journal of Informetrics' editorial board, Elsevier stated:
Elsevier invests significantly in citation extraction technology. While these are made available to those who wish to license this data, Elsevier cannot make such a large corpus of data, to which it has added significant value, available for free.

Sunday, March 8, 2020

Applied Biosystems

From Wikipedia, the free encyclopedia
 
S.A. Edit this on Wikidata
Industrybiotechnology Edit this on Wikidata
Founded1981 Edit this on Wikidata
HeadquartersWaltham, Massachusetts, USA
Key people
Marc N. Casper (President & CEO)
Websitewww.thermofisher.com

Applied Biosystems is one of the various brands under the Life Technologies brand of Thermo Fisher Scientific corporation. The brand is focused on integrated systems for genetic analysis, which include computerized machines and the consumables used within them (such as reagents).

In 2008, a merger between Applied Biosystems and Invitrogen was finalized, creating Life Technologies. The latter was acquired by Thermo Fisher Scientific in 2014. Prior to 2008, the Applied Biosystems brand was owned by various entities in a corporate group parented by PerkinElmer. The roots of Applied Biosystems trace back to GeneCo (Genetic Systems Company), a pioneer biotechnology company founded in 1981 in Foster City, California. Through the 1980s and early 1990s, Applied Biosystems, Inc. operated independently and manufactured biochemicals and automated genetic engineering and diagnostic research instruments, including the principal brand of DNA sequencing machine used by the Human Genome Project consortium centers. Applied Biosystems' close ties to the consortium project led to the idea for the founding of Celera Genomics in 1998 as one of several independent competitors to the consortium.

In 1993 Applied Biosystems, Inc. was delisted from the NASDAQ when it was acquired by the old company known then as Perkin-Elmer. As the PE Applied Biosystems Division under that parent in 1998, it became consolidated with other acquisitions as the primary PE Biosystems Division. In 1999 its parent company reorganized and changed its name to PE Corporation, and the PE Biosystems Group (formerly again became publicly traded, as a tracking stock of its parent, along with its sister tracking stock company, Celera Genomics. In 2000 the parent became Applera Corporation. The Applied Biosystems name also returned that year, in the name change of the tracking stock from PE Biosystems Group to Applera Corporation-Applied Biosystems Group, an S&P 500 company, which remains as a publicly traded operating group within Applera Corp., along with its sibling operating group, Applera Corporation-Celera Group. Applera derives its name from the combination of its two component groups' names, Appl(iedCel)era In November 2008, a merger between Applied Biosystems and Invitrogen was finalized "creating a global leader in biotechnology reagents and systems". The new company was called Life Technologies.

History

Company History
Year Company Name
1981 Genetic Systems Company (GeneCo)
1982 Applied Biosystems, Inc. (ABI)
1993 Applied Biosystems, Perkin-Elmer
1996 PE Applied Biosystems
1998 PE Biosystems
2000 Applied Biosystems Group, Applera Corp
2002 Applied Biosystems
2008 Life Technologies
2014 Thermo Fisher Scientific

In May 1981, the company was founded by two scientist/engineers from Hewlett Packard, Sam Eletr and André Marion based on technology developed by Leroy Hood and Marvin H. Caruthers.

In August 1982, Applied Biosystems released its first commercial instrument, the Model 470A Protein Sequencer. The machine enabled scientists to determine the order of amino acids within a purified protein, which in turn correlated with the protein's function. With 40 employees, the company, reported first-time revenue of US$402,000.

In 1983 the company was led by its president and Chairman of the Board, Sam Eletr and Chief Operating Officer Andre Marion, the company doubled its number of employees to 80, and its stock went public on the NASDAQ exchange under the symbol ABIO, with revenues of US$5.9 million. A new product was a fluorescent molecular tag for immunodiagnostic assays.

The company released its second commercial instrument, the Model 380A DNA Synthesizer, which made oligonucleotides, short DNA strands, for polymerase chain reaction (PCR), DNA sequencing, and gene identification. The two sequencer and synthesizer products allowed molecular biologists to clone genes by building oligonucleotides with the desired protein's DNA sequence.

Automated DNA sequencing began at the California Institute of Technology, using fluorescent dyes, with Rights to the technology granted to Applied Biosystems. At CIT, Dr. Leroy Hood and Dr. Lloyd Smith, together pioneered those first DNA sequencing machines.

In 1984, Applied Biosystems sales revenue tripled to over US$18 million, with a second yearly profit, and with over 200 employees. Services included synthesizing custom DNA and protein fragments, and the sequencing of protein samples submitted from customers. The third major instrument made by Applied, the Model 430A Peptide Synthesizer, was introduced.

In 1985, Applied Biosystems sales revenue grew nearly 70% to over US$35 million, with a third yearly profit. Two new products included the Model 380B DNA Synthesizer and the 381A DNA Synthesizer. That year the company went international for the first time, when it established a wholly owned subsidiary in Great Britain to save shipping costs on chemical sales, which overall by then accounted for 17% of sales.

Also in 1985, Applied Biosystems acquired Brownlee Labs, a manufacturer of columns and pumps for high-performance liquid chromatography (HPLC) systems, after its founder, Robert Brownlee was diagnosed with AIDS-related complex in 1984. Brownlee's technology brought the new on-line 120A PTH Amino Acid Analyzer.

However, Brownlee then began a new company, which was viewed by Applied as a competitor. In 1989 Applied and Brownlee settled in a lawsuit over the conflict. As late as 1990, Brownlee publicly discussed what had been his contributions in the rocky relationship with Applied, before he died early the next year.

In 1986, Andre Marion became President and Chief Executive Officer. Sales revenue increased by 45% to nearly US$52 million. The company introduced six new products, totalling eleven automated instruments. The release of the Model 370A DNA Sequencing System, using fluorescent tags, revolutionized gene discovery. The Model 340A Nucleic Acid Extractor became used in medical labs to isolate DNA from bacteria, blood, and tissue.

In 1987, Sam Eletr resigned for health reasons. Revenues increase by 63% to nearly US$85 million, with 788 employees, and another six new instruments. Applied Biosystems acquired the Kratos Division of Spectros International PLC.

By 1988, the product line had increased to over 25 different automated instruments, over 400 liquid chromatography columns and components, and about 320 chemicals, biochemicals, and consumables. Sales revenue grew to over US$132 million, with almost 1000 employees in eight countries. In that year for the first time, genetic science reached the milestone of being able to identify individuals by their DNA.

In 1989, sales revenue reached nearly $160 million. Applied Biosystems maintained 15 offices in 9 different countries, and introduced four new products. The company developed enzyme-based reagent kits made by Promega Corporation, and in the new field of bioinformatics, licensed with TRW Inc.. Also, joint marketing began with Perkin-Elmer Corporation and Cetus Corporation (formerly of instruments and reagents for DNA replication, the fastest growing segment in biotechnology.

In 1990, instrument sales underwent a cyclical slowdown, as the economy entered the 1990–91 recession. For the first year, Applied revenues did not grow, and came in at less than $159 million, with 1,334 employees. New company developments included new instrumentation for robotics and detection of DNA fragments using the company's fluorescent labelling.

Also in 1990, the U.S. government approved financing to support the Human Genome Project. Dr. James D. Watson, who founded the consortium, forecast that the project could be completed in 15 years from its 1990 starting date, at a cost of cost US$3 billion. Over the next couple years, Japan began a project to sequence the rice genome, and other laboratories initiated programs to sequence the mouse, fruit fly, and yeast genomes.

In 1991, Applied sales revenue grew slightly, to almost $164 million, with consumables and service contracts up by 24% to account for 47% of total sales, and DNA sequencer and DNA synthesis instruments having record sales. Forty-five new consumable products and six new instruments were introduced.

In 1992, sales revenue grew by more than 11% to over $182 million, with Europe representing 25% of revenue, and Asia and the Pacific Rim accounting for 26%. The company formed a new subsidiary, Lynx Therapeutics, Inc., to focus on antisense DNA research in the area of therapeutics for chronic myelogenous leukemia, melanoma, colorectal cancer, and AIDS.

Perkin-Elmer

In February 1993 Applied Biosystems was acquired by Perkin-Elmer, and became the Applied Biosystems Division, as part of the Life Sciences markets segment of that company. Andre Marion, who had been Applied Biosystems's Chairman, President and CEO, became a Senior Vice President of Perkin-Elmer, and President of the Applied Biosystems Division. That year the company was the world's leading manufacturer of instruments and reagents for polymerase chain reaction (PCR). It marketed PCR reagents kits in alliance with Hoffman-La Roche Inc.

In 1994, Perkin-Elmer reported net revenues of over $1 billion, of which Life Sciences accounted for 42% of the business. The company has 5,954 employees. A brand-new highly competitive genomics industry had formed for the development of new pharmaceuticals, based on the work of the Human Genome Project. Companies such as Sequana Therapeutics in San Diego, Human Genome Sciences in Maryland, Myriad Genetics in Utah, INCYTE Pharmaceuticals (later Incyte Genomics) in California, and Millennium Pharmaceuticals relied on the Applied Biosystems Division, which made thermal cyclers and automated sequencers for these new genomics companies.

In 1995, upon Andre Marion retirement, Mike Hunkapiller became President of PE Applied Biosystems Division which sold its 30,000th thermal cycler. To meet Human Genome Project goals, Perkin-Elmer developed mapping kits with markers every 10 million bases along each chromosome. Also that year, DNA fingerprinting using PCR became accepted in court as reliable forensic evidence.

In 1996, Perkin-Elmer acquired Tropix, Inc., a chemiluminescence company, for its life sciences division.

PE Applied Biosystems

In September 1995, Tony L. White from Baxter International Inc. became President and Chief Executive Officer of Perkin-Elmer. In 1996 the company was reorganized into two separate operating divisions, Analytical Instruments and PE Applied Biosystems. The PE Applied Biosystems division accounted for half of Perkin-Elmer's total revenue, with net revenues up by 26%.

In 1997, revenues reached almost US$1.3 billion, of which PE Applied Biosystems was US$653 million. The company acquired GenScope, Inc., and Linkage Genetics, Inc. The Linkage Genetics unit was combined with Zoogen to form PE AgGen, focused on genetic analysis services for plant and animal breeding. The PE Applied Biosystems division partnered with Hyseq, Inc., for work on the new DNA chip technology, and also worked with Tecan U.S., Inc., on combinatorial chemistry automation systems, and also with Molecular Informatics, Inc. on genetic data management and analysis automated systems.

PE Biosystems

In 1998, PE Applied Biosystems became PE Biosystems, and the division's revenues reached US$921.8 million. In January 1998 Perkin-Elmer acquired PerSeptive Biosystems (formerly of Framingham, Massachusetts. It was a leader in the bio-instrumentation field where it made biomolecule purification systems for protein analysis. Noubar B. Afeyan, Ph.D., had been the founder, Chairman, and CEO of PerSeptive, and with the Perkin-Elmer successor company he set up the later tracking stock for Celera.

In 1998, Perkin-Elmer formed the PE Biosystems division, by consolidating Applied Biosystems, PerSeptive Biosystems, Tropix and PE Informatics. Informatics was formed from the Perkin-Elmer combination of two other acquisitions, Molecular Informatics and Nelson Analytical Systems, with existing units of Perkin-Elmer.

While planning the next new generation of machines, PE Biosystems' president, Michael W. Hunkapiller, calculated that it would be possible for their own private industry to decode the human genome before the academic consortium could complete it, by using the resources of a single, industrial-scale center, even though it would require starting from scratch. It was a bold prediction, given that the consortium target date set by Dr. Watson back in 1990 had been the forward year of 2005, only seven years away, and with the consortium already half the way to the completion target date.

Also, it meant that Dr. Hunkapiller's idea would require competing against his own customers, to all of whom Applied Biosystems sold its sequencing machines and their chemical reagents. However, he calculated that it would also mean doubling the market for that equipment.

Hunkapiller brought in Dr. J. Craig Venter to direct the project. Tony White, president of the Perkin-Elmer Corporation backed Hunkapiller on the venture. They organized the new company to accomplish the task. In May 1998, Celera Genomics was formed, to rapidly accelerate the human DNA sequencing process. Dr. Venter boldly declared to the media that he would complete the genome decoding by 2001. That bold announcement prompted the academic consortium to accelerate their own deadline by a couple years, to 2003.

Also in 1998, PE Biosystems partnered with Hitachi, Ltd. to develop electrophoresis-based genetic analysis systems, which resulted in their chief new genomics instrument, the ABI PRISM 3700 DNA Analyzer, which advanced the Human Genome sequencing project by nearly five years ahead of schedule. The partnerships sold hundreds of the 3700 analyzers to Celera, and also to others worldwide.

The new machine cost US$300,000 each, but was a major leap beyond its predecessor, the 377, and was fully automated, allowing genetic decoding to run around the clock with little supervision. According to Venter, the machine was so revolutionary that it could decode in a single day the same amount of genetic material that most DNA labs could produce in a year.

The public consortium also bought one of the PE Biosystems 3700 sequencers, and had plans to buy 200 more. The machine proved to be so fast that by late March 1999 the consortium announced that it had revised its timeline, and would release by the Spring of 2000 a "first draft sequence" for 80% of the human genome.

At year end 1998, the PE Biosystems Group's sales reached US$940 million.

PE Corporation

In 1999, to focus on the new genomics, Perkin-Elmer Corporation was renamed PE Corporation, and sold its old Analytical Instruments division to EG&G, Inc., which also acquired the Perkin-Elmer name. PE Biosystems remained with PE Corp., and became PE Biosystems Group, with 3,500 employees and net revenues of over $1.2 billion. New instruments were developed and sold for forensic human identification, protein identification and characterization, metabolite pathway identification, and lead compound identification from combinatorial libraries.

On April 27, 1999, the shareholders of Perkin-Elmer Corporation approved the reorganization of Perkin-Elmer into PE Corporation, a pure-play life science company. Each share of the Perkin-Elmer stock (PKN) was to be exchanged for one share and for ​ 12 of a share respectively of the two new common share tracking stocks for the two component Life Sciences groups, PE Biosystems Group and Celera Genomics Group.

On April 28, 1999, the two replacement tracking stocks for the new PE Corporation were issued to shareholders. Dr. Michael W. Hunkapiller remained as a Senior Vice President of PE Corporation, and as president of PE Biosystems.

On May 6, 1999, the recapitalization of the company resulted in issuance of the two new classes of common stock, called PE Corporation-PE Biosystems Group Common Stock and PE Corporation-Celera Genomics Group Common Stock. On that date, trading began in both new stocks on the New York Stock Exchange, to great excitement.

On June 17, 1999 the Board of PE Corporation announced a two-for-one split of PE Biosystems Group Common Stock.

By June 2000, the genomics segment of the technology bubble was peaking. Celera Genomics (CRA) and PE Biosystems (PEB) were among five genetics pioneers leading at that time, along with Incyte Genomics, Human Genome Sciences, and Millennium Pharmaceuticals. All five of those stocks by then had exceeded a price above $100 per share in the market, before ultimately crashing back down.

Applera

On November 30, 2000, PE Corporation changed its name to Applera, combining the two partial names Applied and Celera into one, with 5,000 employees. PE Biosystems Group was renamed once again to Applied Biosystems Group, and changed its ticker symbol from PEB to ABI. Its net revenues rose to almost US$1.4 billion. Celera that year made milestone headlines when it announced that it had completed the sequencing and first assembly of the two largest genomes in history, that of the fruit fly, and of the human.

In 2001, the Applied Biosystems division of Applera reached revenues of US$1.6 billion, and developed a new workstation instrument specifically for the new field of proteomics, which had become Celera's new core business focus, as it shifted away from gene discovery. The instrument analyzed 1,000 protein samples per hour.

On April 22, 2002, the Celera Genomics Group announced its decision to shift the role of marketing data from its genetic database over to its sister company, the Applied Biosystems Group. Celera would instead develop pharmaceutical drugs. Applied Biosystems was a better fit for the database, because Applied already had the huge sales force in place for the marketing of its instruments. Plans were to expand those sales and those of the database into an electronic commerce system.

In 2002, Applied Biosystems reached revenues of US$1.6 billion for the year, and took control from Celera of the support of Celera Discovery System (CDS), a data tool to answer specific genomic and proteomic queries, involving the new genetic data field of tens of thousands of single-nucleotide polymorphisms (SNPs) within the human genome. The company developed another new tool, which combined the first ever union of triple quadrupole and ion trap technologies, in proteomics research.

The database itself would remain with Celera, because of shareholder approval complications. Celera would retain responsibility for its maintenance and support to existing customers, and would receive royalties from Applied Biosystems.

In 2003, Catherine Burzik joined Applied's management, from Ortho-Clinical Diagnostics. Applied developed a new tool which measured antibody/antigen binding in real-time kinetic analysis of up to 400 binding interactions simultaneously.

In 2004, Mike Hunkapiller retired and Cathy Burzik replaced him as President of Applied Biosystems. Applera collaborated with General Electric, Abbott Laboratories, Seattle Genetics, and Merck in diagnostics development. Applied Biosystmes also teamed with Northrop Grumman and Cepheid of Sunnyvale, California, to detect Bacillus anthracis during the anthrax contamination case of the U.S. Postal Service.

In 2005, the company released new tools for small molecule quantitation in pharmaceutical drug development. In Mexico, Applied Biosystems collaborated with the National Institute of Genomic Medicine of Mexico (Instituto Nacional de Medicina Genomica or INMEGEN), and established an Applied Biosystems Sequencing and Genotyping Unit at INMEGEN.

In 2006, Applied Biosystems acquired the Research Products Division of Ambion, a supplier of RNA-based reagents and products. That year, with the Influenza A Subtype H5N1 "avian flu" strain scare, the company launched a global initiative to identify and track such infectious diseases.

In 2006, Applied Biosystems also acquired Agencourt Personal Genomics, located in Beverly, MA, to commercialize Agencourt's SOLiD sequencing system.

In 2007, ABI Solid Sequencing - a next-gen DNA sequencing platform was announced. Mark Stevenson was appointed President and Chief Operating Officer of Applied Biosystems.

In November 2008, Applied Biosystems merged with Invitrogen, forming Life Technologies, which was acquired by Thermo Fisher Scientific in 2014.

DNA sequencer

From Wikipedia, the free encyclopedia

DNA-Sequencers from Flickr 57080968.jpg
DNA sequencers
ManufacturersRoche, Illumina, Life Technologies, Beckman Coulter, Pacific Biosciences

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.

The first automated DNA sequencer, invented by Lloyd M. Smith, was introduced by Applied Biosystems in 1987. It used the Sanger sequencing method, a technology which formed the basis of the “first generation” of DNA sequencers and enabled the completion of the human genome project in 2001. This first generation of DNA sequencers are essentially automated electrophoresis systems that detect the migration of labelled DNA fragments. Therefore, these sequencers can also be used in the genotyping of genetic markers where only the length of a DNA fragment(s) needs to be determined (e.g. microsatellites, AFLPs).

The Human Genome Project spurred the development of cheaper, high throughput and more accurate platforms known as Next Generation Sequencers (NGS) to sequence the human genome. These include the 454, SOLiD and Illumina DNA sequencing platforms. Next generation sequencing machines have increased the rate of DNA sequencing substantially, as compared with the previous Sanger methods. DNA samples can be prepared automatically in as little as 90 mins, while a human genome can be sequenced at 15 times coverage in a matter of days.

More recent, third-generation DNA sequencers such as SMRT and Oxford Nanopore measure the addition of nucleotides to a single DNA molecule in real time.

Because of limitations in DNA sequencer technology these reads are short compared to the length of a genome therefore the reads must be assembled into longer contigs. The data may also contain errors, caused by limitations in the DNA sequencing technique or by errors during PCR amplification. DNA sequencer manufacturers use a number of different methods to detect which DNA bases are present. The specific protocols applied in different sequencing platforms have an impact in the final data that is generated. Therefore, comparing data quality and cost across different technologies can be a daunting task. Each manufacturer provides their own ways to inform sequencing errors and scores. However, errors and scores between different platforms cannot always be compared directly. Since these systems rely on different DNA sequencing approaches, choosing the best DNA sequencer and method will typically depend on the experiment objectives and available budget.

History

The first DNA sequencing methods were developed by Gilbert (1973) and Sanger (1975). Gilbert introduced a sequencing method based on chemical modification of DNA followed by cleavage at specific bases whereas Sanger’s technique is based on dideoxynucleotide chain termination. The Sanger method became popular due to its increased efficiency and low radioactivity. The first automated DNA sequencer was the AB370A, introduced in 1986 by Applied Biosystems. The AB370A was able to sequence 96 samples simultaneously, 500 kilobases per day, and reaching read lengths up to 600 bases. This was the beginning of the “first generation” of DNA sequencers, which implemented Sanger sequencing, fluorescent dideoxy nucleotides and polyacrylamide gel sandwiched between glass plates - slab gels. The next major advance was the release in 1995 of the AB310 which utilized a linear polymer in a capillary in place of the slab gel for DNA strand separation by electrophoresis. These techniques formed the base for the completion of the human genome project in 2001. The human genome project spurred the development of cheaper, high throughput and more accurate platforms known as Next Generation Sequencers (NGS). In 2005, 454 Life Sciences released the 454 sequencer, followed by Solexa Genome Analyzer and SOLiD (Supported Oligo Ligation Detection) by Agencourt in 2006. Applied Biosystems acquired Agencourt in 2006, and in 2007, Roche bought 454 Life Sciences, while Illumina purchased Solexa. Ion Torrent entered the market in 2010 and was acquired by Life Technologies (now Thermo Fisher Scientific). These are still the most common NGS systems due to their competitive cost, accuracy, and performance.

More recently, a third generation of DNA sequencers was introduced. The sequencing methods applied by these sequencers do not require DNA amplification (polymerase chain reaction – PCR), which speeds up the sample preparation before sequencing and reduces errors. In addition, sequencing data is collected from the reactions caused by the addition of nucleotides in the complementary strand in real time. Two companies introduced different approaches in their third-generation sequencers. Pacific Biosciences sequencers utilize a method called Single-molecule real-time (SMRT), where sequencing data is produced by light (captured by a camera) emitted when a nucleotide is added to the complementary strand by enzymes containing fluorescent dyes. Oxford Nanopore Technologies is another company developing third-generation sequencers using electronic systems based on nanopore sensing technologies.

Manufacturers of DNA sequencers

DNA sequencers have been developed, manufactured, and sold by the following companies, among others.

Roche

The 454 DNA sequencer was the first next-generation sequencer to become commercially successful. It was developed by 454 Life Sciences and purchased by Roche in 2007. 454 utilizes the detection of pyrophosphate released by the DNA polymerase reaction when adding a nucleotide to the template strain.

Roche currently manufactures two systems based on their pyrosequencing technology: the GS FLX+ and the GS Junior System. The GS FLX+ System promises read lengths of approximately 1000 base pairs while the GS Junior System promises 400 base pair reads. A predecessor to GS FLX+, the 454 GS FLX Titanium system was released in 2008, achieving an output of 0.7G of data per run, with 99.9% accuracy after quality filter, and a read length of up to 700bp. In 2009, Roche launched the GS Junior, a bench top version of the 454 sequencer with read length up to 400bp, and simplified library preparation and data processing.

One of the advantages of 454 systems is their running speed, Manpower can be reduced with automation of library preparation and semi-automation of emulsion PCR. A disadvantage of the 454 system is that it is prone to errors when estimating the number of bases in a long string of identical nucleotides. This is referred to as a homopolymer error and occurs when there are 6 or more identical bases in row. Another disadvantage is that the price of reagents is relatively more expensive compared with other next-generation sequencers.

In 2013 Roche announced that they would be shutting down development of 454 technology and phasing out 454 machines completely in 2016.

Roche produces a number of software tools which are optimised for the analysis of 454 sequencing data. GS Run Processor converts raw images generated by a sequencing run into intensity values. The process consists of two main steps: image processing and signal processing. The software also applies normalization, signal correction, base-calling and quality scores for individual reads. The software outputs data in Standard Flowgram Format (or SFF) files to be used in data analysis applications (GS De Novo Assembler, GS Reference Mapper or GS Amplicon Variant Analyzer). GS De Novo Assembler is a tool for de novo assembly of whole-genomes up to 3GB in size from shotgun reads alone or combined with paired end data generated by 454 sequencers. It also supports de novo assembly of transcripts (including analysis), and also isoform variant detection. GS Reference Mapper maps short reads to a reference genome, generating a consensus sequence. The software is able to generate output files for assessment, indicating insertions, deletions and SNPs. Can handle large and complex genomes of any size. Finally, the GS Amplicon Variant Analyzer aligns reads from amplicon samples against a reference, identifying variants (linked or not) and their frequencies. It can also be used to detect unknown and low-frequency variants. It includes graphical tools for analysis of alignments.

Illumina

Illumina Genome Analyzer II sequencing machine

Illumina produces a number of next-generation sequencing machines using technology acquired from Manteia Predictive Medicine and developed by Solexa. Illumina makes a number of next generation sequencing machines using this technology including the HiSeq, Genome Analyzer IIx, MiSeq and the HiScanSQ, which can also process microarrays.

The technology leading to these DNA sequencers was first released by Solexa in 2006 as the Genome Analyzer. Illumina purchased Solexa in 2007. The Genome Analyzer uses a sequencing by synthesis method. The first model produced 1G per run. During the year 2009 the output was increased from 20G per run in August to 50G per run in December. In 2010 Illumina released the HiSeq 2000 with an output of 200 and then 600G per run which would take 8 days. At its release the HiSeq 2000 provided one of the cheapest sequencing platforms at $0.02 per million bases as costed by the Beijing Genomics Institute.

In 2011 Illumina released a benchtop sequencer called the MiSeq. At its release the MiSeq could generate 1.5G per run with paired end 150bp reads. A sequencing run can be performed in 10 hours when using automated DNA sample preparation.

The Illumina HiSeq uses two software tools to calculate the number and position of DNA clusters to assess the sequencing quality: the HiSeq control system and the real-time analyzer. These methods help to assess if nearby clusters are interfering with each other.

Life Technologies

Life Technologies (now Thermo Fisher Scientific) produces DNA sequencers under the Applied Biosystems and Ion Torrent brands. Applied Biosystems makes the SOLiD next-generation sequencing platform, and Sanger-based DNA sequencers such as the 3500 Genetic Analyzer. Under the Ion Torrent brand, Applied Biosystems produces four next-generation sequencers: the Ion PGM System, Ion Proton System, Ion S5 and Ion S5xl systems. The company is also believed to be developing their new capillary DNA sequencer called SeqStudio that will be released early 2018.

SOLiD systems was acquired by Applied Biosystems in 2006. SOLiD applies sequencing by ligation and dual base encoding. The first SOLiD system was launched in 2007, generating reading lengths of 35bp and 3G data per run. After five upgrades, the 5500xl sequencing system was released in 2010, considerably increasing read length to 85bp, improving accuracy up to 99.99% and producing 30G per 7-day run.
The limited read length of the SOLiD has remained a significant shortcoming and has to some extent limited its use to experiments where read length is less vital such as resequencing and transcriptome analysis and more recently ChIP-Seq and methylation experiments. The DNA sample preparation time for SOLiD systems has become much quicker with the automation of sequencing library preparations such as the Tecan system.

The colour space data produced by the SOLiD platform can be decoded into DNA bases for further analysis, however software that considers the original colour space information can give more accurate results. Life Technologies has released BioScope, a data analysis package for resequencing, ChiP-Seq and transcriptome analysis. It uses the MaxMapper algorithm to map the colour space reads.

Beckman Coulter

Beckman Coulter (now Danaher) has previously manufactured chain termination and capillary electrophoresis-based DNA sequencers under the model name CEQ, including the CEQ 8000. The company now produces the GeXP Genetic Analysis System, which uses dye terminator sequencing. This method uses a thermocycler in much the same way as PCR to denature, anneal, and extend DNA fragments, amplifying the sequenced fragments.

Pacific Biosciences

Pacific Biosciences produces the PacBio RS and Sequel sequencing systems using a single molecule real time sequencing, or SMRT, method. This system can produce read lengths of multiple thousands of base pairs. Higher raw read errors are corrected using either circular consensus - where the same strand is read over and over again - or using optimized assembly strategies. Scientists have reported 99.9999% accuracy with these strategies. The Sequel system was launched in 2015 with an increased capacity and a lower price.

Oxford Nanopore MinION sequencer (lower right) was used in the first-ever DNA sequencing in space in August 2016 by astronaut Kathleen Rubins.

Oxford Nanopore

Oxford Nanopore Technologies has begun shipping early versions of its nanopore sequencing MinION sequencer to selected labs. The device is four inches long and gets power from a USB port. MinION decodes DNA directly as the molecule is drawn at the rate of 450 bases/second through a nanopore suspended in a membrane. Changes in electric current indicate which base is present. It is 60 to 85 percent accurate, compared with 99.9 percent in conventional machines. Even inaccurate results may prove useful because it produces long read lengths. GridION is a slightly larger sequencer that processes up to five MinION flow cells at once. PromethION is another (unreleased) product that will use as many as 100,000 pores in parallel, more suitable for high volume sequencing.

Inequality (mathematics)

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