Editing DNA sequencing (section)

=== High-throughput sequencing (HTS) methods ===
[[File:History of sequencing technology.jpg|thumb|upright=2| History of sequencing technology{{hsp}}<ref>{{cite journal |doi = 10.3389/fbioe.2020.01032|title = Review on the Application of Machine Learning Algorithms in the Sequence Data Mining of DNA|year = 2020|last1 = Yang|first1 = Aimin|last2 = Zhang|first2 = Wei|last3 = Wang|first3 = Jiahao|last4 = Yang|first4 = Ke|last5 = Han|first5 = Yang|last6 = Zhang|first6 = Limin|journal = Frontiers in Bioengineering and Biotechnology|volume = 8|page = 1032|pmid = 33015010|pmc = 7498545|doi-access = free}}</ref>]]

Several new methods for DNA sequencing were developed in the mid to late 1990s and were implemented in commercial [[DNA sequencers]] by 2000. Together these were called the "next-generation" or "second-generation" sequencing (NGS) methods, in order to distinguish them from the earlier methods, including [[Sanger sequencing]]. In contrast to the first generation of sequencing, NGS technology is typically characterized by being highly scalable, allowing the entire genome to be sequenced at once. Usually, this is accomplished by fragmenting the genome into small pieces, randomly sampling for a fragment, and sequencing it using one of a variety of technologies, such as those described below. An entire genome is possible because multiple fragments are sequenced at once (giving it the name "massively parallel" sequencing) in an automated process.

NGS technology has tremendously empowered researchers to look for insights into health, anthropologists to investigate human origins, and is catalyzing the "[[Personalized medicine|Personalized Medicine]]" movement. However, it has also opened the door to more room for error. There are many software tools to carry out the computational analysis of NGS data, often compiled at online platforms such as CSI NGS Portal, each with its own algorithm. Even the parameters within one software package can change the outcome of the analysis. In addition, the large quantities of data produced by DNA sequencing have also required development of new methods and programs for sequence analysis. Several efforts to develop standards in the NGS field have been attempted to address these challenges, most of which have been small-scale efforts arising from individual labs. Most recently, a large, organized, FDA-funded effort has culminated in the [[BioCompute Object|BioCompute]] standard.

On 26 October 1990, [[Roger Tsien]], Pepi Ross, Margaret Fahnestock and Allan J Johnston filed a patent describing stepwise ("base-by-base") sequencing with removable 3' blockers on DNA arrays (blots and single DNA molecules).<ref name=TsienPatent>{{cite web|url=http://worldwide.espacenet.com/publicationDetails/biblio?FT=D&date=19910516&DB=EPODOC&locale=en_EP&CC=WO&NR=9106678A1&KC=A1&ND=4|title=Espacenet – Bibliographic data|website=worldwide.espacenet.com}}</ref>
In 1996, [[Pål Nyrén]] and his student [[Mostafa Ronaghi]] at the Royal Institute of Technology in [[Stockholm]] published their method of [[pyrosequencing]].<ref name=Ronaghi>{{cite journal | vauthors = Ronaghi M, Karamohamed S, Pettersson B, Uhlén M, Nyrén P | title = Real-time DNA sequencing using detection of pyrophosphate release | journal = Analytical Biochemistry | volume = 242 | issue = 1 | pages = 84–89 | year = 1996 | pmid = 8923969 | doi = 10.1006/abio.1996.0432 }}</ref>

On 1 April 1997, [[Pascal Mayer]] and Laurent Farinelli submitted patents to the World Intellectual Property Organization describing DNA colony sequencing.<ref name=DNA_colony_patents>{{cite web | last = Kawashima | first = Eric H. | author2 = Laurent Farinelli | author3 = [[Pascal Mayer]] | title = Patent: Method of nucleic acid amplification | access-date = 2012-12-22 | date = 2005-05-12 | url = http://www.patentlens.net/patentlens/patent/WO_1998_044151_A1/en/ | archive-url = https://archive.today/20130222020134/http://www.patentlens.net/patentlens/patent/WO_1998_044151_A1/en/ | archive-date = 22 February 2013 | url-status = dead }}</ref> The DNA sample preparation and random surface-[[polymerase chain reaction]] (PCR) arraying methods described in this patent, coupled to Roger Tsien et al.'s "base-by-base" sequencing method, is now implemented in [[Illumina (company)|Illumina]]'s Hi-Seq genome sequencers.

In 1998, Phil Green and Brent Ewing of the University of Washington described their [[phred quality score]] for sequencer data analysis,<ref>{{cite journal|vauthors=Ewing B, Green P|date=March 1998|title=Base-calling of automated sequencer traces using phred. II. Error probabilities|journal=Genome Res.|volume=8|issue=3|pages=186–94|doi=10.1101/gr.8.3.186|pmid=9521922|doi-access=free}}</ref> a landmark analysis technique that gained widespread adoption, and which is still the most common metric for assessing the accuracy of a sequencing platform.<ref>{{cite web|url=https://www.illumina.com/documents/products/technotes/technote_Q-Scores.pdf|title=Quality Scores for Next-Generation Sequencing|date=31 October 2011|website=Illumina|access-date=8 May 2018}}</ref>

Lynx Therapeutics published and marketed [[massively parallel signature sequencing]] (MPSS), in 2000. This method incorporated a parallelized, adapter/ligation-mediated, bead-based sequencing technology and served as the first commercially available "next-generation" sequencing method, though no [[DNA sequencers]] were sold to independent laboratories.<ref name="Brenner_2000">{{cite journal | vauthors = Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K | title = Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays | journal = Nature Biotechnology | volume = 18 | issue = 6 | pages = 630–34 | year = 2000 | pmid = 10835600 | doi = 10.1038/76469 | s2cid = 13884154 }}</ref>