Editing DNA sequencing (section)

== Applications ==
DNA sequencing may be used to determine the sequence of individual [[gene]]s, larger genetic regions (i.e. clusters of genes or [[operons]]), full chromosomes, or [[Whole genome sequencing|entire genomes]] of any organism.  DNA sequencing is also the most efficient way to indirectly sequence [[RNA]] or [[protein]]s (via their [[open reading frame]]s). In fact, DNA sequencing has become a key technology in many areas of biology and other sciences such as medicine, [[forensics]], and [[anthropology]].

=== Molecular biology ===
Sequencing is used in [[molecular biology]] to study genomes and the proteins they encode. Information obtained using sequencing allows researchers to identify changes in genes and noncoding DNA (including regulatory sequences), associations with diseases and phenotypes, and identify potential drug targets.

=== Evolutionary biology ===
Since DNA is an informative macromolecule in terms of transmission from one generation to another, DNA sequencing is used in [[evolutionary biology]] to study how different organisms are related and how they evolved. In February 2021, scientists reported, for the first time, the sequencing of [[DNA]] from [[Carrion|animal remains]], a [[mammoth]] in this instance, over a million years old, the oldest DNA sequenced to date.<ref name="CNN-20210217">{{cite news |last=Hunt |first=Katie |title=World's oldest DNA sequenced from a mammoth that lived more than a million years ago |url=https://www.cnn.com/2021/02/17/world/mammoth-oldest-dna-million-years-ago-scn/index.html |date=17 February 2021 |publisher=[[CNN]] |accessdate=17 February 2021 }}</ref><ref name="NAT-20210217">{{cite journal |last=Callaway |first=Ewen |title=Million-year-old mammoth genomes shatter record for oldest ancient DNA – Permafrost-preserved teeth, up to 1.6 million years old, identify a new kind of mammoth in Siberia. |date=17 February 2021 |journal=[[Nature (journal)|Nature]] |volume=590 |issue=7847 |pages=537–538 |doi=10.1038/d41586-021-00436-x |pmid=33597786 |bibcode=2021Natur.590..537C |doi-access=free }}</ref>

=== Metagenomics ===
{{Main|Metagenomics}}
The field of [[metagenomics]] involves identification of organisms present in a body of water, [[sewage]], dirt, debris filtered from the air, or swab samples from organisms. Knowing which organisms are present in a particular environment is critical to research in [[ecology]], [[epidemiology]], [[microbiology]], and other fields. Sequencing enables researchers to determine which types of microbes may be present in a [[microbiome]], for example.

=== Virology ===
{{Main|Virology}}
As most viruses are too small to be seen by a light microscope, sequencing is one of the main tools in virology to identify and study the virus.<ref name=":0c"/> Viral genomes can be based in DNA or RNA. RNA viruses are more time-sensitive for genome sequencing, as they degrade faster in clinical samples.<ref name="Shirlee"/> Traditional [[Sanger sequencing]] and next-generation sequencing are used to sequence viruses in basic and clinical research, as well as for the diagnosis of emerging viral infections, [[molecular epidemiology]] of viral pathogens, and drug-resistance testing. There are more than 2.3 million unique viral sequences in [[GenBank]].<ref name=":0c" /> Recently, NGS has surpassed traditional Sanger as the most popular approach for generating viral genomes.<ref name=":0c">{{cite journal |last1=Castro |first1=Christina |last2=Marine |first2=Rachel |last3=Ramos |first3=Edward |last4=Ng |first4=Terry Fei Fan |title=The effect of variant interference on de novo assembly for viral deep sequencing |journal=BMC Genomics |doi=10.1186/s12864-020-06801-w |biorxiv=10.1101/815480 |year=2019 |volume=21 |issue=1 |page=421 |pmid=32571214 |pmc=7306937 |doi-access=free }}</ref>

During the [[Influenza A virus subtype H5N1#Outbreaks|1997 avian influenza outbreak]], viral sequencing determined that the influenza sub-type originated through [[reassortment]] between [[quail]] and poultry. This led to legislation in [[Hong Kong]] that prohibited selling live quail and poultry together at market. Viral sequencing can also be used to estimate when a viral outbreak began by using a [[molecular clock]] technique.<ref name="Shirlee">{{cite journal|doi=10.1146/annurev-virology-110615-035747|title=Genomic Analysis of Viral Outbreaks|year=2016|last1=Wohl|first1=Shirlee|last2=Schaffner|first2=Stephen F.|last3=Sabeti|first3=Pardis C.|author3-link=Pardis Sabeti|journal=Annual Review of Virology|volume=3|issue=1|pages=173–195|pmid=27501264|pmc=5210220}}</ref>

=== Medicine ===
Medical technicians may sequence genes (or, theoretically, full genomes) from patients to determine if there is risk of genetic diseases. This is a form of [[genetic testing]], though some genetic tests may not involve DNA sequencing.

As of 2013 DNA sequencing was increasingly used to diagnose and treat rare diseases. As more and more genes are identified that cause rare genetic diseases, molecular diagnoses for patients become more mainstream. DNA sequencing allows clinicians to identify genetic diseases, improve disease management, provide reproductive counseling, and more effective therapies.<ref>{{cite journal |last1=Boycott |first1=Kym M. |last2=Vanstone |first2=Megan R. |last3=Bulman |first3=Dennis E. |last4=MacKenzie |first4=Alex E. |title=Rare-disease genetics in the era of next-generation sequencing: discovery to translation |journal=Nature Reviews Genetics |date=October 2013 |volume=14 |issue=10 |pages=681–691 |doi=10.1038/nrg3555 |pmid=23999272 |s2cid=8496181 }}</ref> Gene sequencing panels are used to identify multiple potential genetic causes of a suspected disorder.<ref>{{Cite journal |last1=Bean |first1=Lora |last2=Funke |first2=Birgit |last3=Carlston |first3=Colleen M. |last4=Gannon |first4=Jennifer L. |last5=Kantarci |first5=Sibel |last6=Krock |first6=Bryan L. |last7=Zhang |first7=Shulin |last8=Bayrak-Toydemir |first8=Pinar |date=March 2020 |title=Diagnostic gene sequencing panels: from design to report—a technical standard of the American College of Medical Genetics and Genomics (ACMG) |journal=Genetics in Medicine |volume=22 |issue=3 |pages=453–461 |doi=10.1038/s41436-019-0666-z |issn=1098-3600|doi-access=free |pmid=31732716 }}</ref>

Also, DNA sequencing may be useful for determining a specific bacteria, to allow for more [[Antimicrobial spectrum|precise antibiotics treatments]], hereby reducing the risk of creating [[antimicrobial resistance]] in bacteria populations.<ref>{{cite journal| pmid=28425484 | doi=10.1038/srep46327 | volume=7 | title=''Mycobacterium tuberculosis'' resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools | year=2017 | journal=Sci Rep | page=46327 | vauthors=Schleusener V, Köser CU, Beckert P, Niemann S, Feuerriegel S| pmc=7365310 | bibcode=2017NatSR...746327S | doi-access=free }}</ref><ref>{{cite journal| pmid=31106066 | doi=10.7717/peerj.6857 | volume=7 | title=A large scale evaluation of TBProfiler and Mykrobe for antibiotic resistance prediction in ''Mycobacterium tuberculosis'' | pmc=6500375 | year=2019 | journal=PeerJ | page=e6857 | vauthors=Mahé P, El Azami M, Barlas P, Tournoud M | doi-access=free }}</ref><ref>[https://innovation.ox.ac.uk/wp-content/uploads/2015/04/Mykrobe-predictor-Poster.pdf Mykrobe predictor –Antibiotic resistance prediction for S. aureus and M. tuberculosis from whole genome sequence data]</ref><ref>{{cite journal |last1=Bradley |first1=Phelim |last2=Gordon |first2=N. Claire |last3=Walker |first3=Timothy M. |last4=Dunn |first4=Laura |last5=Heys |first5=Simon |last6=Huang |first6=Bill |last7=Earle |first7=Sarah |last8=Pankhurst |first8=Louise J. |last9=Anson |first9=Luke |last10=de Cesare |first10=Mariateresa |last11=Piazza |first11=Paolo |last12=Votintseva |first12=Antonina A. |last13=Golubchik |first13=Tanya |last14=Wilson |first14=Daniel J. |last15=Wyllie |first15=David H. |last16=Diel |first16=Roland |last17=Niemann |first17=Stefan |last18=Feuerriegel |first18=Silke |last19=Kohl |first19=Thomas A. |last20=Ismail |first20=Nazir |last21=Omar |first21=Shaheed V. |last22=Smith |first22=E. Grace |last23=Buck |first23=David |last24=McVean |first24=Gil |last25=Walker |first25=A. Sarah |last26=Peto |first26=Tim E. A. |last27=Crook |first27=Derrick W. |last28=Iqbal |first28=Zamin |title=Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis |journal=Nature Communications |date=21 December 2015 |volume=6 |issue=1 |page=10063 |doi=10.1038/ncomms10063 |pmid=26686880 |pmc=4703848 |bibcode=2015NatCo...610063B }}</ref><ref>{{Cite web |url=https://www.tvo.org/transcript/115187X/michael-mosley-vs-the-superbugs |title=Michael Mosley vs the superbugs |access-date=21 October 2019 |archive-date=24 November 2020 |archive-url=https://web.archive.org/web/20201124174040/https://www.tvo.org/transcript/115187X/michael-mosley-vs-the-superbugs |url-status=dead }}</ref><ref>{{Citation|title=Mykrobe|date=2022-12-24|url=https://github.com/Mykrobe-tools/mykrobe|publisher=Mykrobe-tools|access-date=2023-01-02}}</ref>

=== Forensic investigation ===
{{Main|Forensic DNA analysis}}
DNA sequencing may be used along with [[DNA profiling]] methods for [[forensic identification]]<ref>{{Cite news|url=https://theconversation.com/from-the-crime-scene-to-the-courtroom-the-journey-of-a-dna-sample-82250|title=From the crime scene to the courtroom: the journey of a DNA sample|last1=Curtis|first1=Caitlin|last2=Hereward|first2=James | name-list-style = vanc |date=29 August 2017|work=The Conversation }}</ref> and [[DNA paternity testing|paternity testing]]. DNA testing has evolved tremendously in the last few decades to ultimately link a DNA print to what is under investigation. The DNA patterns in fingerprint, saliva, hair follicles, etc. uniquely separate each living organism from another. Testing DNA is a technique which can detect specific genomes in a DNA strand to produce a unique and individualized pattern.

DNA sequencing may be used along with [[DNA profiling]] methods for [[forensic identification]] and [[paternity testing]], as it has evolved significantly over the past few decades to ultimately link a DNA print to what is under investigation. The DNA patterns in fingerprint, saliva, hair follicles, and other bodily fluids uniquely separate each living organism from another, making it an invaluable tool in the field of [[forensic science]]. The process of DNA testing involves detecting specific [[genomes]] in a DNA strand to produce a unique and individualized pattern, which can be used to identify individuals or determine their relationships.

The advancements in DNA sequencing technology have made it possible to analyze and compare large amounts of [[genetic data]] quickly and accurately, allowing investigators to gather evidence and solve crimes more efficiently. This technology has been used in various applications, including forensic identification, paternity testing, and human identification in cases where traditional identification methods are unavailable or unreliable. The use of DNA sequencing has also led to the development of new forensic techniques, such as [[DNA phenotyping]], which allows investigators to predict an individual's physical characteristics based on their genetic data.

In addition to its applications in forensic science, DNA sequencing has also been used in medical research and diagnosis. It has enabled scientists to identify genetic mutations and variations that are associated with certain diseases and disorders, allowing for more accurate diagnoses and targeted treatments. Moreover, DNA sequencing has also been used in conservation biology to study the genetic diversity of endangered species and develop strategies for their conservation.

Furthermore, the use of DNA sequencing has also raised important ethical and legal considerations. For example, there are concerns about the privacy and security of genetic data, as well as the potential for misuse or discrimination based on genetic information. As a result, there are ongoing debates about the need for regulations and guidelines to ensure the responsible use of DNA sequencing technology.

Overall, the development of DNA sequencing technology has revolutionized the field of forensic science and has far-reaching implications for our understanding of genetics, medicine, and conservation biology.