Editing Genetics (section)

== Research and technology ==
=== Model organisms ===

[[File:Drosophila melanogaster - side (aka).jpg|thumb|right|The [[common fruit fly]] (''Drosophila melanogaster'') is a popular [[model organism]] in genetics research.]]

Although geneticists originally studied inheritance in a wide variety of organisms, the range of species studied has narrowed. One reason is that when significant research already exists for a given organism, new researchers are more likely to choose it for further study, and so eventually a few [[model organism]]s became the basis for most genetics research. Common research topics in model organism genetics include the study of [[gene regulation]] and the involvement of genes in [[morphogenesis|development]] and [[cancer]]. Organisms were chosen, in part, for convenience—short generation times and easy [[genetic engineering|genetic manipulation]] made some organisms popular genetics research tools. Widely used model organisms include the gut bacterium ''[[Escherichia coli]]'', the plant ''[[Arabidopsis thaliana]]'', baker's yeast (''[[Saccharomyces cerevisiae]]''), the nematode ''[[Caenorhabditis elegans]]'', the common fruit fly (''[[Drosophila melanogaster]]''), the zebrafish (''[[Danio rerio]]''), and the common house mouse (''[[Mus musculus]]'').<ref>{{cite web |url=http://www.loci.wisc.edu/outreach/text/model.html |title=The Use of Model Organisms in Instruction |access-date=15 March 2008 |publisher=University of Wisconsin: Wisconsin Outreach Research Modules |url-status=dead |archive-url=https://web.archive.org/web/20080313023531/http://www.loci.wisc.edu/outreach/text/model.html |archive-date=13 March 2008}}</ref>

=== Medicine ===

[[File:Biochemistry, genetics and molecular biology.svg|alt=|thumb|Schematic relationship between [[biochemistry]], genetics and [[molecular biology]]]]

[[Medical genetics]] seeks to understand how genetic variation relates to human health and disease.<ref>{{cite web |url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=gnd |title=NCBI: Genes and Disease |publisher=NIH: National Center for Biotechnology Information |access-date=15 March 2008 |url-status=dead |archive-url=https://web.archive.org/web/20070220074727/http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=gnd&ref=sidebar |archive-date=20 February 2007}}</ref> When searching for an unknown gene that may be involved in a disease, researchers commonly use genetic linkage and genetic [[pedigree chart]]s to find the location on the genome associated with the disease. At the population level, researchers take advantage of [[Mendelian randomization]] to look for locations in the genome that are associated with diseases, a method especially useful for [[Quantitative trait locus|multigenic traits]] not clearly defined by a single gene.<ref>{{cite journal | vauthors = Smith GD, Ebrahim S | title = 'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease? | journal = International Journal of Epidemiology | volume = 32 | issue = 1 | pages = 1–22 | date = February 2003 | pmid = 12689998 | doi = 10.1093/ije/dyg070 | doi-access =  | author-link1 = George Davey Smith }}</ref> Once a candidate gene is found, further research is often done on the corresponding (or [[Homology (biology)|homologous]]) genes of model organisms. In addition to studying genetic diseases, the increased availability of genotyping methods has led to the field of [[pharmacogenetics]]: the study of how genotype can affect drug responses.<ref>{{cite web|url=http://www.nigms.nih.gov/Initiatives/PGRN/Background/FactSheet.htm |title=Pharmacogenetics Fact Sheet |access-date=15 March 2008 |publisher=NIH: National Institute of General Medical Sciences |url-status=dead |archive-url=https://web.archive.org/web/20080512012316/http://www.nigms.nih.gov/Initiatives/PGRN/Background/FactSheet.htm |archive-date=12 May 2008}}</ref>

Individuals differ in their inherited tendency to develop [[cancer]], and cancer is a genetic disease. The process of cancer development in the body is a combination of events. Mutations occasionally occur within cells in the body as they divide. Although these mutations will not be inherited by any offspring, they can affect the behavior of cells, sometimes causing them to grow and divide more frequently. There are biological mechanisms that attempt to stop this process; signals are given to inappropriately dividing cells that should trigger [[Apoptosis|cell death]], but sometimes additional mutations occur that cause cells to ignore these messages. An internal process of [[natural selection]] occurs within the body and eventually mutations accumulate within cells to promote their own growth, creating a cancerous [[Tumour heterogeneity|tumor]] that grows and invades various tissues of the body. Normally, a cell divides only in response to signals called [[growth factor]]s and [[Contact inhibition|stops growing once in contact with surrounding cells]] and in response to growth-inhibitory signals. It usually then divides a limited number of times and dies, staying within the [[epithelium]] where it is unable to migrate to other organs. To become a cancer cell, a cell has to accumulate mutations in a number of genes (three to seven). A cancer cell can divide without growth factor and ignores inhibitory signals. Also, it is immortal and can grow indefinitely, even after it makes contact with neighboring cells. It may escape from the epithelium and ultimately from the [[primary tumor]]. Then, the escaped cell can cross the endothelium of a blood vessel and get transported by the bloodstream to colonize a new organ, forming deadly [[metastasis]]. Although there are some genetic predispositions in a small fraction of cancers, the major fraction is due to a set of new genetic mutations that originally appear and accumulate in one or a small number of cells that will divide to form the tumor and are not transmitted to the progeny ([[somatic mutation]]s). The most frequent mutations are a loss of function of [[p53 protein]], a [[tumor suppressor]], or in the p53 pathway, and gain of function mutations in the [[Ras proteins]], or in other [[oncogene]]s.<ref>{{cite journal | vauthors = Frank SA | title = Genetic predisposition to cancer - insights from population genetics | journal = Nature Reviews. Genetics | volume = 5 | issue = 10 | pages = 764–772 | date = October 2004 | pmid = 15510167 | doi = 10.1038/nrg1450 | s2cid = 6049662 }}</ref><ref>{{cite book |vauthors=Strachan T, Read AP |title=Human Molecular Genetics 2 |url=https://archive.org/details/humanmolecularge0002stra |url-access=registration |year=1999 |publisher=John Wiley & Sons Inc. |edition=second}} [https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=hmg.chapter.2342 Chapter 18: Cancer Genetics] {{webarchive|url=https://web.archive.org/web/20050926163641/http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=hmg.chapter.2342 |date=26 September 2005 }}</ref>

=== Research methods ===

[[File:Ecoli colonies.png|thumb|right|upright=0.8|[[Colony (biology)|Colonies]] of ''[[Escherichia coli|E. coli]]'' produced by [[Cloning#Unicellular organisms|cellular cloning]]. A similar methodology is often used in [[molecular cloning]].]]

DNA can be manipulated in the laboratory. [[Restriction enzymes]] are commonly used enzymes that cut DNA at specific sequences, producing predictable fragments of DNA.<ref>Lodish et al. (2000), [https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1582 Chapter 7: 7.1. DNA Cloning with Plasmid Vectors] {{webarchive|url=https://web.archive.org/web/20090527183555/http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1582 |date=27 May 2009 }}</ref> DNA fragments can be visualized through use of [[gel electrophoresis]], which separates fragments according to their length.<ref>{{Cite journal |last1=Timms |first1=John F. |last2=Cramer |first2=Rainer |date=December 2008 |title=Difference gel electrophoresis |url=https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.200800298 |journal=Proteomics |language=en |volume=8 |issue=23–24 |pages=4886–4897 |doi=10.1002/pmic.200800298 |pmid=19003860 |issn=1615-9853}}</ref>

The use of [[DNA ligase|ligation enzymes]] allows DNA fragments to be connected. By binding ("ligating") fragments of DNA together from different sources, researchers can create [[recombinant DNA]], the DNA often associated with [[genetically modified organism]]s. Recombinant DNA is commonly used in the context of [[plasmid]]s: short circular DNA molecules with a few genes on them. In the process known as [[molecular cloning]], researchers can amplify the DNA fragments by inserting plasmids into bacteria and then culturing them on plates of agar (to isolate [[Cloning#Unicellular organisms|clones of bacteria cells]]). "Cloning" can also refer to the various means of creating cloned ("clonal") organisms.<ref>{{cite journal | vauthors = Keefer CL | title = Artificial cloning of domestic animals | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 112 | issue = 29 | pages = 8874–8878 | date = July 2015 | pmid = 26195770 | pmc = 4517265 | doi = 10.1073/pnas.1501718112 | bibcode = 2015PNAS..112.8874K | doi-access = free }}</ref>

DNA can also be amplified using a procedure called the [[polymerase chain reaction]] (PCR).<ref>Lodish et al. (2000), [https://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=PCR&rid=mcb.section.1718 Chapter 7: 7.7. Polymerase Chain Reaction: An Alternative to Cloning]</ref> By using specific short sequences of DNA, PCR can isolate and exponentially amplify a targeted region of DNA. Because it can amplify from extremely small amounts of DNA, PCR is also often used to detect the presence of specific DNA sequences.<ref name="Chang_2017">{{cite journal |last1=Chang |first1=Dingran |last2=Tram |first2=Kha |last3=Li |first3=Ben |last4=Feng |first4=Qian |last5=Shen |first5=Zhifa |last6=Lee |first6=Christine H. |last7=Salena |first7=Bruno J. |last8=Li |first8=Yingfu  |date=2017-06-08 |title=Detection of DNA Amplicons of Polymerase Chain Reaction Using Litmus Test |journal=Scientific Reports |volume=7 |issue=3110 |page=3110 |doi=10.1038/s41598-017-03009-z |pmid=28596600 |pmc=5465217 |bibcode=2017NatSR...7.3110C }}</ref><ref name="Garibyan_2013">{{cite journal |last1=Garibyan |first1=Lilit |last2=Nidhi |date=March 2013 |title=Polymerase Chain Reaction |url=https://www.jidonline.org/article/S0022-202X(15)36139-X/fulltext |journal=Journal of Investigative Dermatology |volume=133 |issue=3 |pages=1–4 |doi=10.1038/jid.2013.1 |pmid=23399825 |access-date=2024-02-27|pmc=4102308 }}</ref>

=== DNA sequencing and genomics ===
{{Main|DNA sequencing}}
DNA sequencing, one of the most fundamental technologies developed to study genetics, allows researchers to determine the sequence of nucleotides in DNA fragments. The technique of [[Sanger sequencing|chain-termination sequencing]], developed in 1977 by a team led by [[Frederick Sanger]], is still routinely used to sequence DNA fragments. Using this technology, researchers have been able to study the molecular sequences associated with many human diseases.<ref>{{cite book |vauthors=Brown TA |title=Genomes 2 |edition=2nd |year=2002 |isbn=978-1-85996-228-2 |chapter-url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=genomes.section.6452 |chapter=Section 2, Chapter 6: 6.1. The Methodology for DNA Sequencing |publisher=Bios |location=Oxford}}</ref>

As sequencing has become less expensive, researchers have [[Genome project|sequenced the genomes]] of many organisms using a process called [[genome assembly]], which uses computational tools to stitch together sequences from many different fragments.<ref>Brown (2002), [https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=genomes.section.6481 Section 2, Chapter 6: 6.2. Assembly of a Contiguous DNA Sequence] {{webarchive|url=https://web.archive.org/web/20070208115742/http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=genomes.section.6481 |date=8 February 2007 }}</ref> These technologies were used to sequence the human genome in the Human Genome Project completed in 2003.<ref name=human_genome_project>{{cite web |url=http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml |title=Human Genome Project Information |access-date=15 March 2008 |publisher=Human Genome Project |url-status=dead |archive-url=https://web.archive.org/web/20080315062131/http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml |archive-date=15 March 2008}}</ref> New [[DNA sequencing#New sequencing methods|high-throughput sequencing]] technologies are dramatically lowering the cost of DNA sequencing, with many researchers hoping to bring the cost of resequencing a human genome down to a thousand dollars.<ref>{{cite journal | vauthors = Service RF | title = Gene sequencing. The race for the $1000 genome | journal = Science | volume = 311 | issue = 5767 | pages = 1544–1546 | date = March 2006 | pmid = 16543431 | doi = 10.1126/science.311.5767.1544 | s2cid = 23411598 }}</ref>

[[Next-generation sequencing]] (or high-throughput sequencing) came about due to the ever-increasing demand for low-cost sequencing. These sequencing technologies allow the production of potentially millions of sequences concurrently.<ref name=hall2007>{{cite journal | vauthors = Hall N | title = Advanced sequencing technologies and their wider impact in microbiology | journal = The Journal of Experimental Biology | volume = 210 | issue = Pt 9 | pages = 1518–1525 | date = May 2007 | pmid = 17449817 | doi = 10.1242/jeb.001370 | doi-access = free | bibcode = 2007JExpB.210.1518H }}</ref><ref name=church2006>{{cite journal | vauthors = Church GM | title = Genomes for all | journal = Scientific American | volume = 294 | issue = 1 | pages = 46–54 | date = January 2006 | pmid = 16468433 | doi = 10.1038/scientificamerican0106-46 | s2cid = 28769137 | bibcode = 2006SciAm.294a..46C | author-link1 = George M. Church }}{{subscription required}}</ref> The large amount of sequence data available has created the subfield of [[genomics]], research that uses computational tools to search for and analyze patterns in the full genomes of organisms. Genomics can also be considered a subfield of [[bioinformatics]], which uses computational approaches to analyze large sets of [[biological data]]. A common problem to these fields of research is how to manage and share data that deals with human subject and [[personally identifiable information]].{{cn|date=October 2022}}