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{{Short description|Branch of genetics}}
{{For|the scientific journal
[[Image:Bcrablmet.jpg|right|thumb|A metaphase cell positive for the BCR/ABL rearrangement using FISH]]
'''Cytogenetics''' is essentially a branch of [[genetics]], but is also a part of cell biology/cytology (a subdivision of human anatomy), that is concerned with how the [[chromosome]]s relate to cell behaviour, particularly to their behaviour during [[mitosis]] and [[meiosis]].<ref>{{citation |
==History==
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===Beginnings===
Chromosomes were first observed in plant cells by [[
The next stage took place after the development of genetics in the early 20th century, when it was appreciated that the set of chromosomes (the [[karyotype]]) was the carrier of the genes. Levitsky seems to have been the first to define the karyotype as the [[phenotypic]] appearance of the [[Somatic (biology)|somatic]] chromosomes, in contrast to their [[gene|genic]] contents.<ref>{{cite book |last1=Levitsky |first1=Grigorii Andreevich |title=Material'nye osnovy nasledstvennosti |trans-title=The Material Basis of Heredity |language=ru |location=Kiev |publisher=Gosizdat Ukrainy |year=1924 }}{{page needed|date=October 2020}}</ref><ref>{{cite journal |author=Levitsky GA |year=1931 |title=The morphology of chromosomes |journal=Bull. Applied Bot. Genet. Plant Breed |volume=27 |pages=19–174}}</ref> Investigation into the human karyotype took many years to settle the most basic question: how many chromosomes does a normal [[diploid]] human cell contain?<ref>{{cite journal |last1=Kottler |first1=Malcolm Jay |title=From 48 to 46: cytological technique, preconception, and the counting of human chromosomes. |journal=Bulletin of the History of Medicine |date=1974 |volume=48 |issue=4 |pages=465–502 |id={{ProQuest|1296285397}} |jstor=44450164 |pmid=4618149 }}</ref> In 1912, [[Hans von Winiwarter]] reported 47 chromosomes in [[spermatogonia]] and 48 in [[oogonia]], concluding an [[XO sex-determination system|XX/XO]] [[Sex-determination system|sex determination]] mechanism.<ref>{{cite journal |vauthors=von Winiwarter H |year=1912 |title=Études sur la spermatogenese humaine |trans-title=Human spermatogenesis studies |language=fr |journal=Arch. Biologie |volume=27 |issue=93 |pages=147–149 }}</ref> [[Theophilus Painter|Painter]] in 1922 was not certain whether the diploid number of humans was 46 or 48, at first favoring 46.<ref>Painter T.S. "The spermatogenesis of man" p. 129 in {{cite journal |title=Abstracts |journal=The Anatomical Record |date=January 1922 |volume=23 |issue=1 |pages=89–132 |doi=10.1002/ar.1090230111 |doi-access=free }}</ref> He revised his opinion later from 46 to 48, and he correctly insisted on humans having an [[XY sex-determination system|XX/XY]] system of sex-determination.<ref>{{cite journal |last1=Painter |first1=Theophilus S. |title=Studies in mammalian spermatogenesis. II. The spermatogenesis of man |journal=Journal of Experimental Zoology |date=April 1923 |volume=37 |issue=3 |pages=291–336 |doi=10.1002/jez.1400370303 }}</ref> Considering their techniques, these results were quite remarkable. In science books, the number of human chromosomes remained at 48 for over thirty years. New techniques were needed to correct this error. [[Joe Hin Tjio]] working in [[Albert Levan]]'s lab<ref>{{cite news|url=https://www.theguardian.com/news/2001/dec/11/guardianobituaries.medicalscience|title=Joe Hin Tjio The man who cracked the chromosome count|work=[[The Guardian]]|author=Wright, Pearce|date=11 December 2001|url-status=live|archive-url=https://web.archive.org/web/20170825151411/https://www.theguardian.com/news/2001/dec/11/guardianobituaries.medicalscience|archive-date=25 August 2017}}</ref><ref>{{cite news|url=https://www.nytimes.com/2001/12/07/us/joe-hin-tjio-82-research-biologist-counted-chromosomes.html|title=Joe Hin Tjio, 82; Research Biologist Counted Chromosomes|work=[[The New York Times]]|author=Saxon, Wolfgang|date=7 December 2001|url-status=live|archive-url=https://web.archive.org/web/20130512193836/http://www.nytimes.com/2001/12/07/us/joe-hin-tjio-82-research-biologist-counted-chromosomes.html|archive-date=12 May 2013}}</ref> was responsible for finding the approach:
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:# Cutting up a photomicrograph and arranging the result into an indisputable karyogram.
It took until 1956 for it to be generally accepted that the karyotype of man included only 46 chromosomes.<ref>{{cite journal |last1=Tjio |first1=Joe Hin |last2=Levan |first2=Albert |title=The chromosome number of man |journal=Hereditas |date=9 July 2010 |volume=42 |issue=1–2 |pages=723–4 |doi=10.1111/j.1601-5223.1956.tb03010.x |pmid=345813 |doi-access=free }}</ref><ref>{{cite book |last1=Hsu |first1=T. C. |title=Human and Mammalian Cytogenetics: An Historical Perspective |date=2012 |publisher=Springer Science & Business Media |isbn=978-1-4612-6159-9 }}{{page needed|date=October 2020}}</ref><ref>{{cite web |url=http://www.britannica.com/EBchecked/topic/228983/human-genetics/50731/The-human-chromosomes |title=
== Applications
=== McClintock's work on maize ===
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=== Natural populations of Drosophila ===
In the 1930s, [[Dobzhansky]] and his coworkers collected ''[[Drosophila pseudoobscura]]'' and ''[[Drosophila persimilis|D. persimilis]]'' from wild populations in [[California]] and neighboring states. Using Painter's technique<ref>{{cite journal |last1=Painter |first1=T. S. |title=A new method for the study of chromosome rearrangements and the plotting of chromosome maps |journal=Science |date=22 December 1933 |volume=78 |issue=2034 |pages=585–586 |doi=10.1126/science.78.2034.585 |pmid=17801695 |bibcode=1933Sci....78..585P }}</ref> they studied the [[polytene|polytene chromosomes]] and discovered that the wild populations were polymorphic for [[chromosomal inversions]]. All the flies look alike whatever inversions they carry: this is an example of a cryptic polymorphism.{{cn|date=February 2024}}
Evidence rapidly accumulated to show that [[natural selection]] was responsible. Using a method invented by L'Héritier and Teissier, Dobzhansky bred populations in ''population cages'', which enabled feeding, breeding and sampling whilst preventing escape. This had the benefit of eliminating [[insect migration|migration]] as a possible explanation of the results. Stocks containing inversions at a known initial frequency can be maintained in controlled conditions. It was found that the various chromosome types do not fluctuate at random, as they would if selectively neutral, but adjust to certain frequencies at which they become stabilised. By the time Dobzhansky published the third edition of his book in 1951<ref>Dobzhansky T. 1951. ''Genetics and the origin of species''. 3rd ed, Columbia University Press, New York.</ref> he was persuaded that the chromosome morphs were being maintained in the population by the selective advantage of the heterozygotes, as with most [[polymorphism (biology)|polymorphisms]].<ref>Dobzhansky T. 1970. ''Genetics of the evolutionary process''. Columbia University Press N.Y.</ref><ref>[Dobzhansky T.] 1981. ''Dobzhansky's genetics of natural populations''. eds Lewontin RC, Moore JA, Provine WB and Wallace B. Columbia University Press N.Y.</ref>
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=== Lily and mouse ===
The lily is a favored organism for the cytological examination of meiosis since the chromosomes are large and each morphological stage of meiosis can be easily identified microscopically. Hotta, [[Ann Chester Chandley|Chandley]] et al.<ref name="pmid593319">{{cite journal |last1=Hotta |first1=Yasuo |last2=Chandley |first2=Ann C. |last3=Stern |first3=Herbert |title=Meiotic crossing-over in lily and mouse |journal=Nature |date=September 1977 |volume=269 |issue=5625 |pages=240–242 |doi=10.1038/269240a0 |pmid=593319 |bibcode=1977Natur.269..240H |s2cid=4268089 }}</ref> presented the evidence for a common pattern of DNA nicking and repair synthesis in male meiotic cells of lilies and rodents during the zygotene–pachytene stages of meiosis when crossing over was presumed to occur. The presence of a common pattern between organisms as phylogenetically distant as lily and mouse led the authors to conclude that the organization for meiotic crossing-over in at least higher eukaryotes is probably universal in distribution.{{cn|date=February 2024}}
==Human abnormalities and medical applications==
[[File:T922 CML.jpg|thumb|Philadelphia translocation t(9;22)(q34;q11.2) seen in chronic myelogenous leukemia.]]
Following the advent of procedures that allowed easy enumeration of chromosomes, discoveries were quickly made related to aberrant chromosomes or chromosome number.{{cn|date=February 2024}}
Following the advent of procedures that allowed easy enumeration of chromosomes, discoveries were quickly made related to aberrant chromosomes or chromosome number. In some congenital disorders, such as [[Down syndrome]], cytogenetics revealed the nature of the chromosomal defect: a "simple" trisomy. Abnormalities arising from [[nondisjunction]] events can cause cells with [[aneuploidy]] (additions or deletions of entire chromosomes) in one of the parents or in the fetus. In 1959, Lejeune<ref>{{cite journal |last1=Lejeune |first1=Jérôme |last2=Gautier |first2=Marthe |last3=Turpin |first3=Raymond |title=Étude des chromosomes somatiques des neuf enfants mongoliens |trans-title=Study of somatic chromosomes from 9 mongoloid children |language=fr |journal=Comptes rendus hebdomadaires des séances de l'Académie des Sciences |date=16 March 1959 |volume=248 |issue=11 |pages=1721–1722 |pmid=13639368 |id={{NAID|10008406728}} |oclc=871332352 }}</ref> discovered patients with Down syndrome had an extra copy of chromosome 21. Down syndrome is also referred to as trisomy 21.▼
▲
Other numerical abnormalities discovered include sex chromosome abnormalities. A female with only one X chromosome has [[Turner syndrome]], whereas a male with an additional X chromosome, resulting in 47 total chromosomes, has [[Klinefelter syndrome]]. Many other sex chromosome combinations are compatible with live birth including XXX, XYY, and XXXX. The ability for mammals to tolerate aneuploidies in the sex chromosomes arises from the ability to [[Barr body|inactivate them]], which is required in normal females to compensate for having two copies of the chromosome. Not all genes on the X chromosome are inactivated, which is why there is a phenotypic effect seen in individuals with extra X chromosomes.▼
▲Other numerical abnormalities discovered include sex chromosome abnormalities. A female with only one X chromosome has [[Turner syndrome]], whereas a male with an additional X chromosome, resulting in 47 total chromosomes, has [[Klinefelter syndrome]]. Many other sex chromosome combinations are compatible with live birth including [[Trisomy X|XXX]], [[XYY syndrome|XYY]], and XXXX. The ability for mammals to tolerate aneuploidies in the sex chromosomes arises from the ability to [[Barr body|inactivate them]], which is required in normal females to compensate for having two copies of the chromosome. Not all genes on the X chromosome are inactivated, which is why there is a phenotypic effect seen in individuals with extra X chromosomes.{{cn|date=February 2024}}
Trisomy 13 was associated with [[Patau syndrome]] and trisomy 18 with [[Edwards syndrome]].▼
▲Trisomy 13 was associated with [[Patau syndrome]] and trisomy 18 with [[Edwards syndrome]].{{cn|date=February 2024}}
In 1960, Peter Nowell and David Hungerford<ref>Nowell PC, Hungerford DA. "A minute chromosome in human chronic granulocytic leukemia". pp. 1497–1501 in {{cite journal |title=National Academy of Sciences |journal=Science |date=18 November 1960 |volume=132 |issue=3438 |pages=1488–1501 |doi=10.1126/science.132.3438.1488 |pmid=17739576 }}</ref> discovered a small chromosome in the white blood cells of patients with [[Chronic myelogenous leukemia]] (CML). This abnormal chromosome was dubbed the [[Philadelphia chromosome]] - as both scientists were doing their research in [[Philadelphia, Pennsylvania]]. Thirteen years later, with the development of more advanced techniques, the abnormal chromosome was shown by [[Janet Rowley]] to be the result of a [[chromosomal translocation|translocation]] of chromosomes 9 and 22. Identification of the Philadelphia chromosome by cytogenetics is diagnostic for CML.▼
▲Acquired cytogenetics: In 1960, Peter Nowell and David Hungerford<ref>Nowell PC, Hungerford DA. "A minute chromosome in human chronic granulocytic leukemia". pp. 1497–1501 in {{cite journal |title=National Academy of Sciences |journal=Science |date=18 November 1960 |volume=132 |issue=3438 |pages=1488–1501 |doi=10.1126/science.132.3438.1488 |pmid=17739576 }}</ref> discovered a small chromosome in the white blood cells of patients with [[Chronic myelogenous leukemia]] (CML). This abnormal chromosome was dubbed the [[Philadelphia chromosome]] - as both scientists were doing their research in [[Philadelphia, Pennsylvania]]. Thirteen years later, with the development of more advanced techniques, the abnormal chromosome was shown by [[Janet Rowley]] to be the result of a [[chromosomal translocation|translocation]] of chromosomes 9 and 22. Identification of the Philadelphia chromosome by cytogenetics is diagnostic for CML. More than 780 leukemias and hundreds of solid tumors (lung, prostate, kidney, etc.) are now characterized by an acquired chromosomal abnormality, whose prognostic value is crucial. The identification of these chromosomal abnormalities has led to the discovery of a very large number of "cancer genes" (or [[oncogene]]s). The increasing knowledge of these cancer genes now allows the development of [[targeted therapies]], which transforms the prospects of patient survival. Thus, cytogenetics has had and continues to have an essential role in the progress of cancer understanding. Large databases ([[Atlas of Genetics and Cytogenetics in Oncology and Haematology]], [[COSMIC cancer database]], [[Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer]]) allow researchers and clinicians to have the necessary corpus for their work in this field.
===Advent of banding techniques===
[[Image:NHGRI human male karyotype.png|thumb|right|250px|
[[File:Human karyotype with bands and sub-bands.png|thumb|Schematic [[Karyotype|karyogram]] of a human, with annotated [[Locus (genetics)|bands and sub-bands]] as used in the [[International System for Human Cytogenomic Nomenclature]] for [[chromosomal abnormalities]]. It shows dark and white regions on [[G banding]]. It shows 22 [[homologous chromosome]]s, both the male (XY) and female (XX) versions of the [[sex chromosome]] (bottom right), as well as the [[human mitochondrial genetics|mitochondrial genome]] (at bottom left). {{further|Karyotype}}]]
In the late 1960s, [[Torbjörn Oskar Caspersson|Torbjörn Caspersson]] developed a quinacrine fluorescent staining technique (Q-banding) which revealed unique banding patterns for each chromosome pair. This allowed chromosome pairs of otherwise equal size to be differentiated by distinct horizontal banding patterns. Banding patterns are now used to elucidate the breakpoints and constituent chromosomes involved in [[Chromosomal translocation|chromosome translocations]]. Deletions and inversions within an individual chromosome can also be identified and described more precisely using standardized banding nomenclature. G-banding (utilizing trypsin and Giemsa/ Wright stain) was concurrently developed in the early 1970s and allows visualization of banding patterns using a bright field microscope.▼
▲In the late 1960s, [[Torbjörn Oskar Caspersson|Torbjörn Caspersson]] developed a quinacrine fluorescent staining technique (Q-banding) which revealed unique banding patterns for each chromosome pair. This allowed chromosome pairs of otherwise equal size to be differentiated by distinct horizontal banding patterns. Banding patterns are now used to elucidate the breakpoints and constituent chromosomes involved in [[Chromosomal translocation|chromosome translocations]]. Deletions and inversions within an individual chromosome can also be identified and described more precisely using standardized banding nomenclature. G-banding (utilizing trypsin and Giemsa/ Wright stain) was concurrently developed in the early 1970s and allows visualization of banding patterns using a bright field microscope.{{cn|date=February 2024}}
Diagrams identifying the chromosomes based on the banding patterns are known as ''idiograms''. These maps became the basis for both prenatal and oncological fields to quickly move cytogenetics into the clinical lab where karyotyping allowed scientists to look for chromosomal alterations. Techniques were expanded to allow for culture of free [[amniocyte]]s recovered from [[amniotic fluid]], and elongation techniques for all culture types that allow for higher-resolution banding.{{cn|date=February 2024}}
===Beginnings of molecular cytogenetics===
In the 1980s, advances were made in [[molecular cytogenetics]]. While radioisotope-labeled probes had been hybridized with [[DNA]] since 1969, movement was now made in using fluorescent-labeled probes. Hybridizing them to chromosomal preparations using existing techniques came to be known as [[fluorescence in situ hybridization|fluorescence ''in situ'' hybridization]] (FISH).<ref>{{cite book |last1=Gupta |first1=P. K. |title=Cytogenetics |date=2007 |publisher=Rastogi Publications |isbn=978-81-7133-737-8 }}{{page needed|date=October 2020}}</ref> This change significantly increased the usage of probing techniques as fluorescent-labeled probes are safer. Further advances in micromanipulation and examination of chromosomes led to the technique of [[chromosome microdissection]] whereby aberrations in chromosomal structure could be isolated, cloned, and studied in ever greater detail.{{cn|date=February 2024}}
==Techniques==
===Karyotyping===
The routine [[chromosome]] analysis ([[Karyotyping]]) refers to analysis of [[metaphase]]
Several chromosome-banding techniques are used in cytogenetics laboratories. [[Quinacrine]] banding (Q-banding) was the first staining method used to produce specific banding patterns. This method requires a fluorescence microscope and is no longer as widely used as [[Giemsa]] banding (G-banding). Reverse banding, or R-banding, requires heat treatment and reverses the usual black-and-white pattern that is seen in G-bands and Q-bands. This method is particularly helpful for staining the distal ends of chromosomes. Other staining techniques include C-banding and [[Nucleolus|nucleolar]] organizing region stains (NOR stains). These latter methods specifically stain certain portions of the chromosome. C-banding stains the [[constitutive heterochromatin]], which usually lies near the centromere, and NOR staining highlights the satellites and stalks of [[acrocentric chromosome]]s.{{cn|date=February 2024}}
High-resolution banding involves the staining of chromosomes during [[prophase]] or early [[metaphase]] (prometaphase), before they reach maximal condensation. Because [[prophase]] and [[prometaphase]] chromosomes are more extended than metaphase chromosomes, the number of bands observable for all chromosomes (''bands per haploid set'', bph; "band level") increases from about 300 to 450 to as many as 800. This allows the detection of less obvious abnormalities usually not seen with conventional banding.<ref>{{cite journal |last1=Geiersbach |first1=Katherine B. |last2=Gardiner |first2=Anna E. |last3=Wilson |first3=Andrew |last4=Shetty |first4=Shashirekha |last5=Bruyère |first5=Hélène |last6=Zabawski |first6=James |last7=Saxe |first7=Debra F. |last8=Gaulin |first8=Rebecca |last9=Williamson |first9=Cynthia |last10=Van Dyke |first10=Daniel L. |title=Subjectivity in chromosome band–level estimation: a multicenter study |journal=Genetics in Medicine |date=February 2014 |volume=16 |issue=2 |pages=170–175 |doi=10.1038/gim.2013.95 |pmid=23887773 |doi-access=free}}</ref>
====Slide preparation====
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Analysis of banded chromosomes is done at a [[microscope]] by a clinical laboratory specialist in cytogenetics (CLSp(CG)). Generally 20 cells are analyzed which is enough to rule out mosaicism to an acceptable level. The results are summarized and given to a board-certified cytogeneticist for review, and to write an interpretation taking into account the patient's previous history and other clinical findings. The results are then given out reported in an ''International System for Human Cytogenetic Nomenclature 2009'' (ISCN2009)..
===
[[Image:Bcrablinter.jpg|right|thumb|Interphase cells positive for a t(9;22) rearrangement]]
[[
In addition to standard preparations FISH can also be performed on:
* [[Bone marrow examination|bone marrow smears]]
* [[Blood film|blood smears]]
* paraffin embedded tissue preparations
* enzymatically dissociated tissue samples
* uncultured bone marrow
* uncultured [[amniocyte]]s
* [[Cytospin]] preparations
====Slide preparation====
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====Analysis====
Analysis of FISH specimens is done by [[fluorescence microscope|fluorescence microscopy]] by a clinical laboratory specialist in cytogenetics. For oncology, generally, a large number of [[interphase]] cells are scored in order to rule out low-level residual disease, generally between 200 and 1,000 cells are counted and scored. For congenital problems usually 20 metaphase cells are scored.{{cn|date=February 2024}}
==Future of cytogenetics==
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==External links==
* [http://www.karyotyper.com/ Cytogenetic Directory]
* [http://www.kumc.edu/gec/prof/cytogene.html Cytogenetics Resources] {{Webarchive|url=https://web.archive.org/web/20170526140046/http://www.kumc.edu/gec/prof/cytogene.html |date=2017-05-26 }}
* [https://web.archive.org/web/20070126232310/http://homepage.mac.com/wildlifeweb/cyto/human/ Human Cytogenetics - Chromosomes and Karyotypes]
* [http://www.agt-info.org/ Association for Genetic Technologists]
* [http://cytogenetics.org.uk/ Association of Clinical Cytogeneticists]
* [http://gladwinmedical.blogspot.com/2006/07/intro-to-principles-of-cytogenetics.html Gladwin Medical Blog] {{Webarchive|url=https://web.archive.org/web/20061108003702/http://gladwinmedical.blogspot.com/2006/07/intro-to-principles-of-cytogenetics.html |date=2006-11-08 }}
* [https://web.archive.org/web/20140428161620/http://www.piribo.com/publications/technology/cytogenetics_market_report.html Cytogenetics - Technologies,markets and companies]
* [https://groups.google.com/group/cytogenetics-methods-and-trouble-shooting Cytogenetics-methods-and-trouble-shooting]
* [[
{{Chromosome genetics}}
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[[Category:Cytogenetics| ]]
[[Category:Laboratory healthcare occupations]]
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