Cytogenetics: Difference between revisions

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=General=
=General=
*Detects "large" changes (in chromosomes).
*Detects "large" changes (in chromosomes).
**Conventional karyotyping has a maximum resolution 3-4 megabase pairs (3-4 million base pairs); may be less - dependent on band density.<ref>{{Ref WMSP|695}}</ref>
**Conventional karyotyping has a maximum resolution 3-4 megabase pairs (3-4 million base pairs); may be less - dependent on band density.<ref name=Ref_WMSP695>{{Ref WMSP|695}}</ref>
*Cytogenetics is morphologic data an the interpretation has a greater degree of subjectivity vis-a-vis genetic sequencing.  
*Cytogenetics is morphologic (data); thus, the interpretation has a greater degree of subjectivity vis-à-vis genetic sequencing.


=Techniques (overview)=
=Techniques (overview)=
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***Several different techniques (stains) are used:<ref>URL: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC355922/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC355922/]. Accessed on: 10 May 2011.</ref>
***Several different techniques (stains) are used:<ref>URL: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC355922/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC355922/]. Accessed on: 10 May 2011.</ref>
****Examples: Q-banding (Q=Quinacrine), C-banding (C=constitutive heterchromatin), G-banding (G=Giemsa), R-banding (R=reverse).
****Examples: Q-banding (Q=Quinacrine), C-banding (C=constitutive heterchromatin), G-banding (G=Giemsa), R-banding (R=reverse).
*****Q-banding is the standard at UHN.


Analysis:
Analysis:
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</ref>
</ref>
*Typically done with karyotyping software (e.g. ''Ikaros'' from ''MetaSystems''<ref>URL: [http://www.metasystems-international.com/index.php?option=com_content&view=article&id=46:ikaros-general&catid=34:ikarosisis&Itemid=119 http://www.metasystems-international.com/index.php?option=com_content&view=article&id=46:ikaros-general&catid=34:ikarosisis&Itemid=119]. Accessed on: 12 May 2011.</ref>).
*Typically done with karyotyping software (e.g. ''Ikaros'' from ''MetaSystems''<ref>URL: [http://www.metasystems-international.com/index.php?option=com_content&view=article&id=46:ikaros-general&catid=34:ikarosisis&Itemid=119 http://www.metasystems-international.com/index.php?option=com_content&view=article&id=46:ikaros-general&catid=34:ikarosisis&Itemid=119]. Accessed on: 12 May 2011.</ref>).
Image:
*[http://commons.wikimedia.org/wiki/File:NHGRI_human_male_karyotype.png Karyotype (WC)].


Notes:
Notes:
*Quinacrine dye - AT-rich regions brighter than GC-rich regions.
*Quinacrine dye - AT-rich regions brighter than GC-rich regions.


====Image====
<gallery>
Image:NHGRI_human_male_karyotype.png | Karyotype (WC)
</gallery>
===Virtual karyotyping===
===Virtual karyotyping===
*An evolving technique based on SNP microarrays<ref name=pmid20736741>{{Cite journal  | last1 = Alvarez | first1 = K. | last2 = Kash | first2 = SF. | last3 = Lyons-Weiler | first3 = MA. | last4 = Kim | first4 = HJ. | last5 = Peterson | first5 = LE. | last6 = Mathai | first6 = B. | last7 = Hagenkord | first7 = JM. | last8 = Monzon | first8 = FA. | title = Reproducibility and performance of virtual karyotyping with SNP microarrays for the detection of chromosomal imbalances in formalin-fixed paraffin-embedded tissues. | journal = Diagn Mol Pathol | volume = 19 | issue = 3 | pages = 127-34 | month = Sep | year = 2010 | doi = 10.1097/PDM.0b013e3181d527c5 | PMID = 20736741 }}
*An evolving technique based on SNP microarrays<ref name=pmid20736741>{{Cite journal  | last1 = Alvarez | first1 = K. | last2 = Kash | first2 = SF. | last3 = Lyons-Weiler | first3 = MA. | last4 = Kim | first4 = HJ. | last5 = Peterson | first5 = LE. | last6 = Mathai | first6 = B. | last7 = Hagenkord | first7 = JM. | last8 = Monzon | first8 = FA. | title = Reproducibility and performance of virtual karyotyping with SNP microarrays for the detection of chromosomal imbalances in formalin-fixed paraffin-embedded tissues. | journal = Diagn Mol Pathol | volume = 19 | issue = 3 | pages = 127-34 | month = Sep | year = 2010 | doi = 10.1097/PDM.0b013e3181d527c5 | PMID = 20736741 }}
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===Overview===
===Overview===
*Usually done on interphase nuclei.
*ISH is a relatively high resolution cytogenetic technique (vis-à-vis karyotyping) used to identify specific DNA sequences and, with multiple probes, determine their relative location.
*Probe size ~20-1000 base pairs.
**Usually done on interphase nuclei.
**DNA probe size ~20-1000 base pairs.


Comes in different flavours:
Comes in different flavours:
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* † This could be considered a break apart ''and'' fusion probe; it has both elements.
* † This could be considered a break apart ''and'' fusion probe; it has both elements.


Image:
====Image====
*[http://commons.wikimedia.org/wiki/File:Bcrablmet.jpg Bcr-Abl translocation (WC)].
<gallery>
Image:Bcrablmet.jpg| Fusion signal suggesting a BCR-ABL translocation. (WC/Pmx)
</gallery>


===Tests===
===Tests===
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*[http://homepage.mac.com/wildlifeweb/cyto/human/ Cytogenetics (homepage.mac.com)] - has ideograms (banding maps) of the human chromosomes.
*[http://homepage.mac.com/wildlifeweb/cyto/human/ Cytogenetics (homepage.mac.com)] - has ideograms (banding maps) of the human chromosomes.
*[http://ccr.coriell.org/sections/support/global/iscn_help.aspx?PgId=263 ISCN symbols and abbreviated terms (coriell.org)] - cytogenetics nomenclature.
*[http://ccr.coriell.org/sections/support/global/iscn_help.aspx?PgId=263 ISCN symbols and abbreviated terms (coriell.org)] - cytogenetics nomenclature.
*[http://www.sickkids.ca/paediatriclabmedicinems/test-catalogue/cytogenetics-listing.html Cytogenetics catalogue (sickkids.ca)].


[[Category:Molecular pathology]]
[[Category:Molecular pathology]]
Retrieved from "https://librepathology.org/wiki/Cytogenetics"