Cytogenetics - Revision history

Michael: /* External links */

2016-05-11T12:51:32Z

External links

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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]]

Michael: /* Karyotyping */ clean

2015-05-04T06:38:05Z

Karyotyping: clean

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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:

Michael: /* Image */

2014-11-30T18:11:18Z

Image

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	====Image====		====Image====
	<gallery>		<gallery>
	Image:Bcrablmet.jpg\| ~~Bcr~~-~~Abl~~ translocation (WC)		Image:Bcrablmet.jpg\| Fusion signal suggesting a BCR-ABL translocation. (WC/Pmx)
	</gallery>		</gallery>

Michael: /* Probe types */

2013-05-18T18:40:58Z

Probe types

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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\| Bcr-Abl translocation (WC)
			</gallery>

	===Tests===		===Tests===

Michael: /* Karyotyping */

2013-05-18T18:40:02Z

Karyotyping

← Older revision		Revision as of 18:40, 18 May 2013
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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 }}

Michael: /* General */

2011-11-15T05:09:11Z

General

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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)=

Michael: /* In situ hybridization */

2011-08-22T01:56:02Z

In situ hybridization

← Older revision		Revision as of 01:56, 22 August 2011
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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:

Michael: /* In situ hybridization */ size of probe

2011-08-18T19:15:46Z

In situ hybridization: size of probe

← Older revision		Revision as of 19:15, 18 August 2011
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	===Overview===		===Overview===
	*Usually done on interphase nuclei.		*Usually done on interphase nuclei.
			*Probe size ~20-1000 base pairs.

	Comes in different flavours:		Comes in different flavours:

Michael: /* Probe types */ tweak

2011-06-08T17:49:48Z

Probe types: tweak

← Older revision		Revision as of 17:49, 8 June 2011
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	**Two colour - two different probes with different colours.		**Two colour - two different probes with different colours.
	**Two colour fusion with extra signal - similar two colour fusion.<ref name=pmid12764379>{{Cite journal \| last1 = Primo \| first1 = D. \| last2 = Tabernero \| first2 = MD. \| last3 = Rasillo \| first3 = A. \| last4 = Sayagués \| first4 = JM. \| last5 = Espinosa \| first5 = AB. \| last6 = Chillón \| first6 = MC. \| last7 = Garcia-Sanz \| first7 = R. \| last8 = Gutierrez \| first8 = N. \| last9 = Giralt \| first9 = M. \| title = Patterns of BCR/ABL gene rearrangements by interphase fluorescence in situ hybridization (FISH) in BCR/ABL+ leukemias: incidence and underlying genetic abnormalities. \| journal = Leukemia \| volume = 17 \| issue = 6 \| pages = 1124-9 \| month = Jun \| year = 2003 \| doi = 10.1038/sj.leu.2402963 \| PMID = 12764379 \| url = http://www.nature.com/leu/journal/v17/n6/full/2402963a.html }}</ref>		**Two colour fusion with extra signal - similar two colour fusion.<ref name=pmid12764379>{{Cite journal \| last1 = Primo \| first1 = D. \| last2 = Tabernero \| first2 = MD. \| last3 = Rasillo \| first3 = A. \| last4 = Sayagués \| first4 = JM. \| last5 = Espinosa \| first5 = AB. \| last6 = Chillón \| first6 = MC. \| last7 = Garcia-Sanz \| first7 = R. \| last8 = Gutierrez \| first8 = N. \| last9 = Giralt \| first9 = M. \| title = Patterns of BCR/ABL gene rearrangements by interphase fluorescence in situ hybridization (FISH) in BCR/ABL+ leukemias: incidence and underlying genetic abnormalities. \| journal = Leukemia \| volume = 17 \| issue = 6 \| pages = 1124-9 \| month = Jun \| year = 2003 \| doi = 10.1038/sj.leu.2402963 \| PMID = 12764379 \| url = http://www.nature.com/leu/journal/v17/n6/full/2402963a.html }}</ref>
	**Three-colour - two probes (e.g. red and blue) straddle the break point.<ref>{{Cite journal \| last1 = Sinclair \| first1 = PB. \| last2 = Green \| first2 = AR. \| last3 = Grace \| first3 = C. \| last4 = Nacheva \| first4 = EP. \| title = Improved sensitivity of BCR-ABL detection: a triple-probe three-color fluorescence in situ hybridization system. \| journal = Blood \| volume = 90 \| issue = 4 \| pages = 1395-402 \| month = Aug \| year = 1997 \| doi = \| PMID = 9269756 \| url= http://bloodjournal.hematologylibrary.org/content/90/4/1395.full.html }}</ref>		**Three-colour † - two probes (e.g. red and blue) straddle the break point.<ref>{{Cite journal \| last1 = Sinclair \| first1 = PB. \| last2 = Green \| first2 = AR. \| last3 = Grace \| first3 = C. \| last4 = Nacheva \| first4 = EP. \| title = Improved sensitivity of BCR-ABL detection: a triple-probe three-color fluorescence in situ hybridization system. \| journal = Blood \| volume = 90 \| issue = 4 \| pages = 1395-402 \| month = Aug \| year = 1997 \| doi = \| PMID = 9269756 \| url= http://bloodjournal.hematologylibrary.org/content/90/4/1395.full.html }}</ref>
	***One of the (true) translocations (e.g. presence of a Philadelphia chromosome) will have only two colours (red and green or yellow).		***One of the (true) translocations (e.g. presence of a Philadelphia chromosome) will have only two colours (red and green or yellow).
	***The derivative chromosome (e.g. derivative 9 chromosome in Philadelphia chromosome cells), which may be lost, will have all three colours.		***The derivative chromosome (e.g. derivative 9 chromosome in Philadelphia chromosome cells), which may be lost, will have all three colours.
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	*Break apart - two colour, e.g. [[translocations\|c-MYC rearrangement]].		*Break apart - two colour, e.g. [[translocations\|c-MYC rearrangement]].
	*Deletion/duplication (e.g. trisomy) - one colour.		*Deletion/duplication (e.g. trisomy) - one colour.

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

	Image:		Image:

Michael: /* Probe types */ tweak

2011-05-31T18:19:34Z

Probe types: tweak

← Older revision		Revision as of 18:19, 31 May 2011
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	===Probe types===		===Probe types===
	Types:		Types:
	*Fusion - usually two ~~colours.~~		*Fusion - usually two colours , e.g. [[translocations\|IGH/BCL2 translocation]], BCR/ABL translocation.
	**Two colour - two different probes with different colours, e.g. [[translocations\|IGH/BCL2 translocation]].		**Two colour - two different probes with different colours.
	**Two colour fusion with extra signal - similar two colour fusion.<ref name=pmid12764379>{{Cite journal \| last1 = Primo \| first1 = D. \| last2 = Tabernero \| first2 = MD. \| last3 = Rasillo \| first3 = A. \| last4 = Sayagués \| first4 = JM. \| last5 = Espinosa \| first5 = AB. \| last6 = Chillón \| first6 = MC. \| last7 = Garcia-Sanz \| first7 = R. \| last8 = Gutierrez \| first8 = N. \| last9 = Giralt \| first9 = M. \| title = Patterns of BCR/ABL gene rearrangements by interphase fluorescence in situ hybridization (FISH) in BCR/ABL+ leukemias: incidence and underlying genetic abnormalities. \| journal = Leukemia \| volume = 17 \| issue = 6 \| pages = 1124-9 \| month = Jun \| year = 2003 \| doi = 10.1038/sj.leu.2402963 \| PMID = 12764379 \| url = http://www.nature.com/leu/journal/v17/n6/full/2402963a.html }}</ref>		**Two colour fusion with extra signal - similar two colour fusion.<ref name=pmid12764379>{{Cite journal \| last1 = Primo \| first1 = D. \| last2 = Tabernero \| first2 = MD. \| last3 = Rasillo \| first3 = A. \| last4 = Sayagués \| first4 = JM. \| last5 = Espinosa \| first5 = AB. \| last6 = Chillón \| first6 = MC. \| last7 = Garcia-Sanz \| first7 = R. \| last8 = Gutierrez \| first8 = N. \| last9 = Giralt \| first9 = M. \| title = Patterns of BCR/ABL gene rearrangements by interphase fluorescence in situ hybridization (FISH) in BCR/ABL+ leukemias: incidence and underlying genetic abnormalities. \| journal = Leukemia \| volume = 17 \| issue = 6 \| pages = 1124-9 \| month = Jun \| year = 2003 \| doi = 10.1038/sj.leu.2402963 \| PMID = 12764379 \| url = http://www.nature.com/leu/journal/v17/n6/full/2402963a.html }}</ref>
	**Three-colour ~~where~~ two probes (e.g. red and blue) straddle the break point.		**Three-colour - two probes (e.g. red and blue) straddle the break point.<ref>{{Cite journal \| last1 = Sinclair \| first1 = PB. \| last2 = Green \| first2 = AR. \| last3 = Grace \| first3 = C. \| last4 = Nacheva \| first4 = EP. \| title = Improved sensitivity of BCR-ABL detection: a triple-probe three-color fluorescence in situ hybridization system. \| journal = Blood \| volume = 90 \| issue = 4 \| pages = 1395-402 \| month = Aug \| year = 1997 \| doi = \| PMID = 9269756 \| url= http://bloodjournal.hematologylibrary.org/content/90/4/1395.full.html }}</ref>
	***One of the (true) translocations ~~will have only two colours~~ (e.g. Philadelphia chromosome).		***One of the (true) translocations (e.g. presence of a Philadelphia chromosome) will have only two colours (red and green or yellow).
	***The derivative chromosome (e.g. derivative 9 chromosome in Philadelphia chromosome cells), which may be lost, will have all three colours.		***The derivative chromosome (e.g. derivative 9 chromosome in Philadelphia chromosome cells), which may be lost, will have all three colours.
	***A (non-pathologic) coincidental colocalization (or overlap) of probes will consist of all three colours.		***A (non-pathologic) coincidental colocalization (or overlap) of probes will consist of all three colours.