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Difference between revisions of "Cytogenetics"
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This article deals with '''cytogenetics'''. | This article deals with '''cytogenetics'''. An introduction to molecular pathology is found in the ''[[molecular pathology]]'' article. | ||
=General= | =General= | ||
* | *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 name=Ref_WMSP695>{{Ref WMSP|695}}</ref> | ||
* | *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). | ||
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>). | ||
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. | ||
**Usually done on interphase nuclei. | |||
**DNA probe size ~20-1000 base pairs. | |||
Comes in different flavours: | Comes in different flavours: | ||
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===Probe types=== | ===Probe types=== | ||
Types: | Types: | ||
*Fusion - two colour | *Fusion - usually two colours , e.g. [[translocations|IGH/BCL2 translocation]], BCR/ABL 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> | |||
**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). | |||
***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. | |||
*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==== | |||
<gallery> | |||
Image:Bcrablmet.jpg| Fusion signal suggesting a BCR-ABL translocation. (WC/Pmx) | |||
</gallery> | |||
===Tests=== | ===Tests=== | ||
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=External links= | =External links= | ||
*[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://www.sickkids.ca/paediatriclabmedicinems/test-catalogue/cytogenetics-listing.html Cytogenetics catalogue (sickkids.ca)]. | |||
[[Category:Molecular pathology]] | [[Category:Molecular pathology]] | ||