Difference between revisions of "Cytogenetics"
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***The detail of an ideogram is given in "band levels"; a 850 band ideogram has a higher resolution than a 400 band ideogram. The typical range for band level is 300-850. The band level, for a given specimen, is determined by an empirical standard and based on the number of bands an observer sees in a subset of the chromosomes.<ref name=pmid8291552>{{Cite journal | last1 = Welborn | first1 = JL. | last2 = Welborn | first2 = R. | title = Banding resolution of human chromosomes: a method of accuracy and simplicity. | journal = Am J Med Genet | volume = 47 | issue = 8 | pages = 1180-3 | month = Dec | year = 1993 | doi = 10.1002/ajmg.1320470810 | PMID = 8291552 }} | ***The detail of an ideogram is given in "band levels"; a 850 band ideogram has a higher resolution than a 400 band ideogram. The typical range for band level is 300-850. The band level, for a given specimen, is determined by an empirical standard and based on the number of bands an observer sees in a subset of the chromosomes.<ref name=pmid8291552>{{Cite journal | last1 = Welborn | first1 = JL. | last2 = Welborn | first2 = R. | title = Banding resolution of human chromosomes: a method of accuracy and simplicity. | journal = Am J Med Genet | volume = 47 | issue = 8 | pages = 1180-3 | month = Dec | year = 1993 | doi = 10.1002/ajmg.1320470810 | PMID = 8291552 }} | ||
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*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>). | ||
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*Quinacrine dye - AT-rich regions brighter than GC-rich regions. | *Quinacrine dye - AT-rich regions brighter than GC-rich regions. | ||
===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 }} | |||
</ref> or comparative genomic hybridization (CGH). | |||
==ISH== | ==ISH== | ||
Revision as of 14:15, 12 May 2011
This article deals with cytogenetics.
General
- Large changes (chromosomal).
- Maximum resolution 3-4 megabase pairs (3-4 million base pairs); may be less - dependent on band density.[1]
- Morphologic data.
Techniques (overview)
- ISH = in situ hybridization.
- FISH = fluorescent in situ hybridization.
- SISH = silver in situ hybridization.[2]
- Karyotyping.
Karyotyping
What?
- Metaphase nuclei.
How?
- Chromosomes are identified by:
- Size (chromosome 1 = largest, chromosome 22 = smallest).
- Position of centromere.
- Banding pattern - using (special) stains:
- Several different techniques (stains) are used:[3]
- 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.
- Examples: Q-banding (Q=Quinacrine), C-banding (C=constitutive heterchromatin), G-banding (G=Giemsa), R-banding (R=reverse).
- Several different techniques (stains) are used:[3]
Analysis:
- Based on comparison to maps of the chromosomes (ideograms).
- Detailed ideograms are in ISCN 2009.[4]
- The detail of an ideogram is given in "band levels"; a 850 band ideogram has a higher resolution than a 400 band ideogram. The typical range for band level is 300-850. The band level, for a given specimen, is determined by an empirical standard and based on the number of bands an observer sees in a subset of the chromosomes.[5]
- Detailed ideograms are in ISCN 2009.[4]
- Typically done with karyotyping software (e.g. Ikaros from MetaSystems[6]).
Image:
Notes:
- Quinacrine dye - AT-rich regions brighter than GC-rich regions.
Virtual karyotyping
- An evolving technique based on SNP microarrays[7] or comparative genomic hybridization (CGH).
ISH
- Usu. interphase nuclei.
May be prepared from:
- In situ paraffin sections (section 4 micrometers thick).
- Isolated nuclei (section 10 micrometers thick).
- Cytospin.
- Cultured cells.
Probe types
Types:
- Fusion (two colours).
- Breakapart (two colours).
- Deletion/duplication (e.g. trisomy).
Image:
Tests
ERBB2
- AKA HER2,[8] AKA HER2/neu.
- Important in invasive breast cancer.
Protocol:
- ISH label for HER2.
- ISH label for CEP17 (D17Z1 -- labels centromere of chromosome 17).[9]
- In 60 nuclei:
- Count number of HER2 signals.
- Count number of CEP17 signals.
- Calculate ratio HER2/D17Z1 signals:[10]
- >2.2 --> HER2 amplification.
- 1.8-2.2 --> equivocal.
See also
References
- ↑ Humphrey, Peter A; Dehner, Louis P; Pfeifer, John D (2008). The Washington Manual of Surgical Pathology (1st ed.). Lippincott Williams & Wilkins. pp. 695. ISBN 978-0781765275.
- ↑ URL: http://www.immunoportal.com/modules.php?name=News&file=article&sid=186. Accessed on: 2 May 2011.
- ↑ URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC355922/. Accessed on: 10 May 2011.
- ↑ Shaffer, Lisa G.; Slovak, Marilyn L.; Campbell, Lynda J. (2009). ISCN 2009: an international system for human cytogenetic nomenclature (2009 ed.). S. Karger AG. ISBN 978-3805589857.
- ↑ Welborn, JL.; Welborn, R. (Dec 1993). "Banding resolution of human chromosomes: a method of accuracy and simplicity.". Am J Med Genet 47 (8): 1180-3. doi:10.1002/ajmg.1320470810. PMID 8291552.
- ↑ URL: 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.
- ↑ Alvarez, K.; Kash, SF.; Lyons-Weiler, MA.; Kim, HJ.; Peterson, LE.; Mathai, B.; Hagenkord, JM.; Monzon, FA. (Sep 2010). "Reproducibility and performance of virtual karyotyping with SNP microarrays for the detection of chromosomal imbalances in formalin-fixed paraffin-embedded tissues.". Diagn Mol Pathol 19 (3): 127-34. doi:10.1097/PDM.0b013e3181d527c5. PMID 20736741.
- ↑ Online 'Mendelian Inheritance in Man' (OMIM) 164870
- ↑ URL: http://www.medscape.com/viewarticle/546925_3. Accessed on: 10 May 2011.
- ↑ ASCO/CAP 2007 guidelines. URL: http://www.cap.org/apps/cap.portal?_nfpb=true&cntvwrPtlt_actionOverride=%2Fportlets%2FcontentViewer%2Fshow&_windowLabel=cntvwrPtlt&cntvwrPtlt%7BactionForm.contentReference%7D=committees%2Fimmunohistochemistry%2Fher2_index.html. Accessed on: 10 May 2011.
External links
- Cytogenetics (homepage.mac.com) - has ideograms (banding maps) of the human chromosomes.