Difference between revisions of "Molecular pathology"

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==Molecular==
==Molecular==
General:
===General===
*Very small changes - submicroscopic.
*Very small changes - submicroscopic.
*Sequence data.
*Sequence data.


Techniques:
===Techniques===
*DNA sequencing.
*DNA sequencing.
**Real time-PCR, [[AKA]] real time-quantitative PCR (RQ-PCR).
**Real time-PCR, [[AKA]] real time-quantitative PCR (RQ-PCR).
Line 29: Line 29:
****If the mutation is absent no PCR product is seen.
****If the mutation is absent no PCR product is seen.


===Tests===
====Specific tests====
A list of tests are found in the ''[[Molecular pathology tests]]'' article.
A list of tests are found in the ''[[Molecular pathology tests]]'' article.


===DNA & RNA extraction===
====DNA & RNA extraction====
*Techniques are largely standardized.
*Techniques are largely standardized.
*Protocols exist for fresh tissue and formulin fixed parafin imbeded tissue.
*Protocols exist for fresh tissue and formulin fixed parafin imbeded tissue.
Line 39: Line 39:


==Cytogenetics==
==Cytogenetics==
General:
===General===
*Large changes (chromosomal).
*Large changes (chromosomal).
**Maximum resolution 3-4 megabase pairs (3-4 million base pairs); may be less - dependent on band density.<ref>{{Ref WMSP|695}}</ref>
**Maximum resolution 3-4 megabase pairs (3-4 million base pairs); may be less - dependent on band density.<ref>{{Ref WMSP|695}}</ref>
*Morphologic data.
*Morphologic data.


===Overview===
===Techniques===
Techniques:
*ISH = in situ hybridization.
*ISH = in situ hybridization.
**FISH = fluorescent in situ hybridization.  
**FISH = fluorescent in situ hybridization.  
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*[http://commons.wikimedia.org/wiki/File:Bcrablmet.jpg Bcr-Abl translocation (WC)].
*[http://commons.wikimedia.org/wiki/File:Bcrablmet.jpg Bcr-Abl translocation (WC)].


==World protein databank==
==Other garbage==
===World protein databank===
I can't help think it is ironic that the protein databank goal is to maintain a free and publicly available archive,<ref>Worldwide Protein Data Bank. URL: [http://www.wwpdb.org/faq.html http://www.wwpdb.org/faq.html] Accessed on: April 22, 2009.</ref> yet the announcement is in pay-for-access journal (''Nature Structual Biology'').<ref name=pmid14634627>{{cite journal |author=Berman H, Henrick K, Nakamura H |title=Announcing the worldwide Protein Data Bank |journal=Nat. Struct. Biol. |volume=10 |issue=12 |pages=980 |year=2003 |month=December |pmid=14634627 |doi=10.1038/nsb1203-980 |url=}}</ref>
I can't help think it is ironic that the protein databank goal is to maintain a free and publicly available archive,<ref>Worldwide Protein Data Bank. URL: [http://www.wwpdb.org/faq.html http://www.wwpdb.org/faq.html] Accessed on: April 22, 2009.</ref> yet the announcement is in pay-for-access journal (''Nature Structual Biology'').<ref name=pmid14634627>{{cite journal |author=Berman H, Henrick K, Nakamura H |title=Announcing the worldwide Protein Data Bank |journal=Nat. Struct. Biol. |volume=10 |issue=12 |pages=980 |year=2003 |month=December |pmid=14634627 |doi=10.1038/nsb1203-980 |url=}}</ref>


==Wnt/beta-catenin pathway==
===Wnt/beta-catenin pathway===
Important in hepatoblastomas.<ref name=Ref_PBoD923>{{Ref PBoD|923}}</ref>
Important in hepatoblastomas.<ref name=Ref_PBoD923>{{Ref PBoD|923}}</ref>


Revision as of 16:19, 9 May 2011

Molecular pathology is the future of pathology.

Overview

Molecular pathology can be divided as follows:

 
 
 
Molecular
pathology
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Molecular
techniques
 
 
 
Cytogenetics

Molecular

General

  • Very small changes - submicroscopic.
  • Sequence data.

Techniques

  • DNA sequencing.
    • Real time-PCR, AKA real time-quantitative PCR (RQ-PCR).
  • RNA sequencing.
    • May be examined after reverse transcription (RNA -> DNA), i.e. RT-PCR.
  • Southern blot.
    • Analysis of proteins.
  • Amplification-refractory mutation system (ARMS):[1]
    • Technique for finding a (specific) single base change.
      • The (PCR) primers are designed bind to mutated sequence.
        • If the mutation is present a PCR product is seen.
        • If the mutation is absent no PCR product is seen.

Specific tests

A list of tests are found in the Molecular pathology tests article.

DNA & RNA extraction

  • Techniques are largely standardized.
  • Protocols exist for fresh tissue and formulin fixed parafin imbeded tissue.
    • RNA is usually extracted with acid guanidium thiocyanate, phenol and choroform.[2]
    • DNA is extracted using phenol and isopropanol.[3]

Cytogenetics

General

  • Large changes (chromosomal).
    • Maximum resolution 3-4 megabase pairs (3-4 million base pairs); may be less - dependent on band density.[4]
  • Morphologic data.

Techniques

  • ISH = in situ hybridization.
    • FISH = fluorescent in situ hybridization.
    • SISH = silver in situ hybridization.[5]
  • Karyotyping.

Karyotyping

  • Metaphase nuclei.

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:

Other garbage

World protein databank

I can't help think it is ironic that the protein databank goal is to maintain a free and publicly available archive,[6] yet the announcement is in pay-for-access journal (Nature Structual Biology).[7]

Wnt/beta-catenin pathway

Important in hepatoblastomas.[8]

See also

References

  1. ↑ Little S (May 2001). "Amplification-refractory mutation system (ARMS) analysis of point mutations". Curr Protoc Hum Genet Chapter 9: Unit 9.8. doi:10.1002/0471142905.hg0908s07. PMID 18428319.
  2. ↑ Chomczynski P, Sacchi N (2006). "The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on". Nat Protoc 1 (2): 581–5. doi:10.1038/nprot.2006.83. PMID 17406285.
  3. ↑ Pikor LA, Enfield KS, Cameron H, Lam WL (2011). "DNA extraction from paraffin embedded material for genetic and epigenetic analyses". J Vis Exp (49). doi:10.3791/2763. PMID 21490570.
  4. ↑ 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.
  5. ↑ URL: http://www.immunoportal.com/modules.php?name=News&file=article&sid=186. Accessed on: 2 May 2011.
  6. ↑ Worldwide Protein Data Bank. URL: http://www.wwpdb.org/faq.html Accessed on: April 22, 2009.
  7. ↑ Berman H, Henrick K, Nakamura H (December 2003). "Announcing the worldwide Protein Data Bank". Nat. Struct. Biol. 10 (12): 980. doi:10.1038/nsb1203-980. PMID 14634627.
  8. ↑ Cotran, Ramzi S.; Kumar, Vinay; Fausto, Nelson; Nelso Fausto; Robbins, Stanley L.; Abbas, Abul K. (2005). Robbins and Cotran pathologic basis of disease (7th ed.). St. Louis, Mo: Elsevier Saunders. pp. 923. ISBN 0-7216-0187-1.

External links

Retrieved from "https://librepathology.org/w/index.php?title=Molecular_pathology&oldid=5254"