Difference between revisions of "Molecular pathology tests"

From Libre Pathology
Jump to navigation Jump to search
 
(21 intermediate revisions by 2 users not shown)
Line 12: Line 12:
| PCR
| PCR
| thrombophilia  
| thrombophilia  
| see ''[[Pulmonary_embolism#Risks_factors_.28VTE.29|Risks for VTE]]''
| see ''[[Pulmonary_embolism#Risks_factors_.28VTE.29|Risks for VTE]]'', done together with F5
|-
|-
| F5<ref>{{OMIM|612309}}</ref>
| F5<ref>{{OMIM|612309}}</ref>
| PCR
| PCR
| thrombophilia
| thrombophilia
| see ''[[Pulmonary_embolism#Risks_factors_.28VTE.29|Risks for VTE]]''
| see ''[[Pulmonary_embolism#Risks_factors_.28VTE.29|Risks for VTE]]'', done together with F2
|-
|-
| HFE<ref>{{OMIM|613609}}</ref> Cys282Tyr, His63Asp  
| HFE<ref>{{OMIM|613609}}</ref> Cys282Tyr, His63Asp  
Line 29: Line 29:
| anesthetics
| anesthetics
|-
|-
| several
| APOA1, TTR, FGA, LYZ
| PCR & sequencing
| PCR & sequencing
| herediary [[amyloidosis]]
| herediary [[amyloidosis]]
Line 68: Line 68:
|
|
|-
|-
| HHV-8
| [[HHV-8]]
| PCR, HPV linear array
| PCR
| HHV-8 associated lymphomas (body cavity lymphoma, primary effusion lymphoma)
| HHV-8 associated lymphomas (body cavity lymphoma, primary effusion lymphoma)
|
|
Line 75: Line 75:


===Leukemia===
===Leukemia===
*Several.
Tests for leukemias:<ref name=uhn_molecular_tests>University Health Network. Molecular diagnostics - current testing. Document number: PMD10002. Version 2.0. March 30, 2011.</ref>
{| class="wikitable sortable" style="margin-left:auto;margin-right:auto"
! Target
! Technique
! Disease
! Notes
|-
| BCR-ABL1 t(9;22)
| RQ-PCR
| [[CML]], [[ALL]]
| used to detect residual disease<ref>{{Ref PCPBoD8|175}}</ref>
|-
| MLL-AF4 t(4;11)
| RQ-PCR
|
|
|-
| PML-RARA t(15;17)
| RQ-PCR
| [[Acute promyelocytic leukemia|APL]]
| detect relapse, diagnostic, determines therapy
|-
| RUNX1-RUNX1T1 (AKA AML1/ETO) t(8;21)
| RQ-PCR
| AML-M2
| good prognosis
|-
| CBFB-MYHII t(16;16)
| RQ-PCR
| AML-M4Eo
| good prognosis
|-
| ETV6-RUNX1 t(12;21)
| RQ-PCR
| ALL, AML
| good prognosis
|-
| FLT3, NPM1 (FLT-3, NPM)
| RT-PCR/RE digest
| AML
| prognostic
|-
| 15 STR loci, amelogenin
| PCR
| chimerism (post-[[BMT]]), [[identity testing]]
| monitor transplants, sort-out mixed-up specimens
|}


===Carcinoma===
===Carcinoma===
Line 90: Line 136:
|
|
|-
|-
| HPV several
| [[HPV]] several
| PCR
| PCR
| squamous cell carcinoma ([[cervix]])
| squamous cell carcinoma ([[cervix]])
|
|
|-
|-
| KRAS, BRAF
| [[KRAS mutation|KRAS]], BRAF
| fluorescent RFLP, real time PCR, sequencing
| fluorescent RFLP, real time PCR, sequencing
| netastatic [[colorectal carinoma]]
| metastatic [[colorectal carcinoma]]
|  
|  
|-
|-
Line 105: Line 151:
|
|
|-
|-
| BRAF V600E  
| [[BRAF V600E]]
| ARMS
| ARMS
| [[papillary thyroid carcinoma]]
| [[papillary thyroid carcinoma]]
Line 111: Line 157:
|}
|}


===Other===
===[[Neuropathology]]===
Tests for miscellaneous things:<ref name=uhn_molecular_tests>University Health Network. Molecular diagnostics - current testing. Document number: PMD10002. Version 2.0. March 30, 2011.</ref>
Common tests in neurooncology practice:
{| class="wikitable sortable" style="margin-left:auto;margin-right:auto"
{| class="wikitable sortable" style="margin-left:auto;margin-right:auto"
! Target
! Target
Line 119: Line 165:
! Notes
! Notes
|-
|-
| LOH 1p, 19q
| LOH 1p/19q
| PCR
| PCR
| [[oligodendroglioma]]
| [[oligodendroglioma]]
|
| Prognostic and predicts response to PCV treatment.<ref>{{Cite journal  | last1 = Cairncross | first1 = G. | last2 = Wang | first2 = M. | last3 = Shaw | first3 = E. | last4 = Jenkins | first4 = R. | last5 = Brachman | first5 = D. | last6 = Buckner | first6 = J. | last7 = Fink | first7 = K. | last8 = Souhami | first8 = L. | last9 = Laperriere | first9 = N. | title = Phase III trial of chemoradiotherapy for anaplastic oligodendroglioma: long-term results of RTOG 9402. | journal = J Clin Oncol | volume = 31 | issue = 3 | pages = 337-43 | month = Jan | year = 2013 | doi = 10.1200/JCO.2012.43.2674 | PMID = 23071247 }}</ref>
|-
| [[IDH_mutation|IDH1/2]]
| PCR + [[IDH-1|IDH1 R132H antibody]].
| [[oligodendroglioma]] & [[astrocytoma]].
| Diagnostic and prognostic.<ref>{{Cite journal  | last1 = Hartmann | first1 = C. | last2 = Hentschel | first2 = B. | last3 = Wick | first3 = W. | last4 = Capper | first4 = D. | last5 = Felsberg | first5 = J. | last6 = Simon | first6 = M. | last7 = Westphal | first7 = M. | last8 = Schackert | first8 = G. | last9 = Meyermann | first9 = R. | title = Patients with IDH1 wild type anaplastic astrocytomas exhibit worse prognosis than IDH1-mutated glioblastomas, and IDH1 mutation status accounts for the unfavorable prognostic effect of higher age: implications for classification of gliomas. | journal = Acta Neuropathol | volume = 120 | issue = 6 | pages = 707-18 | month = Dec | year = 2010 | doi = 10.1007/s00401-010-0781-z | PMID = 21088844 }}</ref>
|-
| H3F3A
| PCR + [[H3F3A|H3.3 K27M antibody]].
| [[glioblastoma]] & [[astrocytoma]].
| Diagnostic (K27M-mutant glioma of the midline / pediatric glioblastoma). <ref>{{Cite journal  | last1 = Sturm | first1 = D. | last2 = Witt | first2 = H. | last3 = Hovestadt | first3 = V. | last4 = Khuong-Quang | first4 = DA. | last5 = Jones | first5 = DT. | last6 = Konermann | first6 = C. | last7 = Pfaff | first7 = E. | last8 = Tönjes | first8 = M. | last9 = Sill | first9 = M. | title = Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. | journal = Cancer Cell | volume = 22 | issue = 4 | pages = 425-37 | month = Oct | year = 2012 | doi = 10.1016/j.ccr.2012.08.024 | PMID = 23079654 }}</ref>
|-
| [[MGMT]]
| Methylation-specific PCR, Pyroseq.
| [[glioblastoma]],  [[astrocytoma]] & [[oligodendroglioma]].
| Prognostic & predicts treatment to Temozolomide treatment.<ref>{{Cite journal  | last1 = Stupp | first1 = R. | last2 = Hegi | first2 = ME. | last3 = Mason | first3 = WP. | last4 = van den Bent | first4 = MJ. | last5 = Taphoorn | first5 = MJ. | last6 = Janzer | first6 = RC. | last7 = Ludwin | first7 = SK. | last8 = Allgeier | first8 = A. | last9 = Fisher | first9 = B. | title = Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. | journal = Lancet Oncol | volume = 10 | issue = 5 | pages = 459-66 | month = May | year = 2009 | doi = 10.1016/S1470-2045(09)70025-7 | PMID = 19269895 }}</ref>
|-
| BRAF-Fusion
| RT-PCR, RNAseq + Defuse-Analysis<ref>{{Cite journal  | last1 = McPherson | first1 = A. | last2 = Hormozdiari | first2 = F. | last3 = Zayed | first3 = A. | last4 = Giuliany | first4 = R. | last5 = Ha | first5 = G. | last6 = Sun | first6 = MG. | last7 = Griffith | first7 = M. | last8 = Heravi Moussavi | first8 = A. | last9 = Senz | first9 = J. | title = deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. | journal = PLoS Comput Biol | volume = 7 | issue = 5 | pages = e1001138 | month = May | year = 2011 | doi = 10.1371/journal.pcbi.1001138 | PMID = 21625565 }}</ref>
| [[pilocytic astrocytoma]]
| Diagnostic.<ref>{{Cite journal  | last1 = Hasselblatt | first1 = M. | last2 = Riesmeier | first2 = B. | last3 = Lechtape | first3 = B. | last4 = Brentrup | first4 = A. | last5 = Stummer | first5 = W. | last6 = Albert | first6 = FK. | last7 = Sepehrnia | first7 = A. | last8 = Ebel | first8 = H. | last9 = Gerss | first9 = J. | title = BRAF-KIAA1549 fusion transcripts are less frequent in pilocytic astrocytomas diagnosed in adults. | journal = Neuropathol Appl Neurobiol | volume = 37 | issue = 7 | pages = 803-6 | month = Dec | year = 2011 | doi = 10.1111/j.1365-2990.2011.01193.x | PMID = 21696415 }}</ref>
|-
| Rela-Fusion
| RT-PCR, RNAseq + Defuse-Analysis
| supratentorial [[ependymoma]]
| Diagnostic and prognostic (unfavourable, when present).<ref>{{Cite journal  | last1 = Parker | first1 = M. | last2 = Mohankumar | first2 = KM. | last3 = Punchihewa | first3 = C. | last4 = Weinlich | first4 = R. | last5 = Dalton | first5 = JD. | last6 = Li | first6 = Y. | last7 = Lee | first7 = R. | last8 = Tatevossian | first8 = RG. | last9 = Phoenix | first9 = TN. | title = C11orf95-RELA fusions drive oncogenic NF-κB signalling in ependymoma. | journal = Nature | volume = 506 | issue = 7489 | pages = 451-5 | month = Feb | year = 2014 | doi = 10.1038/nature13109 | PMID = 24553141 }}</ref>
|}
 
===Other===
Tests for miscellaneous things:<ref name=uhn_molecular_tests>University Health Network. Molecular diagnostics - current testing. Document number: PMD10002. Version 2.0. March 30, 2011.</ref>
{| class="wikitable sortable" style="margin-left:auto;margin-right:auto"
! Target
! Technique
! Disease
! Notes
|-
|-
| 15 STRs and amelogenin (XY) loci
| PCR<ref>{{Cite journal  | last1 = Romsos | first1 = EL. | last2 = Vallone | first2 = PM. | title = Rapid PCR of STR markers: Applications to human identification. | journal = Forensic Sci Int Genet | volume =  | issue =  | pages =  | month = Apr | year = 2015 | doi = 10.1016/j.fsigen.2015.04.008 | PMID = 25937291 }}</ref>
|  
|  
| 15 STRs and amelogenin (XY) loci
| [[identity testing]] - chimerism analysis (post-[[BMT]]),<ref>{{Cite journal  | last1 = Borrill | first1 = V. | last2 = Schlaphoff | first2 = T. | last3 = du Toit | first3 = E. | last4 = Marx | first4 = M. | last5 = Wood | first5 = L. | last6 = Jacobs | first6 = P. | title = The use of short tandem repeat polymorphisms for monitoring chimerism following bone marrow transplantation: a short report. | journal = Hematology | volume = 13 | issue = 4 | pages = 210-4 | month = Aug | year = 2008 | doi = 10.1179/102453308X316059 | PMID = 18796246 }}</ref> specimen mix-ups, [[decendent identification]]/evidence ([[forensic pathology]])
| identity testing
|
|-
|-
| KIT, BRAF
| KIT, BRAF
Line 152: Line 232:
==See also==
==See also==
*[[Molecular pathology]].
*[[Molecular pathology]].
*[[Chromosomal translocations]].


==References==
==References==

Latest revision as of 11:25, 23 March 2017

This article is a collection of molecular pathology tests. It is not meant to be complete list. It is there to give a flavour of what is out there and how things are done.

Hereditary

Tests for hereditary conditions:[1]

Target Technique Disease Notes
F2[2] PCR thrombophilia see Risks for VTE, done together with F5
F5[3] PCR thrombophilia see Risks for VTE, done together with F2
HFE[4] Cys282Tyr, His63Asp PCR hemochromatosis -
RYR1 PCR & sequencing malignant hyperthermia anesthetics
APOA1, TTR, FGA, LYZ PCR & sequencing herediary amyloidosis
HBA PCR Alpha thalassemia

Lymphoma

Tests for lymphomas:[1]

Target Technique Disease Notes
BCL2 PCR follicular lymphoma vs. follicular hyperplasia
several Southern / PCR T cell neoplasia
Ig heavy chain, Ig light chain Southern / PCR B cell neoplasia
EBV PTLD vs. rejection
HHV-8 PCR HHV-8 associated lymphomas (body cavity lymphoma, primary effusion lymphoma)

Leukemia

Tests for leukemias:[1]

Target Technique Disease Notes
BCR-ABL1 t(9;22) RQ-PCR CML, ALL used to detect residual disease[5]
MLL-AF4 t(4;11) RQ-PCR
PML-RARA t(15;17) RQ-PCR APL detect relapse, diagnostic, determines therapy
RUNX1-RUNX1T1 (AKA AML1/ETO) t(8;21) RQ-PCR AML-M2 good prognosis
CBFB-MYHII t(16;16) RQ-PCR AML-M4Eo good prognosis
ETV6-RUNX1 t(12;21) RQ-PCR ALL, AML good prognosis
FLT3, NPM1 (FLT-3, NPM) RT-PCR/RE digest AML prognostic
15 STR loci, amelogenin PCR chimerism (post-BMT), identity testing monitor transplants, sort-out mixed-up specimens

Carcinoma

Tests for carcinomas:[1]

Target Technique Disease Notes
EBV quantitation PQ-PCR Nasopharyngeal carcinoma
HPV several PCR squamous cell carcinoma (cervix)
KRAS, BRAF fluorescent RFLP, real time PCR, sequencing metastatic colorectal carcinoma
EGRF fluorescent RFLP non small cell lung cancer
BRAF V600E ARMS papillary thyroid carcinoma

Neuropathology

Common tests in neurooncology practice:

Target Technique Disease Notes
LOH 1p/19q PCR oligodendroglioma Prognostic and predicts response to PCV treatment.[6]
IDH1/2 PCR + IDH1 R132H antibody. oligodendroglioma & astrocytoma. Diagnostic and prognostic.[7]
H3F3A PCR + H3.3 K27M antibody. glioblastoma & astrocytoma. Diagnostic (K27M-mutant glioma of the midline / pediatric glioblastoma). [8]
MGMT Methylation-specific PCR, Pyroseq. glioblastoma, astrocytoma & oligodendroglioma. Prognostic & predicts treatment to Temozolomide treatment.[9]
BRAF-Fusion RT-PCR, RNAseq + Defuse-Analysis[10] pilocytic astrocytoma Diagnostic.[11]
Rela-Fusion RT-PCR, RNAseq + Defuse-Analysis supratentorial ependymoma Diagnostic and prognostic (unfavourable, when present).[12]

Other

Tests for miscellaneous things:[1]

Target Technique Disease Notes
15 STRs and amelogenin (XY) loci PCR[13] identity testing - chimerism analysis (post-BMT),[14] specimen mix-ups, decendent identification/evidence (forensic pathology)
KIT, BRAF sequencying, ARMS malignant melanoma
several PQ-PCR synovial sarcoma
JAK2 V617F ARMS myeloproliferative disorders
KIT sequencing AML, mastocytosis, GIST

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 University Health Network. Molecular diagnostics - current testing. Document number: PMD10002. Version 2.0. March 30, 2011.
  2. ↑ Online 'Mendelian Inheritance in Man' (OMIM) 176930
  3. ↑ Online 'Mendelian Inheritance in Man' (OMIM) 612309
  4. ↑ Online 'Mendelian Inheritance in Man' (OMIM) 613609
  5. ↑ Mitchell, Richard; Kumar, Vinay; Fausto, Nelson; Abbas, Abul K.; Aster, Jon (2011). Pocket Companion to Robbins & Cotran Pathologic Basis of Disease (8th ed.). Elsevier Saunders. pp. 175. ISBN 978-1416054542.
  6. ↑ Cairncross, G.; Wang, M.; Shaw, E.; Jenkins, R.; Brachman, D.; Buckner, J.; Fink, K.; Souhami, L. et al. (Jan 2013). "Phase III trial of chemoradiotherapy for anaplastic oligodendroglioma: long-term results of RTOG 9402.". J Clin Oncol 31 (3): 337-43. doi:10.1200/JCO.2012.43.2674. PMID 23071247.
  7. ↑ Hartmann, C.; Hentschel, B.; Wick, W.; Capper, D.; Felsberg, J.; Simon, M.; Westphal, M.; Schackert, G. et al. (Dec 2010). "Patients with IDH1 wild type anaplastic astrocytomas exhibit worse prognosis than IDH1-mutated glioblastomas, and IDH1 mutation status accounts for the unfavorable prognostic effect of higher age: implications for classification of gliomas.". Acta Neuropathol 120 (6): 707-18. doi:10.1007/s00401-010-0781-z. PMID 21088844.
  8. ↑ Sturm, D.; Witt, H.; Hovestadt, V.; Khuong-Quang, DA.; Jones, DT.; Konermann, C.; Pfaff, E.; Tönjes, M. et al. (Oct 2012). "Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma.". Cancer Cell 22 (4): 425-37. doi:10.1016/j.ccr.2012.08.024. PMID 23079654.
  9. ↑ Stupp, R.; Hegi, ME.; Mason, WP.; van den Bent, MJ.; Taphoorn, MJ.; Janzer, RC.; Ludwin, SK.; Allgeier, A. et al. (May 2009). "Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial.". Lancet Oncol 10 (5): 459-66. doi:10.1016/S1470-2045(09)70025-7. PMID 19269895.
  10. ↑ McPherson, A.; Hormozdiari, F.; Zayed, A.; Giuliany, R.; Ha, G.; Sun, MG.; Griffith, M.; Heravi Moussavi, A. et al. (May 2011). "deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.". PLoS Comput Biol 7 (5): e1001138. doi:10.1371/journal.pcbi.1001138. PMID 21625565.
  11. ↑ Hasselblatt, M.; Riesmeier, B.; Lechtape, B.; Brentrup, A.; Stummer, W.; Albert, FK.; Sepehrnia, A.; Ebel, H. et al. (Dec 2011). "BRAF-KIAA1549 fusion transcripts are less frequent in pilocytic astrocytomas diagnosed in adults.". Neuropathol Appl Neurobiol 37 (7): 803-6. doi:10.1111/j.1365-2990.2011.01193.x. PMID 21696415.
  12. ↑ Parker, M.; Mohankumar, KM.; Punchihewa, C.; Weinlich, R.; Dalton, JD.; Li, Y.; Lee, R.; Tatevossian, RG. et al. (Feb 2014). "C11orf95-RELA fusions drive oncogenic NF-κB signalling in ependymoma.". Nature 506 (7489): 451-5. doi:10.1038/nature13109. PMID 24553141.
  13. ↑ Romsos, EL.; Vallone, PM. (Apr 2015). "Rapid PCR of STR markers: Applications to human identification.". Forensic Sci Int Genet. doi:10.1016/j.fsigen.2015.04.008. PMID 25937291.
  14. ↑ Borrill, V.; Schlaphoff, T.; du Toit, E.; Marx, M.; Wood, L.; Jacobs, P. (Aug 2008). "The use of short tandem repeat polymorphisms for monitoring chimerism following bone marrow transplantation: a short report.". Hematology 13 (4): 210-4. doi:10.1179/102453308X316059. PMID 18796246.
Retrieved from "https://librepathology.org/w/index.php?title=Molecular_pathology_tests&oldid=47165"