Difference between revisions of "Molecular pathology tests"

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Molecular pathology tests (view source)

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| 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  
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| anesthetics
| anesthetics
|-
|-
| several
| APOA1, TTR, FGA, LYZ
| PCR & sequencing
| PCR & sequencing
| herediary [[amyloidosis]]
| herediary [[amyloidosis]]
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|  
|  
|-
|-
| EBV
| [[EBV]]
|
|
| PTLPD vs. rejection
| [[PTLD]] vs. rejection
|
|
|-
|-
| HHV8
| [[HHV-8]]
| PCR, HPV linear array
| PCR
| HHV8 associated lymphomas (body cavity lymphoma, primary effusion lymphoma)
| HHV-8 associated lymphomas (body cavity lymphoma, primary effusion lymphoma)
|
|
|}
|}


===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===
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|
|
|-
|-
| 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]]
|  
|  
|-
|-
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|
|
|-
|-
| BRAF V600E  
| [[BRAF V600E]]
| ARMS
| ARMS
| [[papillary thyroid carcinoma]]
| [[papillary thyroid carcinoma]]
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|}
|}


===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
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! 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
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==See also==
==See also==
*[[Molecular pathology]].
*[[Molecular pathology]].
*[[Chromosomal translocations]].


==References==
==References==
Jensflorian
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