Difference between revisions of "Molecular pathology tests"
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=== | ===[[Neuropathology]]=== | ||
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 168: | Line 168: | ||
| 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> | |||
|- | |- | ||
| IDH1/ | | H3F3A | ||
| PCR | | PCR + [[H3F3A|H3.3 K27M antibody]]. | ||
| [[oligodendroglioma]] [[astrocytoma]] | | [[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 | | 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> | | 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> | ||
| | | | ||
| 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]] - 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]]) | ||
|- | |- | ||
| KIT, BRAF | | KIT, BRAF | ||
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
- ↑ 1.0 1.1 1.2 1.3 1.4 University Health Network. Molecular diagnostics - current testing. Document number: PMD10002. Version 2.0. March 30, 2011.
- ↑ Online 'Mendelian Inheritance in Man' (OMIM) 176930
- ↑ Online 'Mendelian Inheritance in Man' (OMIM) 612309
- ↑ Online 'Mendelian Inheritance in Man' (OMIM) 613609
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.