Molecular pathology tests
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. | glioblastoma, astrocytoma & oligodendroglioma. | Prognostic & predicts treatment to Temozolomide treatment.[9] |
Other
Tests for miscellaneous things:[1]
| Target | Technique | Disease | Notes |
|---|---|---|---|
| 15 STRs and amelogenin (XY) loci | PCR[10] | identity testing - chimerism analysis (post-BMT),[11] 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.
- ↑ 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.