{"entity":{"id":"cytogenetics-fish","kind":"technology","name":"Cytogenetics and FISH","aka":[],"tldr":"Looking at the leukaemia's chromosomes under a microscope, or lighting up specific gene breaks with fluorescent probes, to classify risk.","summary":"Karyotype and FISH remain the backbone of leukaemia risk stratification: t(15;17), t(8;21), inv(16), complex/monosomal karyotype in AML; t(9;22), KMT2A, hypodiploidy, iAMP21 in ALL; del(17p), del(11q), del(13q), trisomy 12 in CLL. Increasingly complemented by optical genome mapping and NGS panels, but still required by ELN and NCCN.","status":"standard-of-care","asOf":"2026-09-07","wikipedia":"https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization","links":[{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization"},{"label":"Horn et al., Blood 2013: MYC, BCL2 and BCL6 rearrangement and expression in 442 RICOVER patients","url":"https://doi.org/10.1182/blood-2012-06-435842"},{"label":"Liu et al., Gastroenterology 2002: t(11;18) marks gastric MALT lymphomas that will not respond to Helicobacter pylori eradication (111 patients)","url":"https://doi.org/10.1053/gast.2002.33047"},{"label":"Roemer et al., J Clin Oncol 2016: PD-L1 and PD-L2 genetic alterations in 108 classical Hodgkin lymphomas","url":"https://doi.org/10.1200/JCO.2016.66.4482"},{"label":"Bea and Amador, Curr Oncol Rep 2017: SOX11 and the genetic events that cooperate with cyclin D1 in mantle cell lymphoma","url":"https://doi.org/10.1007/s11912-017-0598-1"}],"tags":[],"related":[],"cancers":["aml","all-leukemia","cll","nsclc","dlbcl","follicular-lymphoma","mantle-cell-lymphoma","malt-lymphoma","burkitt-lymphoma","hodgkin-lymphoma","non-hodgkin-lymphoma"],"sections":["diagnostics"],"technologies":[],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["eln-risk","del17p-tp53"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":["paper-kris-lung-cancer-mutation-consortium-jama-2014","paper-bergethon-ros1-rearrangements-lung-jco-2012","paper-weiss-fgfr1-amplification-squamous-lung-sci-transl-med-2010"],"journals":["cancer-genetics","genes-chromosomes-and-cancer"],"dependsOn":[],"notes":["Lung cancer: fluorescence in situ hybridisation still finds rearrangements that DNA panels miss, which is why the ALK rate was 8% by this method in the Lung Cancer Mutation Consortium against 3 to 6% on panels (Kris 2014), and it is how ROS1 rearrangement and FGFR1 amplification were first counted (Bergethon 2012, Weiss 2010). It does not identify the fusion partner, which matters for inhibitor choice.","Lymphoma: FISH answers four questions that nothing else answers as cheaply. Is there a MYC rearrangement, and with BCL2 or BCL6 alongside it, which makes this a different WHO entity: in 442 unselected diffuse large B-cell lymphomas the rates were 8.8%, 13.5% and 28.7% (Horn 2013). Is there a t(11;14), which confirms mantle cell lymphoma (Bea and Amador 2017). Is there a t(11;18) in a gastric MALT lymphoma, which predicts that Helicobacter eradication will not work: 47 of the 48 patients who regressed completely after antibiotics were negative for the API2-MALT1 transcript (Liu 2002). And is the 9p24.1 locus gained in a Hodgkin or mediastinal lymphoma, which was found in 97% of 108 classical Hodgkin lymphomas (Roemer 2016). A break-apart probe says a locus is broken, not what it is joined to, which matters for MYC."],"principle":"Metaphase banding for genome-wide structure; interphase FISH for specific loci at single-cell level.","strengths":["Genome-wide, cheap, decades of prognostic validation"],"limitations":["Needs dividing cells; 7-14 days; misses cryptic rearrangements"]},"route":"/technologies/cytogenetics-fish/","neighbours":{"cancer":[{"id":"all-leukemia","kind":"cancer","name":"Acute lymphoblastic leukaemia","route":"/cancers/all-leukemia/"},{"id":"aml","kind":"cancer","name":"Acute myeloid leukaemia","route":"/cancers/aml/"},{"id":"apl","kind":"cancer","name":"Acute promyelocytic leukaemia","route":"/cancers/apl/"},{"id":"burkitt-lymphoma","kind":"cancer","name":"Burkitt lymphoma","route":"/cancers/burkitt-lymphoma/"},{"id":"cll","kind":"cancer","name":"Chronic lymphocytic leukaemia","route":"/cancers/cll/"},{"id":"cll-treatment-naive","kind":"cancer","name":"Chronic lymphocytic leukaemia, first treatment","route":"/cancers/cll-treatment-naive/"},{"id":"cml","kind":"cancer","name":"Chronic myeloid leukaemia (CML)","route":"/cancers/cml/"},{"id":"cml-advanced-phase","kind":"cancer","name":"Chronic myeloid leukaemia, accelerated and blast phase","route":"/cancers/cml-advanced-phase/"},{"id":"cml-chronic-phase","kind":"cancer","name":"Chronic myeloid leukaemia, chronic phase","route":"/cancers/cml-chronic-phase/"},{"id":"cmml","kind":"cancer","name":"Chronic myelomonocytic leukaemia and MDS/MPN overlap neoplasms","route":"/cancers/cmml/"},{"id":"colorectal","kind":"cancer","name":"Colorectal cancer","route":"/cancers/colorectal/"},{"id":"dlbcl","kind":"cancer","name":"Diffuse large B-cell lymphoma","route":"/cancers/dlbcl/"},{"id":"malt-lymphoma","kind":"cancer","name":"Extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma)","route":"/cancers/malt-lymphoma/"},{"id":"follicular-lymphoma","kind":"cancer","name":"Follicular lymphoma","route":"/cancers/follicular-lymphoma/"},{"id":"hodgkin-lymphoma","kind":"cancer","name":"Hodgkin lymphoma","route":"/cancers/hodgkin-lymphoma/"},{"id":"leukaemia","kind":"cancer","name":"Leukaemia (all types)","route":"/cancers/leukaemia/"},{"id":"mantle-cell-lymphoma","kind":"cancer","name":"Mantle cell lymphoma","route":"/cancers/mantle-cell-lymphoma/"},{"id":"marginal-zone-lymphoma","kind":"cancer","name":"Marginal zone lymphoma","route":"/cancers/marginal-zone-lymphoma/"},{"id":"mds","kind":"cancer","name":"Myelodysplastic syndromes / neoplasms (MDS)","route":"/cancers/mds/"},{"id":"non-hodgkin-lymphoma","kind":"cancer","name":"Non-Hodgkin lymphoma (all types)","route":"/cancers/non-hodgkin-lymphoma/"},{"id":"nsclc","kind":"cancer","name":"Non-small-cell lung cancer","route":"/cancers/nsclc/"},{"id":"primary-mediastinal-b-cell-lymphoma","kind":"cancer","name":"Primary mediastinal (thymic) large B-cell lymphoma","route":"/cancers/primary-mediastinal-b-cell-lymphoma/"},{"id":"prostate","kind":"cancer","name":"Prostate cancer","route":"/cancers/prostate/"},{"id":"richter-transformation-cll","kind":"cancer","name":"Richter transformation of chronic lymphocytic leukaemia","route":"/cancers/richter-transformation-cll/"}],"section":[{"id":"diagnostics","kind":"section","name":"Diagnostics & Biomarkers","route":"/fronts/diagnostics/"}],"term":[{"id":"del17p-tp53","kind":"term","name":"del(17p) / TP53 aberration in CLL","route":"/terms/del17p-tp53/"},{"id":"eln-risk","kind":"term","name":"ELN 2022 risk classification","route":"/terms/eln-risk/"},{"id":"lymphoma-bio-transformation","kind":"term","name":"Transformation: when a slow lymphoma turns into a fast one","route":"/terms/lymphoma-bio-transformation/"}],"paper":[{"id":"paper-yu-acquired-resistance-rebiopsy-egfr-ccr-2013","kind":"paper","name":"Analysis of tumor specimens at the time of acquired resistance to EGFR-TKI therapy in 155 patients with EGFR-mutant lung cancers","route":"/key-papers/paper-yu-acquired-resistance-rebiopsy-egfr-ccr-2013/"},{"id":"paper-valtorta-her2-scoring-colorectal-heracles-mod-pathol-2015","kind":"paper","name":"Assessment of a HER2 scoring system for colorectal cancer: results from a validation study","route":"/key-papers/paper-valtorta-her2-scoring-colorectal-heracles-mod-pathol-2015/"},{"id":"paper-weiss-fgfr1-amplification-squamous-lung-sci-transl-med-2010","kind":"paper","name":"Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer","route":"/key-papers/paper-weiss-fgfr1-amplification-squamous-lung-sci-transl-med-2010/"},{"id":"paper-richman-her2-amplification-quasar-focus-piccolo-j-pathol-2016","kind":"paper","name":"HER2 overexpression and amplification as a potential therapeutic target in colorectal cancer: analysis of 3256 patients enrolled in the QUASAR, FOCUS and PICCOLO colorectal cancer trials","route":"/key-papers/paper-richman-her2-amplification-quasar-focus-piccolo-j-pathol-2016/"},{"id":"paper-visakorpi-androgen-receptor-amplification-nat-genet-1995","kind":"paper","name":"In vivo amplification of the androgen receptor gene and progression of human prostate cancer","route":"/key-papers/paper-visakorpi-androgen-receptor-amplification-nat-genet-1995/"},{"id":"paper-beltran-nepc-aurka-mycn-cancer-discov-2011","kind":"paper","name":"Molecular characterisation of neuroendocrine prostate cancer and identification of new drug targets","route":"/key-papers/paper-beltran-nepc-aurka-mycn-cancer-discov-2011/"},{"id":"paper-tomlins-tmprss2-ets-fusion-science-2005","kind":"paper","name":"Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer","route":"/key-papers/paper-tomlins-tmprss2-ets-fusion-science-2005/"},{"id":"paper-bergethon-ros1-rearrangements-lung-jco-2012","kind":"paper","name":"ROS1 rearrangements define a unique molecular class of lung cancers","route":"/key-papers/paper-bergethon-ros1-rearrangements-lung-jco-2012/"},{"id":"paper-lindeman-lung-molecular-testing-guideline-jto-2018","kind":"paper","name":"Updated molecular testing guideline for the selection of lung cancer patients for treatment with targeted tyrosine kinase inhibitors","route":"/key-papers/paper-lindeman-lung-molecular-testing-guideline-jto-2018/"},{"id":"paper-kris-lung-cancer-mutation-consortium-jama-2014","kind":"paper","name":"Using multiplexed assays of oncogenic drivers in lung cancers to select targeted drugs","route":"/key-papers/paper-kris-lung-cancer-mutation-consortium-jama-2014/"}],"journal":[{"id":"cancer-genetics","kind":"journal","name":"Cancer genetics","route":"/journals/cancer-genetics/"},{"id":"genes-chromosomes-and-cancer","kind":"journal","name":"Genes, chromosomes & cancer","route":"/journals/genes-chromosomes-and-cancer/"}],"biomarker":[{"id":"pd-ligand-9p24-alteration","kind":"biomarker","name":"9p24.1 alteration of the PD-1 ligand loci","route":"/biomarkers/pd-ligand-9p24-alteration/"},{"id":"bcl2-rearrangement","kind":"biomarker","name":"BCL2 rearrangement, t(14;18)","route":"/biomarkers/bcl2-rearrangement/"},{"id":"double-hit-rearrangement","kind":"biomarker","name":"Double-hit and triple-hit: MYC with BCL2 and BCL6 rearrangement","route":"/biomarkers/double-hit-rearrangement/"},{"id":"tmprss2-erg-fusion","kind":"biomarker","name":"TMPRSS2-ERG fusion (and the other ETS rearrangements)","route":"/biomarkers/tmprss2-erg-fusion/"}],"person":[{"id":"janet-rowley","kind":"person","name":"Janet Rowley","route":"/people/janet-rowley/"}],"target":[{"id":"ewsr1-fli1","kind":"target","name":"EWSR1-FLI1 fusion","route":"/targets/ewsr1-fli1/"}],"drug":[{"id":"her2-testing-assays","kind":"drug","name":"HER2 IHC and ISH companion assays (HercepTest, PATHWAY 4B5, HER2 Dual ISH)","route":"/drugs/her2-testing-assays/"},{"id":"urovysion","kind":"drug","name":"UroVysion Bladder Cancer Kit","route":"/drugs/urovysion/"}],"company":[{"id":"abbott","kind":"company","name":"Abbott Laboratories","route":"/companies/abbott/"}],"roadmap":[{"id":"diagnostics-roadmap","kind":"roadmap","name":"Diagnostics roadmap: stains → gene panels → blood tests that decide treatment","route":"/roadmaps/diagnostics-roadmap/"}],"technology":[{"id":"sarcoma-methylation-classifier","kind":"technology","name":"Methylation classifier for sarcomas","route":"/technologies/sarcoma-methylation-classifier/"},{"id":"urine-bladder-cancer-tests","kind":"technology","name":"Urine tests for bladder cancer (cytology, FISH, RNA and methylation)","route":"/technologies/urine-bladder-cancer-tests/"}]}}