Fluorescence in situ hybridization (FISH)

Overview

Cytogenetic technique using fluorescent DNA probes to detect specific genomic rearrangements, fusions, and copy-number changes on interphase or metaphase nuclei.

Used by

  • PMID:37315267 — used with custom BAC probes flanking FOXO1, PAX3, and PAX7 to detect FOXO1 fusions in extremity rhabdomyosarcoma; complemented Archer FusionPlex testing. 85% of cases were FOXO1 fusion-positive ARMS, 70% of which carried PAX3::FOXO1 PMID:37315267.
  • PMID:38497151 — FISH translocation data for BCL2 and BCL6 used as input to the LymphGen probabilistic algorithm in 320 of 396 DLBCL cases sequenced by MSK-IMPACT Heme PMID:38497151.
  • PMID:38758238 — FISH on five pituitary neuroendocrine tumor patients to validate chromosomal losses identified by FACETS and MSK-IMPACT PMID:38758238.
  • PMID:27806376 — FISH with probes on 1p36/1q25 and 19q13/19p13 to confirm 1p/19q co-deletion in 6 IDH-mutant oligodendrogliomas; complemented bulk WES and Smart-Seq2 scRNA-seq in defining the genetic composition of each tumor’s subclones PMID:27806376.
  • PMID:30325352 — FISH used to detect EML4-ALK translocation status in 196/211 NSCLC subjects in the Stanford radiogenomics dataset; complement to SNaPshot PCR for EGFR/KRAS single-gene testing PMID:30325352.
  • PMID:39305899 — FISH performed by NeoGenomics to confirm MDM2 amplification in a well-differentiated liposarcoma (WDLS) patient-derived tumor organoid (PDTO) and matched primary tumor (SARC0120); separately used to evaluate NTRK1/2/3 status in SARC0127, where ETV6-FISH negativity and larotrectinib resistance helped reclassify the tumor from infantile fibrosarcoma to high-grade sclerosing rhabdomyosarcoma (SCSRMS) PMID:39305899.
  • Used to confirm EWSR1::KLF15 rearrangement in MEC Patient 2 alongside RNA-seq and RT-PCR/Sanger validation PMID:36577525
  • FISH used to validate copy-number alterations in prostate adenocarcinoma tumors from the Broad WES cohort PMID:22610119
  • FISH used to validate KIT and BRAF copy-number alterations in melanoma WGS study PMID:22622578
  • FISH used to validate copy-number alterations and structural rearrangements in pediatric medulloblastoma cases (ICGC, n=125); confirmed chromosome gains and fusion gene events PMID:22832583
  • Used in CLCGP SCLC study (29 tumors) to validate focal amplifications of oncogenes including SOX2 and MYCL identified by WGS PMID:22941188
  • Used fluorescence in situ hybridization (FISH) to validate ETS gene fusions (ETV1 and ERG) in prostate tumors alongside dRanger WGS rearrangement calling PMID:23622249
  • Used in adenoid cystic carcinoma study (n=60 tumor/normal pairs) to detect MYB-NFIB translocations on tissue microarrays via 3-color BAC probes; confirmed fusion in 57% (34/60) of cases PMID:23685749
  • Used in ACC exome study to determine MYB-NFIB fusion status alongside fusion-transcript sequencing, qRT-PCR, and 3’ RACE; confirmed translocations in 19/24 cases PMID:23778141
  • Used to validate DHFR amplification at 5q detected in 14/99 (14%) TCC bladder tumors by WGS-based CNA analysis PMID:24121792
  • Applied to FFPE sections of 7 pancreatic neoplasms with acinar differentiation using proximal/distal labeled probes targeting chromosomes 11 (ATM locus), 15, and 22; revealed polysomy and dramatic intratumoral heterogeneity in 3 of 7 tumors and absence of chromosomal gains/losses in the MSI-H case PMID:24293293.
  • Break-apart and dual-fusion FISH probes for MYB, MYBL1, NFIB, and EWSR1 applied to 88 sinonasal adenoid cystic carcinoma cases; rescued 9 additional fusion-positive cases among TruSight Oncology 500-negative tumors, demonstrating complementarity with NGS panels for detection of MYB-family rearrangements PMID:24418857
  • Routine clinical FISH testing for t(4;14) and t(11;14) applied to 50 of 203 multiple myeloma patients in the MMRC cohort, complementing whole-exome and whole-genome sequencing for cytogenetic characterization PMID:24434212
  • Validated FGFR1 amplification in an additional 53 ESCC tumors; FISH confirmed amplification in 11/53 cases (20.8%) PMID:24686850
  • Used to confirm high-level focal EGFR amplification in a metastasis sample (chr 7p) from a RAS/RAF wild-type CRC patient in whom the primary showed only 7p polysomy. PMID:25164765
  • Used in nccRCC study to validate ASPSCR1-TFE3 and PRCC-TFE3 fusions in translocation RCCs, and to confirm TFEB focal amplification and CLTC-TFEB fusion PMID:25401301
  • Vysis LSI MYC dual-colour break-apart FISH probe used to confirm 8q24.13 MYC amplification (without translocation) in PDA; MYC amplification uniquely associated with poor OS (P=0.0013) and adenosquamous histology. PMID:25855536
  • Interphase FISH applied to assess IGH-BCL6, PRKCD, and TOX rearrangements in 11 PCNSL cases; IGH-BCL6 translocations detected in 2/11 cases. PMID:25991819
  • FISH used to validate copy-number alterations identified in adrenocortical carcinoma genomic profiling PMID:26095796
  • FISH used to assess gene amplification status in breast cancer samples PMID:26168399
  • FISH used for gene copy-number assessment in proteogenomic analysis of ovarian cancer PMID:26200345
  • Applied with BAC probes CTD-2191M2 and CTD-2511M20 flanking the TERT/CLPTM1L locus to detect TERT 5p15.33 rearrangements in the 161-sample neuroblastoma validation cohort; required alongside targeted sequencing to call a rearrangement PMID:26466568
  • Used with MYBL1 (RP11-271O1) and NFIB (RP11-54D21, RP11-79B9) BAC probes to detect t(8;9) translocations in 81 salivary adenoid cystic carcinoma validation samples; identified t(8;9) in 27.8% of t(6;9)-negative ACCs PMID:26631609.
  • FISH used to validate MYB rearrangements and characterize the spectrum of structural variants in adenoid cystic carcinoma tumors and primagrafts PMID:26829750
  • FISH used to verify CYLD focal deletion in CRPC-NE samples; confirmed deletion in 51% of CRPC-NE metastatic biopsies with concordant mRNA downregulation PMID:26855148
  • FISH used on 53 tumors from 13 men to assess TMPRSS2-ERG fusion status; found 100% intra-individual concordance for TMPRSS2-ERG status across metastatic sites in mCRPC. PMID:26928463
  • Used with custom three-probe NF2/22q11/Cen10 assay and ALK break-apart probes to confirm NF2 22q hemizygous loss and TPM3-ALK fusion in uRCC tumours. PMID:27713405
  • Used to confirm sub-clonal to clonal progression of CDKN2A deletion (from heterozygous in the primary to homozygous in distant metastases) in the WCM117 rapid-autopsy urothelial carcinoma case. PMID:27749842
  • Used to validate IGH-DUX4 rearrangements and ERG deletions in the DUX4/ERG B-ALL subtype in cell lines and patient-derived xenografts; DUX4 rearrangement is not detectable by conventional FISH due to repetitive subtelomeric DUX4 locus. PMID:27776115
  • Used fluorescence in situ hybridization (FISH) to detect chromosomal copy number alterations and gene fusions PMID:28199314
  • Used FISH to detect copy number alterations and gene fusions in pediatric tumor specimens PMID:28445112
  • Used to independently validate ERBB2 amplification calls from ASCAT/SNP-array analysis in ICGC CCA cohort; enrichment confirmed for Fluke-Pos CCAs (10.4% vs 2.7% in Fluke-Neg, p < 0.01) PMID:28667006
  • Applied to detect MYC and BCL2 translocations in the 1001-patient DLBCL cohort; MYC FISH translocations associated with MYC mutations and high MYC expression PMID:28985567
  • Used for HER2 (ERBB2) status assessment per CAP/ASCO criteria as part of standard clinical workup in the BLCA TCGA cohort PMID:28988769
  • FISH used for HER2 status assessment per CAP/ASCO criteria in 295 metastatic EGC patients; NGS-based ERBB2 amplification showed 93.7% overall concordance with IHC/FISH, with NGS predicting trastuzumab benefit more precisely PMID:29122777

Notes

  • FISH and Archer FusionPlex were used together for fusion confirmation in the extremity RMS cohort PMID:37315267.
  • In the NSCLC radiogenomics dataset, FISH was the sole assay for ALK/EML4 translocation detection (n=196/211); SNaPshot PCR covered EGFR and KRAS PMID:30325352.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:36577525

This page was processed by crosslinker on 2026-05-14. - PMID:22610119

This page was processed by crosslinker on 2026-05-14. - PMID:22622578

This page was processed by crosslinker on 2026-05-14. - PMID:22832583

This page was processed by crosslinker on 2026-05-14. - PMID:22941188

This page was processed by crosslinker on 2026-05-14. - PMID:23622249

This page was processed by crosslinker on 2026-05-14. - PMID:23685749

This page was processed by crosslinker on 2026-05-14. - PMID:23778141

This page was processed by crosslinker on 2026-05-14. - PMID:24121792

This page was processed by crosslinker on 2026-05-14. - PMID:24293293

This page was processed by crosslinker on 2026-05-14. - PMID:24418857

This page was processed by crosslinker on 2026-05-14. - PMID:24434212

This page was processed by crosslinker on 2026-05-14. - PMID:24686850

This page was processed by crosslinker on 2026-05-14. - PMID:25164765

This page was processed by crosslinker on 2026-05-14. - PMID:25401301

This page was processed by crosslinker on 2026-05-14. - PMID:25855536

This page was processed by crosslinker on 2026-05-14. - PMID:25991819

This page was processed by crosslinker on 2026-05-14. - PMID:26095796

This page was processed by crosslinker on 2026-05-14. - PMID:26168399

This page was processed by crosslinker on 2026-05-14. - PMID:26200345

This page was processed by crosslinker on 2026-05-14. - PMID:26466568

This page was processed by crosslinker on 2026-05-14. - PMID:26631609

This page was processed by crosslinker on 2026-05-14. - PMID:26829750

This page was processed by entity-page-writer on 2026-05-15. - PMID:26855148

This page was processed by entity-page-writer on 2026-05-15. - PMID:26928463

This page was processed by entity-page-writer on 2026-05-15. - PMID:27713405

This page was processed by entity-page-writer on 2026-05-15. - PMID:27749842

This page was processed by entity-page-writer on 2026-05-15. - PMID:27776115

This page was processed by entity-page-writer on 2026-05-15. - PMID:28199314

This page was processed by wiki-cli on 2026-05-14. - PMID:28445112

This page was processed by wiki-cli on 2026-05-14. - PMID:28667006

This page was processed by entity-page-writer on 2026-05-15. - PMID:28985567

This page was processed by entity-page-writer on 2026-05-15. - PMID:28988769

This page was processed by entity-page-writer on 2026-05-15. - PMID:29122777

This page was processed by entity-page-writer on 2026-05-15.