Fluorescence In Situ Hybridization

Fluorescence in situ hybridization (FISH) is a technique that uses fluorescent probes that bind only to parts of a chromosome with a high degree of sequence complementarity. The fluorescence-labeled DNA probes specific to chromosomal regions of interest are used to identify DNA changes on a chromosome. FISH is used to identify numerical abnormalities of chromosomes as well as deletions, duplications, translocations and inversions of certain disease-specific regions. FISH is very useful in identifying deletions, duplications and rearrangements of small disease regions when the presence of these anomalies is unidentifiable by standard chromosome analysis. In hematopoietic neoplasms, FISH aids in diagnosis, prognosis and choice of treatment options.

FISH PANELS: HEMATOLOGY

ALL
MYC Breakapart (MYC rearrangement), CDKN2A/D9Z3 (9p deletion), BCR/ABL1-ASS (t(9;22)), D10Z1/D17Z1/CHIC2 (hyperdiploidy), KMT2A (KMT2A or MLL rearrangement), ETV6/RUNX1 (TEL/AML1; t(12;21)), IGH Breakapart (IGH rearrangement), TCF3 Breakapart (TCF3 or E2A rearrangement)
AML
5p15.3/EGR1 (5q deletion), RELN/TES (7q deletion), D8Z2 (Trisomy 8), RUNX1/RUNX1T1 (AML1/ETO; t(8;21), PML/RARA (t(15;17), CBFB/MYH11 (inv(16))
CLL
MYB/D6Z1 (6q deletion), IGH/CCND1 (t(11;14)), ATM/D11Z1 (ATM deletion), D12Z1 (Trisomy 12), 13q14.3/13q34 (13q deletion or monosomy 13), TP53/D17Z1 (TP53 deletion)
CML
BCR/ABL1-ASS (t(9;22)), D8Z2 (Trisomy 8)
Myeloma
CKS1B/CDKN2C (1q gain/1p deletion), CEP3 (trisomy 3), CEP9 (trisomy 9), IGH/FGFR3 (t(4;14)), IGH/CCND1 (t(11;14)), 13q14.3/13q34 (13q deletion), TP53/D17Z1 (TP53 deletion)

MDS
5p15.3/EGR1 (5q deletion), RELN/TES (7q deletion), D8Z2 (Trisomy 8), KMT2A Breakapart (KMT2A or MLL rearrangement), TP53/D17Z1 (TP53 deletion), PTPRT/MYBL2 (20q deletion)
Eosinophilia
FIP1L1/CHIC2/PDGFRA Deletion/Fusion (CHIC2 deletion and FIP1L1-PDGFRA fusion), FGFR1 Breakapart (FGFR1 rearrangement), PDGFRB Breakapart (PDGFRB rearrangement)
High-Grade/Large B-Cell Lymphoma
BCL6 Breakapart (BCL6 rearrangement), MYC Breakapart (MYC rearrangement), BCL2 Breakapart (BCL2 rearrangement)
B-Cell NHL
BCL6 Breakapart (BCL6 rearrangement), MYC Breakapart (MYC rearrangement), IGH/CCND1 (t(11;14)), IGH/BCL2 (t(14;18)), MALT1 Breakapart (MALT1 rearrangement)

FISH Probes: Hematology

ALK/Lymphoma (2p23)
Break-Apart probe covers ALK gene on chromosome 2 at locus p23
ATM (11q22)
Probe covers ATM gene on chromosome 9 at locus q22.3. D11Z1 is as a control probe for chromosome 11
BCL6 (3q27)
Break-Apart probe covers BCL6 gene on chromosome 3 at locus q27
BCR-ABL/ASS1 t(9;22)
Translocation, dual fusion probe covering BCR gene on chromosome 22 at locus q11.22-q11.23 and ABL1-ASS genes on chromosome 9 at locus q34.11-q34.12
CBFB/MYH11 inv(16)
Translocation, dual fusion probe covering CBFB gene at locus q22.1 and MYH11 gene at locus p13.11
CKS1B/CDKN2C (1p/1q)
Probe covers CDKN2C gene locus p32.3 and CKS1B gene at locus q21.3, both on chromosome 1
ETV6/RUNX1 t(12;21)
Break-Apart probe covers ETV6 gene on chromosome 12 at locus p13.2
FGFR1 (8p11)
Break-Apart/amplification probe covers FGFR1 gene on chromosome 8 at locus 8p11
IGH (14q32)
Break-Apart probe covers IGH gene on chromosome 14 at locus q32.3
IGH/BCL2 t(14;18)
Translocation probe covering IGH gene on chromosome 14 at locus q32.3 and BCL2 gene on chromosome 18 at locus q21
IGH/CCND1 t(11;14)
Translocation probe covering IGH gene on chromosome 14 at locus q32.3 and CCND1 gene on chromosome 11 at locus q13
IGH/FGFR3 t(4;14)
Translocation probe covering IGH gene on chromosome 14 at locus q32.3 and FGFR3 gene on chromosome 4 at locus p16.3
IGH/MAF t(14;16)
Translocation probe covering IGH gene on chromosome 14 at locus q32.3 and MAF gene on chromosome 16 at locus q23
IGH/MYC t(8;14)
Translocation probe covering IGH gene on chromosome 14 at locus q32.3 and MYC gene on chromosome 8 at locus q24.21
MALT1 (18q21)
Break-Apart probe covers MALT1 gene on chromosome 18 at locus q21
MLL (11q23)
Break-Apart probe covers MLL gene on chromosome 11 at locus q23.3
c-MYC (8q24)
Break-Apart probe covers cMYC gene on chromosome 8 at locus q24
PDGFRA (4q12)
Deletion/fusion probe covering FIP1L1/CHIC2/PDGFRA genes on chromosome 4 at locus 4q12
PDGFRB (5q32)
Break-Apart probe covers PDGFRB gene on chromosome 5 at locus q32
PML/RARA t(15;17)
Translocation probe covering PML gene on chromosome 15 at locus q24.1 and RARA gene on chromosome 17 at locus q21.1-q21.2
RUNX1T1/RUNX1 (ETO/AML1) t(8;21)
Translocation probe covering ETO(RUNX1T1) gene on chromosome 8 at locus q21.3 and AML1(RUNX1) gene on chromosome 21 at locus q22.12
TP53 (17p13)
Probe covers TP53 gene on chromosome 17 at locus p13. D17Z1 is a control probe for chromosome 17
5q-/-5/+5
Probe covers EGR1 gene on chromosome 5 at locus q31.2. The control probe is located on chromosome 5 at locus p15.31
6q21/6q23
Probe covers MYB gene on chromosome 6 at locus q23.3. D6Z1 is a control probe for chromosome 6
7q-/-7
Probe covers RELN gene at locus q22.1-q22.2 and TES gene at locus q31.2, both on chromosome 7
+8
Enumeration probe located in the centromeric, pericentromic or heterochromatic region of chromosome 8
+12
Enumeration probe located in the centromeric, pericentromic or heterochromatic region of chromosome 12
13q-/-13
13q14.3 probe covers D13S319 and D13S25 markers. 13qter probe acts as a control probe.
20q-
Probe covers PTPRT gene at locus q12 and MYBL2 gene at locus q13.12, both on chromosome 20

FISH: SOLID TUMOR

ALK Rearrangement
The FDA-approved Vysis® ALK Break Apart FISH Probe Kit detects rearrangements involving the ALK gene via fluorescence in situ hybridization (FISH) in formalin-fixed paraffin-embedded (FFPE) non-small cell lung cancer (NSCLC) tissue specimens.
HER2 Amplification
Amplification of the ERBB2 gene (encoding for HER2 protein) is detected by fluorescent in situ hybridization (FISH) in human breast and esophagogastric cancer tissue specimens.
EWSR1 Rearrangement
Probes: EWSR1 (22q12)
Disease(s): Ewing sarcoma, primitive neuroectodermal tumor (PNET)

MET Amplification
Amplification of the MET gene is detected by fluorescence in situ hybridization (FISH)
ROS1 Rearrangement
Probes: ROS1 (6q22.1)
Disease(s): Non-small cell lung carcinoma (NSCLC)

FISH: POC PLOIDY

FISH on Formalin Fixed Products of Conception, Common Trisomies and Triploidies, Chromosomes 13/16/18/21/X/Y