Oncology Fluorescence in situ Hybridization (FISH)
Diagnostic gene rearrangements at or below the resolution of cytogenetics may be defined by FISH protocol. Disease-specific translocations can be detected in nondividing (interphase) cells by implementing multicolor fluorescence probes specific for the involved genes that reciprocally merge to form a third color. Oncogenes that have multiple reciprocal translocation sites can be sensitively evaluated by “break-apart” probes in which the neoplastic splitting of the critical sequence separates the normal fusion color into distinct colors regardless of the variant reciprocal site. Disease-causing deletions relating to the loss of known or putative tumor suppressor genes (TSGs) are readily identified by the detection of cells with only a single signal, as in loss of the 5q31 locus-specific probe characteristic of 5q- syndrome in myelodysplasia.
Specially designed profiles targeting the most common genetic changes can effectively detect indolent CLL and myeloma clones that are often normal in cytogenetic analysis due the slow cell division of the clones. MDS and AML profiles can effectively be used as an interphase adjunct to cytogenetic analysis with no mitotic activity. The ALL profile not only detects the submicroscopic t(12;21) but is not affected by the poor chromosome morphology problems that often beset this type of leukemia. The CML probeset now includes the argininosuccinate synthetase (ASS) gene probe as a control to confirm any ABL deletions thought to be associated with poor prognosis CML by some investigators. A CML FISH+chromosome analysis profile is available for monitoring residual disease in marrow samples (FISH alone is better for blood samples since therapy usually blocks peripheral leukemia cell division). A new Aggressive B-Cell Lymphoma Profile, FISH (510344) with three break-apart probes can reliably identify double/triple “hit” NHL.
Opposite sex bone marrow transplants can be monitored by either sex chromosome-specific probes or (cases of same-sex transplants) a leukemia clone-specific probe previously identified by cytogenetics, eg, a centromere 8 probe for trisomy 8 or BCR/ABL fusion probes for CML. Engraftment Monitoring, Pre (168138) is also available.
Clone specific probes may also monitor residual disease. These studies offer the advantage of not requiring mitotic cells in the often hypocellular posttreatment aspirates. Newly available dual fusion and break-apart probes more accurately rule out low level residual disease by dramatically reducing background.
FISH is also readily applicable to blood smears; touch preps; formalin-fixed, paraffin-embedded samples; and frozen sections.
See table for available probes and test numbers.
|
Gene/Region |
Rearrangement/Target (Test Number) |
|---|---|
|
Note: Additional probes may become available. Call 800-345-4363 for more information. |
|
|
TSG = tumor suppressor gene. |
|
|
*Molecular analysis also available. |
|
|
†Approved. |
|
|
‡Immunohistochemistry also available. |
|
|
Xcen, Yq12 |
Chimeric opposite sex bone marrow transplant study |
|
MDS |
Available profile (511060) targets loci below and cen 8 |
|
5q |
5q31 Deletion (probe locus linked with putative TSG) |
|
7q |
7q31 Deletion (probe locus linked with putative TSG) |
|
8† |
Trisomy 8 (centromere) probe (also in AML/MPD) |
|
20q |
20q12 Deletion (probe locus linked with putative TSG) |
|
MPN (With Hypereosinophilia) |
Available profile (511444) targets loci below |
|
FIP1L1/PDGFR-α |
4q12 Two-color dual fusion probe for HES/CEL rearrangements |
|
PDGFR-β |
5q32 Two-color break-apart probe for CMML Gleevec-sensitive rearrangements |
|
FGFR1 |
8p12 Two-color break-apart probe for stem-cell myeloproliferative neoplasms |
|
MPN/CML |
Available profile (511425) targets loci below |
|
BCR/ABL1* |
t(9;22) Two-color dual-fusion signal for CML |
|
8† |
Trisomy 8 (centromere) probe (also in AML/MPD) |
|
20q |
20q12 Deletion (probe locus linked with putative TSG) |
|
p16 (CDKN2A) |
9p21 Deletion (probe-specific for p16 TSG) |
|
13q |
13q14.3 Deletion (probe locus linked with putative TSG) |
|
CML |
CML Profile: BCR/ABL FISH Plus Chromosome Analysis (150500) |
|
BCR/ABL1* |
t(9;22) Two-color dual-fusion signal for CML (511520) |
|
ALL (Pediatric) |
Available profile (510324) targets loci below |
|
BCR/ABL1* |
t(9;22) Two-color dual-fusion signal |
|
MLL (KMT2A) |
11q23 Two-color break-apart probe for all translocation variants |
|
p16 (CDKN2A) |
9p21 Deletion (probe-specific for p16 TSG) |
|
TCF3 (E2A) |
19p13 Two-color break-apart probe for t(1;19) |
|
TEL/AML1 (ETV6/RUNX1) |
t(12;21) Two-color dual-fusion signal |
|
4, 10, 17 |
Centromere probe set for hyperdiploid signal |
|
ALL (Adult) |
Available profile (511077) targets loci below |
|
BCR/ABL1* |
t(9;22) Two-color dual-fusion signal |
|
MLL (KMT2A) |
11q23 Two-color break-apart probe for all translocation variants |
|
MYC |
8q24 Two-color break-apart probe for all Burkitt lymphoma variants |
|
Cep 6/21q |
Two-color enumeration probes for ALL |
|
ALL |
Profile not available; probes are ordered separately |
|
ABL1 |
9q34.12 Dual color break-apart probe |
|
ABL2 |
1q25.2 Dual color break-apart probe |
|
AML |
Available profile (510336) targets loci below (except EVI1) |
|
PML/RARA |
t(15;17) Two-color dual fusion probe (APL variants split RARA probe) |
|
CBFB |
inv(16) Two-color break-apart probe |
|
ETO/AML1 (RUNX1T1/RUNX1) |
t(8;21) Two-color dual-fusion signal |
|
MLL (KMT2A) |
11q23 Two-color break-apart probe for all translocation variants |
|
5q/7q |
5q31/7q31 Deletions (probe locus linked with putative TSG) |
|
EVI1 (MECOM) |
3q26 Two-color break-apart probe in AML |
|
AML |
Profile not available; probes are ordered separately |
|
NUP98 |
11p15.4 Dual color break-apart probe |
|
CBFB/MYH11 |
16q22.1/16p13.11 inv(16) Dual color dual fusion signal |
|
CLL (LPD) |
Available profile (510340) targets loci below |
|
ATM |
11q23 Deletion (probe locus linked with putative TSG) |
|
12† |
Trisomy 12 (centromere) probe |
|
13q |
13q14.3 Deletion (probe locus linked with putative TSG) |
|
IgH Cyclin D1 (CCND1) |
t(11;14) Two-color dual-fusion signal in leukemic phase of MCL |
|
TP53 |
17p13.1 TSG deleted in many malignancies (including CLL and MM) |
|
MM |
Available profile (510325) targets loci below |
|
13q |
13q14.3 Deletion (probe locus linked with putative TSG) |
|
IgH Cyclin D1 (CCND1) |
t(11;14) Two-color dual fusion signal in MM/PCL/MGUS |
|
IgH/FGFR3 |
t(4;14) Two-color dual fusion signal in MM/PCL/MGUS |
|
TP53 |
17p13.1 TSG deleted in many malignancies (including CLL and MM) |
|
IgH/C-MAF |
t(14;16) Two-color dual fusion signal in MM/PCL/MGUS |
|
1p/1q |
1p36/1q21 Two-color probe set for genomic imbalance in MM |
|
7,9,15 |
Centromere probe set for hyperdiploid signal |
|
Lymphoma |
|
|
BCL2 |
18q21.3 Two color break-apart probe for follicular lymphoma and DLBCL |
|
MYC |
8q24 Two-color break-apart probe for all Burkitt lymphoma variants |
|
BCL6 |
3q27 Two-color break-apart probe in centroblastic lymphoma and DLBCL |
|
Lymphoma |
Profile not available; probes are ordered separately |
|
IgH/Cyclin D1(BCL1) |
*t(11;14) Two-color dual fusion signal in mantle cell lymphoma (MCL) |
|
MYC |
8q24 Two-color break-apart probe for all Burkitt lymphoma variants |
|
IgH/BCL2* |
t(14;18) Two-color merged signal in follicular lymphoma |
|
BCL6 |
3q27 Two-color break-apart probe in centroblastic lymphoma |
|
MALT1 |
18q21 Two-color break-apart probe in MALT lymphoma |
|
ALK |
2p23 Two-color break-apart probe for ALK (Ki-1) lymphomas |
|
TCR |
Two-color break-apart probe at 14q11 for T-cell leukemia/lymphoma |
|
MYB |
6q22 Locus linked with putative TSG in NHL and other lymphoid malignancies |
|
Cancer |
|
|
EWSR1 |
Two-color break-apart probe at 22q12 in PNETs (all variants) (510379) |
|
MYCN† |
Two-color probe detects amplification in neuroblastoma (510945) |
|
1p,19q |
Deletion detection of putative TSGs in diffuse gliomas (510360) |
|
HER-2/neu† |
Amplified in breast cancer (PathVysion, 483248) |
|
c-MET |
Two-color 7q31/SE7 amplification probe detects deletions of the hepatocyte growth factor receptor gene associated with ovarian, breast, lung, thyroid, and gastric tumor growth (510890) |
|
TP53‡ |
17p13.1 TSG deleted in many malignancies (including CLL and MM) (510940) |
|
ALK |
2p23 Two-color break-apart probe for ALK rearrangement in NSCLC (510950) |
|
RB1 |
13q14 TSG deleted in retinoblastoma and other malignancies (510374) |
|
SYT |
Two-color break-apart probe at 18q11.2 for synovial sarcoma (510384) |
|
EGFR |
Two-color probe detects amplification in lung, colon, breast cancer (510355) |
|
FKHR (FOXO1) |
Two-color break-apart probe at 13q14 in alveolar rhabdomyosarcoma (510371) |
|
CHOP (DDIT3) |
Two-color break-apart probe at 12q13 in myxoid/round cell liposarcomas (510349) |
|
PTEN |
Two-color deletion probe at 10q23 associated with prostate, endometrial, breast, renal/bladder, lung, thyroid tumors. Also associated with hematological neoplasms, melanomas, polyposis/colon cancer. |
|
ROS1 |
6q22 Two-color break-apart probe for ROS1 rearrangement (510312) |
|
RET |
10q11 Two-color break-apart probe for RET rearrangement (510315) |
|
Options for Fluorescence in situ Hybridization (FISH) Analysis |
Test Number(s) |
|---|---|
|
FISH analysis from blood, bone marrow, lymph node, or slides (include probe desired) |
|
|
FISH analysis ordered in conjunction with classical G-band chromosome analysis |
|
|
CML Profile (BCR/ABL): FISH analysis with classical G-band chromosome analysis |
|
|
FISH analysis on paraffin-embedded tissue (include probe or profile desired) |
|
1p, 19q |
C-MYC Break-apart |
MYC-N |
|
ALK Break-apart |
Cyclin D1 (CCND1) Break-apart |
PDGFR-α Break-apart |
|
BCL2 Break-apart |
EGFR Break-apart |
PDGFR-β Break-apart |
|
BCL6 Break-apart |
EWSR1 Break-apart |
PTEN |
|
CHOP Break-apart |
LSI 13/21 |
ROS1 |
|
c-MET |
MALT1 Break-apart |
TCR-α Break-apart |
SNP Microarray—Oncology (Reveal®) (510146)
Cancer microarray analysis has the resolution to identify significant acquired genetic alterations that would remain undefined by routine chromosome analysis and not targeted by the DNA probes employed in routine FISH analysis, as well as better defining existing abnormalities. Chromosome studies can only detect copy number abnormalities (ie, deletions or duplications), in the size range of 5 to 10 megabases. Contrary to FISH analysis that is limited to specific target sites; the dense whole genome microarray coverage substantially increases the potential detection rate. MDS analysis can be performed from blood, as opposed to standard chromosome analysis that requires mitotic activity.
The Reveal SNP (2.69 million probe) microarray analysis has the resolution to detect copy number changes about 200 times (50-100 kb range) better than cytogenetics, while detecting copy-neutral loss of heterozygosity (CN-LOH). CN-LOH is a common form of clonal evolution that results in homozygosity of a gene mutation, biallelic loss of a tumor suppressor, or doubling of a gene fusion. The precise whole-genome high-resolution detection of copy number changes combined with the dynamic resolution of CN-LOH provided by SNP arrays is revolutionizing DNA-based clonal analysis in cancer diagnostics.
In general, array analysis is recommended for an initial diagnosis (and after clinical progression) to determine whether new abnormalities are present. It cannot be used for the detection of balanced rearrangements and should not be used for detection of residual disease. FISH (see above for FISH test numbers), Chromosome Analysis, Leukemia/Lymphoma (510999), and possibly qPCR (eg, BCR/ABL1) should be used for MRD (minimal residual disease).
Any FISH or chromosome testing suggested as a result of the array will be added upon receiving authorization from the physician. Array testing may be added at the request of the client within one week of initial test resulting or may be ordered as a standalone test. Array may also be ordered as a reflex from a normal chromosome analysis, ie, Chromosome Analysis, Leukemia/Lymphoma With Reflex to Chromosome Microarray (CMA) (511040).
Diagnosis Required
|
Diagnosis |
Clinical Use |
Specimen Type |
|---|---|---|
|
CLL |
Array analysis can be used for the staging of the disease, either in conjunction with the numerical FISH probes (11q-, +12. 13q-. 17p-) or as a standalone test. If the array results are normal; the CCND1/IGH probe set may be used to rule out a circulating mantle cell lymphoma. The array not only detects the standard regions targeted by FISH but will provide the whole genome perspective that can change good prognosis FISH results to poor prognosis-related clonal evolution. |
Peripheral blood, bone marrow |
|
MDS, MPN |
Array analysis can be used in place of standard cytogenetic analysis, especially for blood samples, or it can be added to: (1) detect copy-neutral LOH or changes below the level of standard cytogenetic resolution after normal results; (2) resolve abnormal cytogenetic results better. |
Bone marrow or peripheral blood |
|
ALL, AML |
Array analysis can be used in conjunction with standard cytogenetic and FISH analysis. It can also be added either to: (1) detect copy-neutral LOH or changes below the level of standard cytogenetic resolution after normal results; (2) resolve abnormal cytogenetic results better. Cytogenetics and /or FISH must be used to rule out common balanced translocations or inversions associated with specific subgroups of these acute diseases. |
Bone marrow or peripheral blood |
|
MM |
Plasma cells are enriched using a CD138+ sorting protocol before array analysis. The analysis can be used for the detection of residual disease/clonal evolution. Use in conjunction with specific IGH translocation FISH probes is recommended for prognosis. |
Bone marrow (CD138-enriched) |
|
Tumor |
Array analysis can be used in resolving genomic imbalance in complex tumors, either in conjunction with cytogenetics/FISH or as a standalone technique. If there is a known specific balanced translocation associated with the tumor type, gene-targeted FISH (see probe list) is recommended. |
Fresh tissue or formalin-fixed, paraffin-embedded tissue |
Frozen Gel Packs. To ensure specimen integrity during warm weather, follow these Instructions for Use of frozen gel packs and specimen lockboxes.