Oncology Fluorescence in situ Hybridization (FISH)

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.

Oncology-based FISH

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

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

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

Aggressive B-cell Lymphoma Profile (510344)

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)

510669

FISH analysis ordered in conjunction with classical G-band chromosome analysis

510669, 510999

CML Profile (BCR/ABL): FISH analysis with classical G-band chromosome analysis

150500

FISH analysis on paraffin-embedded tissue (include probe or profile desired)

510825

Available Probes for Paraffin-blocked Tissue

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

BCR/ABL+ASS

FKHR (FOXO1) Break-apart

RET Break-apart

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.

For Providers

Please login to order a test.