Test Id : CILPF

This test includes a charge for application of the first probe set (2 fluorescence in situ hybridization [FISH] probes) and professional interpretation of results. Additional charges will be incurred for all reflex probes performed. Analysis charges will be incurred based on the number of cells analyzed per probe set. If no cells are available for analysis, no analysis charges will be incurred.

This FISH test allows different combinations of probes to be utilized based on the patient’s age and clinical question, per client request.

All probes marked with an asterisk* will be performed as reflex testing, without notification, if the corresponding region was disrupted or potentially disrupted. Patients found to have a MYC rearrangement will be reflexed to the break-apart BCL6 and BCL2 probe sets. Patients found to have 3 copies of KAT6A will be reflexed with D8Z2/MYC.

The FISH panel for patients younger than 3 months includes testing for the following abnormalities using the FISH probes listed:

11q23 rearrangement, MLL (KMT2A)

*t(4;11)(q21;q23) AFF1/MLL

*t(9;11)(p22;q23) MLLT3/MLL

*t(10;11)(p12;q23) MLLT10/MLL

*t(11;19)(q23;p13.1) MLL/ELL

*t(11;19)(q23;p13.3) MLL/MLLT1-

t(8;16), [M4,M5], KAT6A/CREBBP

*D8Z2/MYC for trisomy 8

t(1;22), [M7], RBM15/MKL1

+13/+21, 13q14 and 21q22

If no classic abnormalities are observed, other FISH probes may be offered by the laboratory.

The FISH panel is dependent on the reason for testing and the patient’s diagnosis (acute myeloid leukemia [AML], B-cell acute lymphoblastic leukemia [ALL], or T-cell ALL).

The initial FISH panel for patients 3 months to 18 months of age with AML includes testing for the following abnormalities:

11q23 rearrangement, MLL (KMT2A)

*t(4;11)(q21;q23) AFF1/MLL

*t(9;11)(p22;q23) MLLT3/MLL

*t(10;11)(p12;q23) MLLT10/MLL

*t(11;19)(q23;p13.1) MLL/ELL

If an MLL disruption is not identified, the following secondary AML FISH probes will be evaluated:

inv(16), [M4, Eos], MYH11/CBFB

t(8;21), [M2], RUNX1T1/RUNX1

t(15;17), [M3], PML/RARA

12p13 rearrangement, ETV6 break-apart

*t(7;12)(q36;p13), MNX1/ETV6

t(8;16), [M4,M5], KAT6A/CREBBP

inv(16), GLIS2/CBFA2T3

11p15.4 rearrangement, NUP98 break-apart

t(1;22), [M7], RBM15/MKL1

The initial FISH panel for patients 3 to 18 months of age with B-cell ALL includes testing for the following abnormalities:

11q23 rearrangement, MLL (KMT2A)

*t(4;11)(q21;q23) AFF1/MLL

*t(9;11)(p22;q23) MLLT3/MLL

*t(10;11)(p12;q23) MLLT10/MLL

*t(11;19)(q23;p13.3) MLL/MLLT1

If an MLL disruption is not identified, the following secondary panel of B-cell ALL FISH probes will be evaluated:

+9/9p-, CDKN2A/D9Z1

t(9;22) BCR/ABL1 fusion

-17/17p-, TP53/D17Z1

t(1;19)(q23;p13), PBX1/TCF3 fusion

Hyperdiploidy, +4,+10,+17: D4Z1/D10Z1/D17Z1

t(12;21)(p13;q22), ETV6/RUNX1 fusion and iAMP21

*12p13 rearrangement, ETV6 break-apart

14q32 rearrangement, IGH break-apart

8q24.1 rearrangement, MYC

*3q27 rearrangement, BCL6 break-apart

*18q21 rearrangement, BCL2 break-apart

If a classic B-cell ALL abnormality is not identified in the first 11 probes analyzed, the following tertiary panel of B-cell ALL FISH probes will be evaluated, 9p24.1 rearrangement, JAK2.

The initial FISH panel for patients 3 to 18 months of age with T-cell ALL includes testing for the following abnormalities:

11q23 rearrangement, MLL (KMT2A)

*t(6;11)(q27;q23) MLLT4(AFDN)/MLL

*t(9;11)(p22;q23) MLLT3/MLL

*t(10;11)(p12;q23) MLLT10/MLL

*t(11;19)(q23;p13.3) MLL/MLLT1

*t(11;19)(q23;p13.1) MLL/ELL

If an MLL disruption is not identified, the following secondary panel of T-cell ALL FISH probes will be evaluated:

+9/9p-, CDKN2A/D9Z1

t(9;22) BCR/ABL1

-17/17p-, TP53/D17Z1

t(5;14), TLX3/BCL11B

7q34 rearrangement, TRB

*t(7;10) - TRB/TLX1

14q11.2 rearrangement, TRAD

*t(10;14) - TLX1/TRAD

t(10;11), MLLT10/PICALM

1p33 rearrangement, TAL1/STIL

Appropriate ancillary probes may be performed at consultant discretion to render comprehensive assessment. Any additional probes will have the results included within the final report and will be performed at an additional charge.

This test is only performed on specimens from patients with acute leukemia who are 18 months of age or younger.

For testing bone marrow or blood specimens from patients with congenital infantile leukemia, order CILDF / Congenital Infantile Leukemia, Diagnostic FISH, Varies.

If this test is ordered on a patient older than 18 months of age and the reason for testing is B-cell or T-cell acute lymphocytic leukemia (B-ALL or T-ALL), this test will be canceled and automatically reordered by the laboratory as BLBLF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma, FISH, Tissue or TLBLF / T-Cell Acute Lymphoblastic Leukemia/Lymphoma, FISH, Tissue.

If this test is ordered on a patient older than 18 months of age and the reason for testing is acute myeloid leukemia (AML), this test will be canceled and automatically reordered by the laboratory as MSTF / Myeloid Sarcoma, FISH, Tissue.

This test does not include a pathology consult. If a pathology consultation is requested, PATHC / Pathology Consultation should be ordered and the appropriate FISH test will be ordered and performed at an additional charge.

Advise Express Mail or equivalent if not on courier service.

A reason for testing and pathology report are required for testing to be performed. Send information with specimen. Acceptable pathology reports include working drafts, preliminary pathology or surgical pathology reports. The laboratory will not reject testing if this information is not provided, but appropriate testing and interpretation may be compromised or delayed. If this information is not provided, an appropriate indication for testing may be entered by Mayo Clinic Laboratories.

Submit only 1 of the following specimens:

Specimen Type: Tissue

Preferred: Tissue block

Collection Instructions: Submit a formalin-fixed, paraffin-embedded (FFPE) tumor tissue block. Blocks prepared with alternative fixation methods may be acceptable; provide fixation method used.

Additional Information:

1. The paraffin embedded specimen can be from any anatomic location (skin, soft tissue, lymph node, etc.).

2. Bone specimens that have been decalcified will be attempted for FISH, with a success rate of approximately 50%.

Acceptable: Slides

Collection Instructions: 20 Consecutive, unstained, 5 micron-thick sections placed on positively charged slides, and 1 hematoxylin and eosin-stained slide.

If not ordering electronically, complete, print, and send a Hematopathology/Cytogenetics Test Request (T726) with the specimen.

15 consecutive, unstained, 5-micron-thick sections placed on positively charged slides, and 1 hematoxylin and eosin-stained slide.

Detecting a neoplastic clone associated with the common chromosome abnormalities and classic rearrangements seen in infant patients with leukemia using tissue specimens

This test includes a charge for application of the first probe set (2 fluorescence in situ hybridization [FISH] probes) and professional interpretation of results. Additional charges will be incurred for all reflex probes performed. Analysis charges will be incurred based on the number of cells analyzed per probe set. If no cells are available for analysis, no analysis charges will be incurred.

This FISH test allows different combinations of probes to be utilized based on the patient’s age and clinical question, per client request.

All probes marked with an asterisk* will be performed as reflex testing, without notification, if the corresponding region was disrupted or potentially disrupted. Patients found to have a MYC rearrangement will be reflexed to the break-apart BCL6 and BCL2 probe sets. Patients found to have 3 copies of KAT6A will be reflexed with D8Z2/MYC.

The FISH panel for patients younger than 3 months includes testing for the following abnormalities using the FISH probes listed:

11q23 rearrangement, MLL (KMT2A)

*t(4;11)(q21;q23) AFF1/MLL

*t(9;11)(p22;q23) MLLT3/MLL

*t(10;11)(p12;q23) MLLT10/MLL

*t(11;19)(q23;p13.1) MLL/ELL

*t(11;19)(q23;p13.3) MLL/MLLT1-

t(8;16), [M4,M5], KAT6A/CREBBP

*D8Z2/MYC for trisomy 8

t(1;22), [M7], RBM15/MKL1

+13/+21, 13q14 and 21q22

If no classic abnormalities are observed, other FISH probes may be offered by the laboratory.

The FISH panel is dependent on the reason for testing and the patient’s diagnosis (acute myeloid leukemia [AML], B-cell acute lymphoblastic leukemia [ALL], or T-cell ALL).

The initial FISH panel for patients 3 months to 18 months of age with AML includes testing for the following abnormalities:

11q23 rearrangement, MLL (KMT2A)

*t(4;11)(q21;q23) AFF1/MLL

*t(9;11)(p22;q23) MLLT3/MLL

*t(10;11)(p12;q23) MLLT10/MLL

*t(11;19)(q23;p13.1) MLL/ELL

If an MLL disruption is not identified, the following secondary AML FISH probes will be evaluated:

inv(16), [M4, Eos], MYH11/CBFB

t(8;21), [M2], RUNX1T1/RUNX1

t(15;17), [M3], PML/RARA

12p13 rearrangement, ETV6 break-apart

*t(7;12)(q36;p13), MNX1/ETV6

t(8;16), [M4,M5], KAT6A/CREBBP

inv(16), GLIS2/CBFA2T3

11p15.4 rearrangement, NUP98 break-apart

t(1;22), [M7], RBM15/MKL1

The initial FISH panel for patients 3 to 18 months of age with B-cell ALL includes testing for the following abnormalities:

11q23 rearrangement, MLL (KMT2A)

*t(4;11)(q21;q23) AFF1/MLL

*t(9;11)(p22;q23) MLLT3/MLL

*t(10;11)(p12;q23) MLLT10/MLL

*t(11;19)(q23;p13.3) MLL/MLLT1

If an MLL disruption is not identified, the following secondary panel of B-cell ALL FISH probes will be evaluated:

+9/9p-, CDKN2A/D9Z1

t(9;22) BCR/ABL1 fusion

-17/17p-, TP53/D17Z1

t(1;19)(q23;p13), PBX1/TCF3 fusion

Hyperdiploidy, +4,+10,+17: D4Z1/D10Z1/D17Z1

t(12;21)(p13;q22), ETV6/RUNX1 fusion and iAMP21

*12p13 rearrangement, ETV6 break-apart

14q32 rearrangement, IGH break-apart

8q24.1 rearrangement, MYC

*3q27 rearrangement, BCL6 break-apart

*18q21 rearrangement, BCL2 break-apart

If a classic B-cell ALL abnormality is not identified in the first 11 probes analyzed, the following tertiary panel of B-cell ALL FISH probes will be evaluated, 9p24.1 rearrangement, JAK2.

The initial FISH panel for patients 3 to 18 months of age with T-cell ALL includes testing for the following abnormalities:

11q23 rearrangement, MLL (KMT2A)

*t(6;11)(q27;q23) MLLT4(AFDN)/MLL

*t(9;11)(p22;q23) MLLT3/MLL

*t(10;11)(p12;q23) MLLT10/MLL

*t(11;19)(q23;p13.3) MLL/MLLT1

*t(11;19)(q23;p13.1) MLL/ELL

If an MLL disruption is not identified, the following secondary panel of T-cell ALL FISH probes will be evaluated:

+9/9p-, CDKN2A/D9Z1

t(9;22) BCR/ABL1

-17/17p-, TP53/D17Z1

t(5;14), TLX3/BCL11B

7q34 rearrangement, TRB

*t(7;10) - TRB/TLX1

14q11.2 rearrangement, TRAD

*t(10;14) - TLX1/TRAD

t(10;11), MLLT10/PICALM

1p33 rearrangement, TAL1/STIL

Appropriate ancillary probes may be performed at consultant discretion to render comprehensive assessment. Any additional probes will have the results included within the final report and will be performed at an additional charge.

While pediatric leukemia is the most common malignancy affecting children, acute leukemia occuring prior to the age of 18 months (infant leukemia) or occuring within the first 3 months of life (congenital leukemia) are relatively rare in occurrence. The incidence of congenital and infant acute leukemia cases (through 12 months of age) is estimated at only 30 to 40 cases/million/year, with the majority comprising infant cases. Nearly all cases of congenital and infant acute leukemia represent either acute myeloid leukemia (AML) or B-cell acute lymphocytic leukemia/lymphoblastic lymphoma (B-ALL/LBL) with only very rare cases of T-cell-ALL/LBL identified in this age group.

Characteristic genetic abnormalities have been identified in both the congenital acute leukemia and infant acute leukemia setting, each with uniquely associated clinical-pathologic correlations. Rare but important patients with KAT6A/CREBBP translocations and congenital acute leukemia have been described with spontaneously remitting AML despite the lack of therapeutic intervention. In addition, transient abnormal myelopoiesis associated with Down syndrome is another common manifestation encountered in the neonatal setting that can be associated with the development of frank acute leukemia. In contrast, nearly 80% of infant acute leukemia cases are associated with MLL(KMT2A) translocation events with varying percentages of translocation partners based on an AML versus B-ALL/LBL presentation.

Due to the underlying genetic heterogeneity associated with both congenital and infant leukemia and the important prognostic, diagnostic, and occasional therapeutic targets identified, appropriate genetic characterization of this uncommon acute leukemia presentation is critical. These thorough fluorescence in situ hybridization (FISH) panels have been developed by Mayo Clinic Laboratories to interrogate the more common AML and B-ALL abnormalities associated with both congenital and infant acute leukemias. These FISH probes have been validated both in bone marrow/blood CILDF / Congenital Infantile Leukemia, Diagnostic FISH, Varies and in paraffin CILPF / Congenital Infantile Leukemia, FISH, Tissuesince a significant minority of these patient’s present clinically with isolated extramedullary (tissue) manifestations (ie, myeloid sarcoma).

An interpretive report will be provided.

A neoplastic clone is detected when the percent of cells with an abnormality exceeds the normal reference range for any given probe.

A positive result is not diagnostic for congenital or infantile leukemia but may provide relevant prognostic information.

The absence of an abnormal clone does not rule out the presence of neoplastic disorder.

This test is not approved by the US Food and Drug Administration, and it is best used as an adjunct to existing clinical and pathologic information.

Fixatives other than formalin (eg, Prefer, Bouin’s) may not be successful for fluorescence in situ hybridization (FISH) assays. Although FISH testing will not be rejected due to non-formalin fixation, results may be compromised.

Paraffin-embedded tissues that have been decalcified may be unsuccessful for FISH analysis. FISH studies will be attempted if sufficient tumor is present for analysis. The pathologist reviewing the hematoxylin and eosin-stained slide may find it necessary to cancel testing. If no FISH signals are observed post-hybridization, the case will be released indicating a lack of FISH results.

For each probe set, blinded fluorescence in situ hybridization (FISH) analysis was performed on 20 to 25 normal paraffin-embedded, formalin-fixed tissue controls and between 2 and 20 paraffin-embedded, formalin-fixed tissue samples from patients diagnosed with B-cell lymphoblastic leukemia or lymphoma. Results from the 25 controls were used to generate the normal cutoff values.

1. Swerdlow SH, Campo E, Harris NL, et al, eds: WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues. 4th ed. IARC Press; 2017

2. Tomizawa D: Recent progress in the treatment of infant acute lymphoblastic leukemia. Pediatr Int. 2015;57(5):811-819. doi: 10.1111/ped.12758

3. Inaba H, Zhou Y, Abla O, et al: Heterogeneous cytogenetic subgroups and outcomes in childhood acute megakaryoblastic leukemia: a retrospective international study. Blood. 2015;126(13):1575-1584. doi: 10.1182/blood-2015-02-629204

4. Coenen EA, Zwaan CM, Reinhardt D, et al: Pediatric acute myeloid leukemia with t(8;16)(p11;p13), a distinct clinical and biological entity: a collaborative study by the International-Berlin-Frankfurt-Munster AML-study group. Blood. 2013;122(15):2704-2713. doi: 10.1182/blood-2013-02-485524

This test is performed using commercially available and laboratory-developed probes. Gain or loss of chromosomes 4, 8, 10, 13, 17, and 21 are detected using enumeration strategy probes. Deletion of the CDKN2A locus on chromosome 9 and TP53 on chromosome 17 are detected using enumeration strategy. Rearrangements involving genes involving MLL (KMT2A), NUP98, ETV6, MYC, JAK2, IGH, TAL1/STIL, TRB, and TRAD are detected using a dual-color break-apart (BAP) strategy probe. If a MYC gene region separation is identified, break-apart BCL2 and BCL6 will be evaluated using a dual-color break-apart (BAP) strategy probe. Dual-color, dual-fusion fluorescence in situ hybridization (D-FISH) strategy probe sets are used to detect inv(16), t(8;21), t(15;17), t(8;16), t(1;22),  t(7;12), t(9;22), t(12;21), t(1;19), t(5;14), t(9;22), t(10;11),  and in reflex testing when a rearrangement of the MLL, TRB, TRAD gene region is observed. Amplification of ABL1 (9q34) is detected using a D-FISH probe strategy.

Paraffin-embedded tissues are cut at 5 microns and mounted on positively charged glass slides. The selection of tissue and the identification of target areas on the hematoxylin and eosin (H and E)-stained slide are performed by a pathologist. Using the H and E-stained slide as a reference, target areas are etched with a diamond-tipped etcher on the back of the unstained slide to be assayed. For each probe set, the probes are hybridized to the appropriate target areas and 2 technologists each analyze 50 interphase nuclei (100 total) per probe set with the results expressed as the percent abnormal nuclei.(Unpublished Mayo method)

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This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.

88271 x2, 88291-DNA probe, each (first probe set), interpretation and report

88271 x2-DNA probe, each; each additional probe set (if appropriate)

88271-DNA probe, each; coverage for sets containing 3 probes (if appropriate)

88271 x 2-DNA probe, each; coverage for sets containing 4 probes (if appropriate)

88271 x 3-DNA probe, each; coverage for sets containing 5 probes (if appropriate)

88274 w/modifier 52-Interphase in situ hybridization, <25 cells, each probe set (if appropriate)

88274-Interphase in situ hybridization, 25 to 99 cells, each probe set (if appropriate)

88275-Interphase in situ hybridization, 100 to 300 cells, each probe set (if appropriate)