Test Id : BALMF

This test includes a charge for the probe application, analysis, and professional interpretation of results for 1 probe set (2 individual fluorescence in situ hybridization (FISH) probes or 3 individual FISH probes). Additional charges will be incurred for all reflex or additional probe sets performed.

If the patient is being treated for known abnormalities, indicate the abnormality and which probes should be used.

Testing will be performed using the probes specified by the client:

t(1q25;var) or ABL2 rearrangement, request probe ABL2 break-apart

t(5q32;var) or PDGFRB rearrangement, request probe PDGFRB break-apart

7p- or IKZF1 deletion, request probe: IKZF1/CEP7

t(9p24.1;var) or JAK2 rearrangement, request probe JAK2 break-apart

+9/9p- or trisomy 9, CDKN2A deletion, request probe CDKN2A/D9Z1

t(9;22)(q34;q11.2) or BCR::ABL1 fusion, request probe BCR/ABL1

t(9q34;var) or ABL1 rearrangement, request probe: ABL1 break-apart

t(11q23;var) or MLL(KMT2A) rearrangement, request probe MLL break-apart

t(4;11)(q21;q23) or AFF1::MLL(KMT2A) fusion, request probe AFF1/MLL

t(6;11)(q27;q23) or MLLT4(AFDN)::MLL(KMT2A) fusion, request probe MLLT4/MLL

t(9;11)(p21;q23) or MLLT3::MLL(KMT2A) fusion, request probe MLLT3/MLL

t(10;11)(p13;q23) or MLLT10::MLL(KMT2A) fusion, request probe MLLT10/MLL

t(11;19)(q23;p13.3) or MLL::MLLT1(KMT2A) fusion, request probe MLL/MLLT1

t(11;19)(q23;p13.1) or MLL(KMT2A)::ELL fusion, request probe MLL/ELL

-17/17p- or TP53 deletion, request probe TP53/D17Z1

t(1;19)(q23;p13) or PBX1::TCF3 fusion, request probe PBX1/TCF3

Hyperdiploidy or +4,+10,+17, request probe D4Z1/D10Z1/D17Z1

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

t(12p13;var) or ETV6 rearrangement, request probe ETV6 break-apart

t(14q32;var) or IGH rearrangement, request probe IGH break-apart

t(Xp22.33;var) or t(Yp11.32;var) or P2RY8 rearrangement, request probe P2RY8 break-apart

t(Xp22.33;var) or t(Yp11.32;var) or CRLF2 rearrangement, request probe CRLF2 break-apart

t(X;14)(p22.33;q32) or t(Y;14)(p11.32;q32) or CRLF2::IGH fusion, request probe CRLF2/IGH

t(8q24.2;var) or MYC rearrangement, request probe MYC break-apart

For more information see:

-B-Lymphoblastic Leukemia/Lymphoma Algorithm

-Acute Leukemias of Ambiguous Lineage Testing Algorithm

This test is intended for instances when targeted B-cell acute lymphoblastic leukemia/lymphoma (B-ALL/LBL) fluorescence in situ hybridization (FISH) probes are needed based on specific abnormality or abnormalities identified in the diagnostic sample. The FISH probes must be specified on the request when ordering.

If targeted FISH probes are not included with this test order, test processing will be delayed, and the test may be canceled by the laboratory.

If targeted probes are not included with this test request, the test may be canceled and automatically reordered by the laboratory as BALAF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL), FISH, Adult, Varies or BALPF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL), FISH, Pediatric, Varies depending on the age of the patient.

For an adult patient, if the entire B-cell ALL FISH panel is preferred, order BALAF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL), FISH, Adult, Varies.

For a pediatric patient, if the entire B-cell ALL FISH panel is preferred, order BALPF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL), FISH, Pediatric, Varies.

At diagnosis, both conventional cytogenetic studies (CHRBM / Chromosome Analysis, Hematologic Disorders, Bone Marrow) and either BALAF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL), FISH, Adult, Varies or BALPF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL), FISH, Pediatric, Varies should be performed.

If the patient clinically relapses, a conventional chromosome study may be useful to identify cytogenetic changes in the neoplastic clone or the possible emergence of a therapy-related myeloid clone.

If this test is ordered and the laboratory is informed that the patient is 30 years of age and under AND is on a Children's Oncology Group (COG) protocol, this test will be canceled and automatically reordered by the laboratory COGBF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL), Children's Oncology Group Enrollment Testing, FISH, Varies.

For patients with B-cell lymphoma, order BLPMF / B-Cell Lymphoma, Specified FISH, Varies.

For testing paraffin-embedded tissue samples from patients with B-ALL/LBL, order BLBLF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma, FISH, Tissue. If a paraffin-embedded tissue sample is submitted for this test, it will be canceled and BLBLF will be added and performed as the appropriate test.

Advise Express Mail or equivalent if not on courier service.

1. A list of probes requested for analysis is required. Probes available for this test are listed in the Testing Algorithm section.

2. A reason for testing and a flow cytometry and/or a bone marrow pathology report should be submitted with each specimen. The laboratory will not reject testing if this information is not provided; however, appropriate testing and/or interpretation may be compromised or delayed in some instances. If not provided, an appropriate indication for testing may be entered by Mayo Clinic Laboratories.

Submit only 1 of the following specimens:

Preferred

Specimen Type: Bone marrow

Container/Tube:

Preferred: Yellow top (ACD)

Acceptable: Green top (heparin) or lavender top (EDTA)

Specimen Volume: 2 to 3 mL

Collection Instructions:

1. It is preferable to send the first aspirate from the bone marrow collection.

2. Invert several times to mix bone marrow.

3. Send bone marrow specimen in original tube. Do not aliquot.

Acceptable

Specimen Type: Whole blood

Container/Tube:

Preferred: Yellow top (ACD)

Acceptable: Green top (heparin) or lavender top (EDTA)

Specimen Volume: 6 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send whole blood specimen in original tube. Do not aliquot.

• B-Lymphoblastic Leukemia/Lymphoma Algorithm
• Acute Leukemias of Ambiguous Lineage Testing Algorithm

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

Whole blood: 2 mL; Bone marrow: 1 mL

Detecting a neoplastic clone associated with recurrent common chromosome abnormalities associated with B-cell acute lymphoblastic leukemia/lymphoma (B-ALL/LBL) and Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) using client specified probes

As an adjunct to conventional chromosome studies in patients with B-ALL/LBL

Evaluating specimens in which chromosome studies are unsuccessful

This test should not be used to screen for residual B-ALL/LBL.

This test includes a charge for the probe application, analysis, and professional interpretation of results for 1 probe set (2 individual fluorescence in situ hybridization (FISH) probes or 3 individual FISH probes). Additional charges will be incurred for all reflex or additional probe sets performed.

If the patient is being treated for known abnormalities, indicate the abnormality and which probes should be used.

Testing will be performed using the probes specified by the client:

t(1q25;var) or ABL2 rearrangement, request probe ABL2 break-apart

t(5q32;var) or PDGFRB rearrangement, request probe PDGFRB break-apart

7p- or IKZF1 deletion, request probe: IKZF1/CEP7

t(9p24.1;var) or JAK2 rearrangement, request probe JAK2 break-apart

+9/9p- or trisomy 9, CDKN2A deletion, request probe CDKN2A/D9Z1

t(9;22)(q34;q11.2) or BCR::ABL1 fusion, request probe BCR/ABL1

t(9q34;var) or ABL1 rearrangement, request probe: ABL1 break-apart

t(11q23;var) or MLL(KMT2A) rearrangement, request probe MLL break-apart

t(4;11)(q21;q23) or AFF1::MLL(KMT2A) fusion, request probe AFF1/MLL

t(6;11)(q27;q23) or MLLT4(AFDN)::MLL(KMT2A) fusion, request probe MLLT4/MLL

t(9;11)(p21;q23) or MLLT3::MLL(KMT2A) fusion, request probe MLLT3/MLL

t(10;11)(p13;q23) or MLLT10::MLL(KMT2A) fusion, request probe MLLT10/MLL

t(11;19)(q23;p13.3) or MLL::MLLT1(KMT2A) fusion, request probe MLL/MLLT1

t(11;19)(q23;p13.1) or MLL(KMT2A)::ELL fusion, request probe MLL/ELL

-17/17p- or TP53 deletion, request probe TP53/D17Z1

t(1;19)(q23;p13) or PBX1::TCF3 fusion, request probe PBX1/TCF3

Hyperdiploidy or +4,+10,+17, request probe D4Z1/D10Z1/D17Z1

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

t(12p13;var) or ETV6 rearrangement, request probe ETV6 break-apart

t(14q32;var) or IGH rearrangement, request probe IGH break-apart

t(Xp22.33;var) or t(Yp11.32;var) or P2RY8 rearrangement, request probe P2RY8 break-apart

t(Xp22.33;var) or t(Yp11.32;var) or CRLF2 rearrangement, request probe CRLF2 break-apart

t(X;14)(p22.33;q32) or t(Y;14)(p11.32;q32) or CRLF2::IGH fusion, request probe CRLF2/IGH

t(8q24.2;var) or MYC rearrangement, request probe MYC break-apart

For more information see:

-B-Lymphoblastic Leukemia/Lymphoma Algorithm

-Acute Leukemias of Ambiguous Lineage Testing Algorithm

In the United States, the incidence of B-lymphoblastic leukemia/lymphoma (B-ALL/LBL) is roughly 6000 new cases per year or approximately 1 in 50,000. B-ALL/LBL accounts for approximately 70% of all childhood leukemia cases (ages 0 to 19 years), making it the most common type of childhood cancer. It has a peak incidence at 2 to 5 years of age. This incidence decreases with age before increasing again at around 50 years of age. B-ALL/LBL is slightly more common in male patients than female patients. There is also an increased incidence of B-ALL/LBL in individuals with genetic conditions such as Down syndrome, Fanconi anemia, Bloom syndrome, ataxia telangiectasia, Li-Fraumeni syndrome, X-linked agammaglobulinemia, and severe combined immunodeficiency. The overall cure rate for B-ALL/LBL in children is approximately 90%, and about 45% to 60% of adults have long-term disease-free survival. Of note, CRLF2::IGH fusion is more commonly observed in patients with Down syndrome or of Hispanic descent.

Specific cytogenetic abnormalities are identified in the majority of cases of B-ALL/LBL, by conventional chromosome studies or fluorescence in situ hybridization (FISH) studies. B-ALL genetic subgroups are important to detect and can be critical prognostic markers. For example, a decision for early transplantation may be made if BCR::ABL1 fusion, KMT2A rearrangement, iAMP21, or a hypodiploid clone is identified. In contrast, if the ETV6::RUNX1 fusion or hyperdiploidy is identified, the patient has a more favorable prognosis and transplantation is rarely initially considered.

A newly recognized World Health Organization entity called BCR-ABL1-like ALL, also known as Philadelphia chromosome-like acute lymphoblastic leukemia, is increasing in importance due to the poor prognosis seen in pediatric, adolescent, and young adult ALL. Common features of this entity involve rearrangements with tyrosine kinase genes involving the following genes: ABL2, PDGFRB, JAK2, ABL1, CRLF2, and P2RY8, as well as deletions involving IKZF1. Patients who have failed conventional therapies have demonstrated favorable responses to targeted therapies when rearrangements involving these specific gene regions have been identified.

Evaluation of the MYC gene region is included in all diagnostic pediatric B-ALL panels to evaluate for Burkitt lymphoma. If a positive result is obtained, additional testing for the BCL2 and BCL6 gene regions may be considered.

Per National Comprehensive Cancer Network guidelines, a combination of cytogenetic and FISH testing is currently recommended in all pediatric and adult patients with B-ALL/lymphoblastic lymphoma (LBL). Additional cytogenetic techniques such as chromosomal microarray (CMAH / Chromosomal Microarray, Hematologic Disorders, Varies) may be helpful to resolve questions related to ploidy (hyperdiploid clone vs doubled hypodiploid clone) or to resolve certain clonal structural rearrangements such as the presence or absence of intra-chromosomal amplification of chromosome 21 (iAMP21). A summary of the characteristic chromosome abnormalities identified in B-ALL is listed in the following table.

Table. Common Chromosome Abnormalities in B-cell Acute Lymphoblastic Leukemia

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 set.

The absence of an abnormal clone does not rule out the presence of an acute B-cell lymphoblastic leukemia/lymphoma or another neoplastic disorder.

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

Fluorescence in situ hybridization (FISH) is not a substitute for conventional chromosome studies because the latter detects chromosome abnormalities associated with other hematological disorders that would be missed in a targeted B-cell acute lymphoblastic leukemia/lymphoma FISH panel test.

Bone marrow is the preferred specimen type for this fluorescence in situ hybridization test. If bone marrow is not available, a blood specimen may be used if there are circulating malignant cells in the blood specimen (as verified by a hematopathologist).

1. Moorman AV, Harrison CJ, Buck GA, et al. Karyotype is an independent prognostic factor in adult acute lymphoblastic leukemia (ALL): analysis of cytogenetic data from patients treated on the Medical Research Council (MRC) UKALLXII/Eastern Cooperative Oncology Group (ECOG) 2993 trial. Blood. 2007;109(8):3189-3197. doi:10.1182/blood-2006-10-051912

2. Moorman AV. The clinical relevance of chromosomal and genetic abnormalities in B-cell precursor acute lymphoblastic leukemia. Blood Rev. 2012;26(3):123-135. doi:10.1016/j.blre.2012.01.001

3. Roberts KG, Li Y, Payne-Turner D, et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med. 2014;371(11):1005-1015. doi:10.1056/NEJMoa1403088

4. Mullighan CG. The genomic landscape of acute lymphoblastic leukemia in children and young adults. Hematology Am Soc Hematol Educ Program. 2014;2014(1):174-180. doi:10.1182/asheducation-2014.1.174

5. Arber DA, Orazi A, Hasserjian R, et al: The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016;127(20):2391-2405. doi:10.1182/blood-2016-03-643544

This test is performed using commercially available and laboratory-developed probes. Deletion of the CDKN2A locus on chromosome 9, TP53 on chromosome 17, deletion of IKZF1 on chromosome 7, and gain of chromosomes 4, 10, and 17 are detected using enumeration strategy probes. Rearrangements involving ABL2, PDGFRB, MYC, JAK2, ABL1, MLL, ETV6, IGH, MYC, CRLF2, and P2RY8 are detected 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 t(X/Y;14), t(9;22), t(12;21), t(1;19), and in reflex testing when rearrangements of the MLL gene is detected. Amplification of RUNX1 (21q22) is detected using a D-FISH probe set to enumerate copies of the RUNX1 probe. For enumeration and BAP strategy probe sets, 100 interphase nuclei are scored; 200 interphase nuclei are scored when D-FISH probes are used. Results are expressed as the percent abnormal nuclei.(Unpublished Mayo method)

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• Prospective clients should contact their account representative. For assistance, contact Customer Service.

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, 88275 x1, 88291 x1- FISH Probe, Analysis, Interpretation; 1 probe sets

88271 x2, 88275 x1 - FISH Probe, Analysis; each additional probe set (if appropriate)

88271 x1 -FISH Probe; coverage for sets containing 3 probes (if appropriate)