Test Id : BALMF

This test includes a charge for the probe application, analysis, and professional interpretation of results for one probe set (2 individual fluorescence in situ hybridization [FISH] probes). Additional charges will be incurred for all reflex or additional probe sets 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 test is performed using client-specified FISH probes and is not intended as a panel test. Specific probes must be listed in the probe request field. Reflex probes can be performed when appropriate if specified in the order request field.

When specified, any of the following probes will be performed:

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 IGH::CRLF2 fusion, request probe CRLF2/IGH

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

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

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

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

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

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

t(8;14)(q24.21;q32) or IGH::MYC fusion, request probe MYC/IGH

t(8q24.21;var) or MYC rearrangement, request probe MYC break-apart

t(3q27;var) or BCL6 rearrangement, request probe BCL6 break-apart

t(18q21;var) or BCL2 rearrangement, request probe BCL2 break-apart

t(14;18)(q32;q21) or IGH::BCL2 fusion, request probe BCL2/IGH

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

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

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

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

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

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

t(9;11)(p22;q23) or KMT2A::MLLT3 fusion, request probe MLLT3/KMT2A

t(10;11)(p12;q23) or KMT2A::MLLT10 fusion, request probe MLLT10/KMT2A

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

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

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

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.

For more information see:

-B-Lymphoblastic Leukemia/Lymphoma Genetic Testing Guidelines

-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 Genetic Testing Guidelines
• 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 one probe set (2 individual fluorescence in situ hybridization [FISH] probes). Additional charges will be incurred for all reflex or additional probe sets 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 test is performed using client-specified FISH probes and is not intended as a panel test. Specific probes must be listed in the probe request field. Reflex probes can be performed when appropriate if specified in the order request field.

When specified, any of the following probes will be performed:

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 IGH::CRLF2 fusion, request probe CRLF2/IGH

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

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

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

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

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

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

t(8;14)(q24.21;q32) or IGH::MYC fusion, request probe MYC/IGH

t(8q24.21;var) or MYC rearrangement, request probe MYC break-apart

t(3q27;var) or BCL6 rearrangement, request probe BCL6 break-apart

t(18q21;var) or BCL2 rearrangement, request probe BCL2 break-apart

t(14;18)(q32;q21) or IGH::BCL2 fusion, request probe BCL2/IGH

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

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

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

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

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

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

t(9;11)(p22;q23) or KMT2A::MLLT3 fusion, request probe MLLT3/KMT2A

t(10;11)(p12;q23) or KMT2A::MLLT10 fusion, request probe MLLT10/KMT2A

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

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

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

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.

For more information see:

-B-Lymphoblastic Leukemia/Lymphoma Genetic Testing Guidelines

-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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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)