26459 B-Lymphoblastic Leukemia/Lymphoma, Children's Oncology Group Enrollment Testing, FISH (COGBF)

+4,+10,+17

17p- (17p deletion) or TP53

9p- (9p deletion) or CDKN2A or p16

ABL1 (9q34) rearrangement

ABL2 (1q25) rearrangement

BCR-ABL1 like ALL

CRLF2 (Xp22.33) or (Yp11.32) rearrangement

Hyperdiploidy

iAMP21

IGH (14q32) rearrangement

JAK2 (9p24.1) rearrangement

MLL or KMT2A (11q23) rearrangement

MYC (8q24.1) rearrangement

P2RY8 (Xp22.33) or (Yp11.32) rearrangement

PDGFRB (5q33) rearrangement

IKZF1 deletion

Ph-like ALL

t(1;19)(q23;p13.3) - PBX1/TCF3

t(10;11)(p12;q23) - MLLT10/MLL or AF10/MLL

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

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

t(12;21)(p13;q22) - TEL/AML1 or ETV6/RUNX1

t(4;11)(q21;q23) - AFF1/MLL or AF4/MLL

t(6;11)(q27;q23) - MLLT4/MLL or AF6/MLL

t(9;11)(p22;q23) - MLLT3/MLL or AF9/MLL

t(X;14)(p22.3;q32) - CRLF2/IGH

Hypodiploid/pseudo-hyperdiploid

Hypotriploid/Near-Triploid

Philadelphia-like ALL

t(9;22)(9q34;q11.2) - BCR/ABL1

t(Y;14)(p11.32;q32) - CRLF2/IGH

12p13 rearrangement, ETV6

Children's Oncology Group, COG

The FISH panel includes testing for the following abnormalities using the fluorescence in situ hybridization (FISH) probes listed:

+9/9p-, CDKN2A/D9Z1

t(9;22) BCR/ABL1

11q23 rearrangement, MLL (KMT2A) break-apart

-17/17p-, TP53/D17Z1

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

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

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

14q32 rearrangement, IGH break-apart

t(Xp22.33;var) or t(Yp11.32;var), P2RY8 rearrangement

t(Xp22.33;var) or t(Yp11.32;var), CRLF2 rearrangement

8q24.1 rearrangement, MYC break-apart

If the FISH panel demonstrates normal or nonclassical abnormalities, BALPF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL), FISH, Pediatric Varies panel will be performed.

The Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL)panel includes testing for the following kinase activating chromosome abnormalities, using the FISH probes listed below as well as IKZF1 deletion, which often accompanies Ph-like ALL:

1q25 rearrangement, ABL2 break-apart

5q33 rearrangement, PDGFRB break-apart

9p24.1 rearrangement, JAK2 break-apart

9q34 rearrangement, ABL1 break-apart

7p-, IKZF1/CEP7

When an MLL (KMT2A) rearrangement is identified, reflex testing will be performed to identify the translocation partner. Probes include identification of:

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

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;p13.1) MLL/ELL

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

When an IGH and/or CRLF2 rearrangement is identified, reflex testing will be performed using the CRLF2/IGH fusion probe set to identify a potential t(X;14)(p22.33;q32) or t(Y;14)(p11.32;q32) cryptic translocation.

In the absence of BCR/ABL1 fusion, when an extra ABL1 signal is identified, reflex testing will be performed using the ABL1 break-apart probe set to evaluate for the presence or absence of an ABL1 rearrangement.

In the absence of ETV6/RUNX1 fusion, when an extra ETV6 signal is identified, reflex testing will be performed using the ETV6 break-apart probe set to evaluate for the presence or absence of an ETV6 rearrangement.

If a MYC rearrangement is identified, both the BCL2 and BCL6 probe sets will be performed.

Evaluation of pediatric bone marrow and peripheral blood specimens by fluorescence in situ hybridization probe analysis for classic rearrangements and chromosomal copy number changes associated with B-cell acute lymphoblastic leukemia/lymphoma (B-ALL) and Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) in patients being considered for enrollment in Children's Oncology Group (COG) clinical trials and research protocols

As an adjunct to conventional chromosome studies in performed in pediatric patients with B-ALL and Ph-like ALL being considered for enrollment in COG protocols

Ordering Guidance:

This test is only performed on specimens from pediatric patients being considered for enrollment in a Children's Oncology Group (COG) protocol. If this test is ordered and the laboratory is informed that the patient is not on a COG protocol, this test will be canceled and automatically reordered by the laboratory as BALPF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL), FISH, Pediatric Varies.

At follow-up, conventional cytogenetic studies (CHRBM / Chromosome Analysis, Hematologic Disorders, Bone Marrow) and targeted B-cell ALL fluorescence in situ hybridization (FISH) probes can be evaluated based on the abnormalities identified in the diagnostic study. Order BALMF / B-Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL), Specified FISH, Varies and request specific probes or abnormalities.

This test is only performed on specimens from pediatric patients being considered for enrollment in a Children's Oncology Group (COG) protocol.

Bone Marrow:

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

2. Invert several times to mix bone marrow.

Whole Blood:

Invert several times to mix blood.

Necessary Information:

1. A reason for testing, a flow cytometry and/or a bone marrow pathology report, and a Children's Oncology Group (COG) registration number and protocol number should be submitted with each specimen. 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.

2. If a patient has received an opposite sex bone marrow transplant prior to specimen collection for this protocol, note this information on the request.

​All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

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.

Fluorescence in situ hybridization (FISH) is not a substitute for conventional chromosome studies because the latter detects many chromosome abnormalities associated with other hematological disorders that would be missed by this FISH panel test.

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

In the United States the incidence of acute lymphoblastic leukemia (ALL) is roughly 6000 new cases per year (as of 2019). ALL accounts for approximately 70% of all childhood leukemia cases (ages 0-19 years), making it the most common type of childhood cancer. Approximately 85% of pediatric cases of ALL are B-cell lineage (B-ALL) and 15% are T-cell lineage (T-ALL). It has a peak incidence at 2 to 5 years of age. The incidence decreases with increasing age, before increasing again at around 50 years of age. ALL is slightly more common in males than females. There is an increased incidence of ALL in individuals with Down syndrome, Fanconi anemia, Bloom syndrome, ataxia telangiectasia, X-linked agammaglobulinemia, and severe combined immunodeficiency. The overall cure rate for ALL in children is about 90% and about 45% to 60% of adults have long-term disease-free survival. CRLF2/IGH rearrangements are more commonly observed in patients with Down syndrome or of Hispanic descent.

Specific genetic abnormalities are identified in the majority of cases of B-ALL, either by conventional chromosome studies or fluorescence in situ hybridization (FISH) studies. For more than 25 years, the Mayo Clinic Genomics Laboratory has served as a Children's Oncology Group (COG) accredited laboratory for the performance of cytogenetic testing in pediatric patients being considered for enrollment in COG clinical trials and research. The laboratory is highly equipped to perform the time sensitive and critical cytogenetic testing necessary to assign risk stratification and facilitate enrollment in COG protocols.

Each of the B-ALL genetic subgroups are important to detect and can be critical prognostic markers. The decision for early transplantation may be made if t(9;22)(q34;q11.2), MLL (KMT2A) translocations, RUNX1 duplication/amplification (iAMP21) or a hypodiploid clone is identified. In contrast, if ETV6/RUNX1 fusion is detected by FISH or hyperdiploidy is identified by chromosome studies, the patient has a favorable prognosis and transplantation is rarely considered.

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

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

Metaphase FISH confirmation of classic translocations that are cryptic and not visually detectable by chromosome analysis (ie, t(12;21) associated with ETV6/RUNX1 fusion) is performed, as required by COG, and is included as part of the electronic case submission by the Mayo Clinic Genomics Laboratory to COG for central review.

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).

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.

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