Test Id : COGBF

This test is only performed on specimens from pediatric patients being considered for enrollment in a Children's Oncology Group (COG) protocol. 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 as panel testing only using the following analysis algorithm.

The diagnostic pediatric/young adult B-cell acute lymphoblastic leukemia/lymphoma (B-ALL) fluorescence in situ hybridization (FISH) panel includes testing for the following abnormalities using the FISH probes listed:

CRLF2 (Xp22.33) or (Yp11.32) rearrangement, CRLF2 break-apart probe set

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

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

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

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

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

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

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

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

If results for the initial panel are negative or demonstrate nonclassical abnormalities, the B-ALL with BCR::ABL1-like features panel will be performed as a secondary panel. This panel includes testing for the following kinase activating chromosome abnormalities, using the FISH probes listed below, as well as IKZF1 deletion, which often accompanies BCR::ABL1-like ALL.

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

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

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

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

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

Appropriate ancillary probes may be performed at consultant discretion to render comprehensive assessment. Any additional probes used will have the results included within the final report and will be performed at an additional charge. In the following situations, additional (reflex) testing may be performed at the laboratory's discretion and may be influenced by available karyotype results or other FISH testing.

When a KMT2A rearrangement is identified, testing with 1 or more dual-fusion (D-FISH) probe sets in an attempt to identify the translocation partner for the following abnormalities:

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

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

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

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

t(11;19)(q23;p13.1) or KMT2A::MLLT1 fusion, KMT2A/ELL probe set

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

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

In the absence of BCR::ABL1 fusion, when an extra or atypical ABL1 signal is identified, testing using the ABL1 break-apart probe set to identify a potential variant translocation involving ABL1, t(9;var)(q34;?) may be performed.

In the absence of ETV6::RUNX1 fusion, when an extra ETV6 signal is identified, testing using the ETV6 break-apart probe set to evaluate for the presence or absence of a potential rearrangement involving ETV6 t(12;var)(p13;?) may be performed.

When a MYC rearrangement is identified, both the BCL2 and BCL6 break-apart probe sets will be performed.

If an unbalanced rearrangement of BCL2 is identified, testing using the IGH/BCL2 probe to identify a potential t(14;18)(q32;q21) or IGH::BCL2 fusion may be performed.

For more information see B-Lymphoblastic Leukemia/Lymphoma Genetic Testing Guidelines.

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 BALFP / Pediatric B-Lymphoblastic Leukemia/Lymphoma panel, FISH, Varies.

At follow-up, conventional cytogenetic studies (CHRBM / Chromosome Analysis, Hematologic Disorders, Bone Marrow) and targeted B-cell ALL fluorescence in situ hybridization 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.

At diagnosis, conventional cytogenetic studies (COGBM / Chromosome Analysis, Hematologic Disorders, Children's Oncology Group Enrollment Testing, Bone Marrow) and this panel should be performed. If there is limited specimen available, only this test will be performed.

Advise Express Mail or equivalent if not on courier service.

1. 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; however, appropriate testing may be compromised or delayed.

2. A reason for testing must be provided. If this information is not provided, an appropriate indication for testing may be entered by Mayo Clinic Laboratories.

3. 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, but appropriate testing and interpretation may be compromised or delayed.

4. If the patient has received an opposite sex bone marrow transplant, note this information on the request.

5. If the patient has Down syndrome, note this information on the request.

Submit only 1 of the following specimens:

Preferred

Specimen Type: Bone marrow

Container/Tube:

Preferred: Yellow top (ACD)

Acceptable: Green top (sodium 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 (sodium 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

If not ordering electronically, complete, print, and send a Children's Oncology Group Test Request (T829) with the specimen.

Bone marrow: 1 mL; Whole blood: 2 mL

Detecting, at diagnosis, recurrent common chromosome abnormalities associated with B-cell acute lymphoblastic leukemia/lymphoma (B-ALL) and BCR::ABL1-like acute lymphoblastic leukemia/lymphoma 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 pediatric patients with B-ALL and Ph-like ALL being considered for enrollment in COG protocols

Evaluating specimens in which chromosome studies are unsuccessful

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

This test is only performed on specimens from pediatric patients being considered for enrollment in a Children's Oncology Group (COG) protocol. 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 as panel testing only using the following analysis algorithm.

The diagnostic pediatric/young adult B-cell acute lymphoblastic leukemia/lymphoma (B-ALL) fluorescence in situ hybridization (FISH) panel includes testing for the following abnormalities using the FISH probes listed:

CRLF2 (Xp22.33) or (Yp11.32) rearrangement, CRLF2 break-apart probe set

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

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

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

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

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

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

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

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

If results for the initial panel are negative or demonstrate nonclassical abnormalities, the B-ALL with BCR::ABL1-like features panel will be performed as a secondary panel. This panel includes testing for the following kinase activating chromosome abnormalities, using the FISH probes listed below, as well as IKZF1 deletion, which often accompanies BCR::ABL1-like ALL.

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

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

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

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

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

Appropriate ancillary probes may be performed at consultant discretion to render comprehensive assessment. Any additional probes used will have the results included within the final report and will be performed at an additional charge. In the following situations, additional (reflex) testing may be performed at the laboratory's discretion and may be influenced by available karyotype results or other FISH testing.

When a KMT2A rearrangement is identified, testing with 1 or more dual-fusion (D-FISH) probe sets in an attempt to identify the translocation partner for the following abnormalities:

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

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

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

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

t(11;19)(q23;p13.1) or KMT2A::MLLT1 fusion, KMT2A/ELL probe set

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

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

In the absence of BCR::ABL1 fusion, when an extra or atypical ABL1 signal is identified, testing using the ABL1 break-apart probe set to identify a potential variant translocation involving ABL1, t(9;var)(q34;?) may be performed.

In the absence of ETV6::RUNX1 fusion, when an extra ETV6 signal is identified, testing using the ETV6 break-apart probe set to evaluate for the presence or absence of a potential rearrangement involving ETV6 t(12;var)(p13;?) may be performed.

When a MYC rearrangement is identified, both the BCL2 and BCL6 break-apart probe sets will be performed.

If an unbalanced rearrangement of BCL2 is identified, testing using the IGH/BCL2 probe to identify a potential t(14;18)(q32;q21) or IGH::BCL2 fusion may be performed.

For more information see B-Lymphoblastic Leukemia/Lymphoma Genetic Testing Guidelines.

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 (aged 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 age 2 to 5 years. The incidence decreases with increasing age, before increasing again at around age 50 years. ALL is slightly more common in male patients than female patients. 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 most 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 is 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 the 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 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 ALL. 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 in 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). 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/Lymphoma

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 a 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 FISH 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).

If no FISH signals are observed post-hybridization, the case will be released indicating a lack of FISH results.

1. Moorman AV, Harrison CJ, Buck GAN, 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

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

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

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. Swerdlow SH, Campo E, Harris NL, et al, eds: WHO Classification of Tumours. Vol 2. WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues. 4th ed. IARC Press; 2017

This test is performed using commercially available and laboratory-developed probes. Deletion of IKZF1 on chromosome 7 and gain or losses of chromosomes 4, 10, and 17 are detected using enumeration strategy probes. Rearrangements involving CRLF2, ABL2, BCL3, PDGFRB, MYC, JAK2, ABL1, MLL, ETV6, IGH, and BCL2 are detected using dual-color break-apart (BAP) strategy probes. Dual-color, dual-fusion fluorescence in situ hybridization (D-FISH) strategy probe sets are used to detect t(X/Y;14), t(1;19), t(8;14), t(9;22), t(12;21), t(14;18), and  in reflex testing when a rearrangement of the KMT2A gene is detected. Amplification of the RUNX1 gene region is detected using a D-FISH probe 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 x 2, 88275, 88291-FISH Probe, Analysis, Interpretation; 1 probe set

88271 x 2, 88275-FISH Probe, Analysis; each additional probe set (if appropriate)