Indications for Testing
ALL testing should be considered for patients presenting with signs of bone marrow failure (eg, anemia, thrombocytopenia, leukopenia) and constitutional symptoms (eg, fever, lethargy, weight loss). In children, joint or extremity pain may be the only presenting symptom.
Laboratory Testing
Diagnosis
Bone marrow aspirate and biopsy allow bone marrow blasts to be enumerated and provide material for ancillary testing, including immunophenotyping, morphology, cytogenetics, and fluorescence in situ hybridization (FISH) or molecular testing. These studies allow for characterization, prognostication, and treatment planning. For patients with diagnosed ALL, it is also important to obtain a cerebrospinal fluid (CSF) sample; ALL may involve the central nervous system (CNS) both at diagnosis and at relapse. Knowledge of CSF status at diagnosis directs appropriate therapy.
Immunophenotyping
Flow cytometric immunophenotyping is performed to identify certain cell surface markers associated with leukemia subtypes and predict outcome. ALL is broadly classified into two immunophenotypic groups: B-cell ALL and T-cell ALL. B-cell ALL is predominantly seen in children (roughly 88% of cases). Refer to the tables below for markers commonly associated with B-cell and T-cell ALL.
Cytogenetics
Cytogenetics are an important part of the diagnosis, prognosis, and treatment of ALL in pediatric and adult patients. These studies further characterize ALL subtypes and provide prognostic stratification, especially in children. The majority of B-ALLs involve chromosomal abnormalities; hyperdiploidy and the ETV6-RUNX1 subtype (resulting from chromosomal translocation t[12;21]) are among the most commonly occurring subtypes in children. Both have favorable prognosis. In adults, Philadelphia chromosome-positive (Ph-positive) ALL is the most common subtype and is associated with a poor prognosis. BCR-ABL1-like ALL, often referred to as Ph-like ALL, a recently identified subtype, is also associated with a poor prognosis. Refer to the tables below for more information about recurrent genetic abnormalities.
Cytogenetic testing methodologies include karyotyping, FISH, and single nucleotide polymorphism (SNP) microarray. Karyotyping, or chromosome analysis, is used to identify recurrent cytogenetic abnormalities. FISH is more sensitive than karyotyping in detecting cytogenetic aberrations, such as the ETV6-RUNX1 fusion. Microarray is capable of detecting some abnormalities that may be missed by chromosome analysis or FISH, like focal deletions, but it will not detect balanced translocations.
Recurrent Genetic Abnormalities Associated with B-ALL
| Translocation/Gene |
Frequency |
Immunophenotype |
Prognosis/Predictive Factors |
|---|
|
t(9;22)(q34.1;q11.2)
BCR-ABL1
|
Children, 2-4%
Adults, 25%
|
CD10, CD19, TdT, CD25 (in adults) positivity
CD13, CD33 frequently expressed
|
Considered worst prognosis of all major ALL subtypes
|
|
BCR-ABL1-like
|
10%-25% of all ALL cases
|
CD19, CD10 positivity
|
Poor prognosis
Higher risk of MRD
|
|
t(v;11q23.3)
KMT2A (MLL)-rearranged
|
Most common in infants <1 yr
Becomes increasingly common in adulthood
|
CD19, CD15 positivity
CD10, CD24 absent
|
Poor prognosis
|
|
t(1;19)(q23;p13.3)
TCF3-PBX1
|
Children, 6%
Adults, rare
|
CD19, CD10 positivity
Cytoplasmic mu heavy chain
|
Poor prognosis; may be improved with intensive therapy
Increased risk of CNS relapse
|
|
t(5;14)(q31.1;q32.1)
IGH/IL3
|
<1% of all cases of ALL
|
CD19, CD10 positivity
|
No different than that of other types of ALL
|
|
iAMP21
|
2% of all cases of B-ALL
More common in children
|
Unknown
|
Poor prognosis; may be improved with intensive therapy
|
|
t(12;21)(p13.2;q22.1)
ETV6-RUNX1
|
Children, 25%
Adults, rare
|
CD19, CD10, CD34 positivity
|
Favorable prognosis, with cure seen in >90% of children
|
|
Hyperdiploidy (>50 chromosomes)
|
Children, 25%
Adults, rare
|
CD19, CD10, CD34 positivity
CD45 often absent
|
Favorable prognosis, with cure seen in >90% of children
|
|
Hypodiploidy (<46 chromosomes)
|
5% of all cases of ALL
|
CD19, CD10 positivity
|
Poor prognosis
|
|
MRD, minimal residual disease
Source: Borowitz, 2017 ; Arber, 2017
|
Common T-ALL Rearrangements
| Translocation/Gene |
Frequency |
Immunophenotype |
Prognosis/Predictive Factors |
|---|
|
10q24
TLX1 (HOX11)
|
Children, 7%
Adults, 30%
|
TdT positive
Variable expression of CD1a, CD2, CD3, CD4, CD5, CD7, and CD8
|
Worse prognosis in childhood than B-ALL
Associated with higher risk of induction failure, early relapse, and isolated CNS relapse
|
|
t(5;14)
TLX3 (HOX11L2)
|
Children, 20%
Adults, 10-15%
|
CD1a, CD10 positivity
|
Poor prognosis
|
|
Source: Borowitz, 2017
|
In addition to the gene fusions and numerical abnormalities above, other gene alterations that have been shown to carry prognostic importance in ALL include PAX5, JAK1/2, IKZF1, CRLF2, and NOTCH1.
Monitoring
Monitoring is performed using the leukemia-associated phenotype defined at diagnosis for the detection of MRD. Virtually all pediatric and many adult patients with ALL are monitored with MRD techniques to assess treatment effectiveness and determine risk stratification. The most frequently used methods include flow cytometry for abnormal immunophenotypes, polymerase chain reaction (PCR), and NGS-based assays to detect fusion genes (eg, BCR-ABL1), clonal rearrangements, and/or T-cell receptor genes. B-cell lineage MRD can be detected using bone marrow, while T-cell lineage MRD can be detected using peripheral blood. Relapse mandates new immunophenotyping and molecular testing. Karyotyping may change and, rarely, a second de novo ALL may be discovered. Ph-positive cases should be tested for BCR-ABL1 tyrosine kinase inhibitor (TKI) mutations.
Pharmacogenetics
The increased survival rates of patients with ALL are due in large part to the identification of effective regimens, treatment durations, and chemotherapeutic agents. For example, combining imatinib with chemotherapy has shown to be effective in cases of Ph-positive ALL. Thiopurine S-methyltransferase (TPMT) activity and genetic testing is available to guide appropriate thiopurine dosing and mitigate the risk of toxicity.
