Acute Lymphoblastic Leukemia - ALL

Indications for Testing

ALL testing should be considered for patients who present 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 enable 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-cell ALLs involve chromosomal abnormalities; high hyperdiploidy and the ETV6-RUNX1 subtype (which results from chromosomal translocation t[12;21]) are among the subtypes that most commonly occur in children.    Both have favorable prognoses.  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, such as focal deletions, but it will not detect balanced translocations.

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 next generation sequencing (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, whereas 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. Refer to current National Comprehensive Cancer Network (NCCN) guidelines for specific guidance for adult and pediatric patients.

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 and NUDT15 genetic testing are available to guide appropriate thiopurine dosing and mitigate the risk of toxicity.   Refer to the Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for thiopurine dosing based on TPMT and NUDT15 genotypes.