Genetic Testing in the Diagnosis and Biology of Acute Leukemia

2017 Society for Hematopathology/European Association for Haematopathology Workshop Report

Marian H. Harris, MD, PhD; David R. Czuchlewski, MD; Daniel A. Arber, MD; Magdalena Czader, MD, PhD


Am J Clin Pathol. 2019;152(3):322-346. 

In This Article


The diagnostic workup of acute leukemia has become increasingly complex. The testing required today to provide a complete diagnosis, as well as clinically significant prognostic and therapeutic information, includes not only morphologic assessment, immunophenotype, and classic cytogenetics, but also molecular genetic techniques. DNA sequence analysis is particularly important in the diagnosis of AML as there are now a number of subtypes defined by gene mutations, as well as mutations with known prognostic (eg, KIT mutations in CBF AML) or therapeutic (eg, FLT3) significance. This use of DNA sequencing was represented in this workshop by the high number of cases of AML with mutated RUNX1, which require sequencing for diagnosis. RNA sequencing is becoming increasingly available, particularly targeted RNA sequencing, and may be particularly useful in the workup of B-ALL, as this technique is capable of identifying BCR-ABL1-like fusions, which is a current challenge in the field. Similarly, gene expression profiling via a low-density array card for identifying BCR-ABL1–like cases is increasingly available outside of the clinical trial setting. RNA sequencing can also identify cytogenetically cryptic fusions.

DNA and RNA sequencing are also used in evaluation of posttreatment and relapse samples. In these settings, interpretation of molecular studies may be confounded by genetic evolution of the original leukemic clone, and molecular abnormalities unrelated to the original leukemia such as CHIP, germline mutations, and even a previously undiagnosed underlying neoplasm. At times, testing individual cell populations, for example, analysis of BCR-ABL1 fusion in segmented neutrophils or confirmation of germline mutation in cultured skin fibroblasts, may clarify the significance of a genetic finding. The awareness of this complex environment is critical in quantitative evaluation of residual disease, especially during therapy leading to HSCT. Lastly, an increasing number of therapies can induce differentiation of leukemic blasts, which emphasizes the importance of integrating treatment information with morphologic and molecular evaluation in order not to overinterpret molecular genetic findings.