Molecular Testing

Whereas cytogenetic analysis can screen for chromosomal abnormalities, molecular profiling can identify changes or mutations to the DNA sequence. Molecular profiling has the ability to identify mutations that can help refine prognostic groups, particularly in patients with a normal-karyotype (NK).1 One of the ways the National Comprehensive Cancer Network (NCCN) confers favorable, intermediate, and poor/adverse risk is based on validated genetic abnormalities.1 As a result, testing for certain molecular genetic lesions, such as NPM1 and biallelic CEBPA, is now becoming a part of the initial diagnostic workup to risk stratify acute myeloid leukemia (AML) and, consequently, may influence treatment decisions.1

NCCN recommendations for molecular testing at diagnosis include screening for the following mutations1:

  • ASXL1
  • c-KIT
  • FLT3-ITD
  • FLT3-TKD
  • NPM1
  • CEBPA (biallelic)
  • IDH1
  • IDH2
  • RUNX1
  • TP53
  • PML-RARA
  • BCR-ABL

Common techniques for molecular testing include:

  • Quantitative polymerase chain reaction, or qPCR, for screening for recurring gene fusions and somatically acquired AML-related mutations2
    • Genome-wide studies for gene mutations and deregulated gene expression are optional2
  • Next generation sequencing (NGS) has recently been used to identify rare variants that may confer disease susceptibility and to classify genomes of individual patients.3 NGS is recommended for comprehensive prognostic assessment.1 In whole-genome sequencing4:
    • DNA is isolated from a patient
    • The whole sequence is determined
    • A bioinformatics computer system compares the patient’s sequence to a reference sequence and then:
      • Notes any differences
      • Determines which differences could hold clinical relevance

NGS has been useful in sequencing a large number of novel abnormalities in cancer genomes.3 NGS has discovered major driver mutations in both solid and hematopoietic malignancies, such as DNMT3A in acute myeloid leukemia (AML).3

NGS can improve tumor classification, diagnosis, and management for some cancer patients. However, there are limitations to the technology, and many challenges remain, including4:

  • The storage and interpretation of vast amounts of sequence data
  • Training physicians
  • Slow turnaround time
  • Healthcare professionals whose knowledge of genetics may be insufficient
  • Effective genetic counseling and communication of results to patients
  • Establishing standards for the appropriate use of the technology

References: 1. Referenced with permission from the NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®) for Acute Myeloid Leukemia V.3.2021. © National Comprehensive Cancer Network, Inc. 2021. All rights reserved. Accessed April 22, 2021. To view the most recent and complete version of the guideline, go online to NCCN.org. NCCN makes no warranties of any kind whatsoever regarding their content, use or application and disclaims any responsibility for their application or use in any way. 2. Roug AS, Hansen MC, Nederby L, Hokland P. Diagnosing and following adult patients with acute myeloid leukaemia in the genomic age. Br J Haematol. 2014;167(2):162-176. 3. Xuan J, Yu Y, Qing T, Guo L, Shi L. Next-generation sequencing in the clinic: promises and challenges. Cancer Lett. 2013;340(2):284-295. 4. Johansen Taber KA, Dickinson BD, Wilson M. The promise and challenges of next-generation genome sequencing for clinical care. JAMA Intern Med. 2014;174(2):275-280.