Fluorescence in situ hybridization (FISH)

FISH is a cytogenetic method that uses fluorescent probes for the visual detection of specific structural chromosome alterations, including translocations, inversions, amplifications, or deletions.1 It is most commonly used to confirm1:

  • t(15;17) and its variants in acute promyelocytic leukemia (APL)
  • Presence of KMT2A (MLL) gene fusion partners

The speed of interphase FISH (iFISH) adds important diagnostic information, as it provides for an unequivocal diagnosis, or exclusion, of APL through the identification of the RARA-involved translocations [t(15;17)].1

Advantages of FISH2:

  • Generally faster than traditional karyotyping and involves a fairly straightforward protocol
  • Can be applied to both metaphase and interphase cells, whereas karyotyping can only analyze cells that are actively dividing
  • Can identify small microdeletions
  • PML-RARA FISH may confirm APL faster than conventional cytogenetics2

Disadvantages of FISH2:

  • Certain mutations or abnormalities cannot be detected
  • Requires existing and correct FISH probes to make an accurate diagnosis


Karyotyping or routine cytogenetic analysis helps detect clonal aberrations via assessment of characteristic banding patterns on chromosomes. It is an important diagnostic and prognostic tool because more than half of patients have an abnormal karyotype, which could impact response to treatment.1

Bone marrow or peripheral blood cells can be used for karyotyping.1

Standard karyotyping can detect recurrent balanced translocations, balanced inversions, partial deletions, and complex/normal karyotypes.1

Karyotyping can take at least 2-3 working days to complete and is heavily reliant on the expertise of an accomplished technician to interpret results.1

Advantages of karyotyping2:

  • In contrast to molecular techniques, karyotyping shows the entire genome at once
  • Suitable when a specific cytogenetic anomaly is suspected
  • Useful in monitoring disease progression
  • Can be used to compare karyotypes from multiple patients to find critical disease-associated regions

Disadvantages of karyotyping2:

  • Most techniques can only detect large structural abnormalities and not smaller DNA gains or losses
  • Can only be used to analyze actively dividing cells
  • Labor intensive and dependent on experience and skill of technician

The current WHO 2016 classifications recognize 9 cytogenetic abnormalities in their classification of AML with recurrent genetic abnormalities (please see section on WHO 2016 Classification Scheme); however, additional aberrations (eg, -5 or del(5q), -7, -17/abn(17p)) may be present in AML.3

References: 1. 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. 2. Schrijver I, Zehnder JL. Tools for genetics and genomics: cytogenetics and molecular genetics. UpToDate website. Updated May 8, 2019. Accessed April 22, 2021. 3. Döhner H, Estey E, Grimwade D, et al. Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel. Blood. 2017;129(4):424-447.