Episode 003: Heme Path Series Pt 2 - Cytogenetics

In Part 2 of our Heme Path series, we get into the details of cytogenetics (conventional karyotype and FISH)

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Take Aways:

1. “Cytogenetics” is the analysis of chromosomal changes in a cell, which includes additions, deletions, inversions, and translocations of important regions of genetic information. 

2. We typically use cytogenetic information to help in disease diagnosis, decide treatment options, determine prognostic information, and, historically, assess response to treatment. 

3. Two different techniques fall under this umbrella: conventional karyotype and fluorescence in situ hybridization (FISH)

4. Conventional karyotype: 

   • What does this mean?: 

     • Assessment of large changes in chromosomes (Megabase sized)

     • Bone marrow specimen is arrested in metaphase with microtubule inhibitors, stained with Giemsa stain, and then cells are analyzed; a total of 20 cells are analyzed 

     • The changes seen provide genetic and prognostic information 

     • Example is in chronic myelogenous leukemia (CML), with pathognomonic t(9;22) which encodes the Philadelphia chromosome (ASH Image Bank example: https://imagebank.hematology.org/image/60150/t922-karyotype)

   • Pros:

     1. Provides important information regarding diagnosis, treatment options, and prognosis particularly for MDS and acute leukemia. 

   • Cons/caveats: 

     1. Can only be run on actively dividing cells (cannot be run on peripheral blood)

     2. Very labor intensive, therefore slower turnaround time 

     3. Cannot detect smaller genetic changes

5. FISH 

   • What does this mean?

     • More sensitive and targeted technique compared to conventional karyotype (Down to kilbased sized changes)

     • Uses fluorescently-labeled probes that target DNA regions that are pathognomonic for the suspected disease. Therefore, which probes are used is based on the clinical context 

     • Example is in acute promyelocytic leukemia (APL), with pathognomonic t(15;17) which encodes PML-RARA gene (ASH Image Bank example: https://imagebank.hematology.org/image/61450/fish-showing-t1517q24q21-pmlrara-translocation)

     • Can also be run on fixed specimens. For example, FISH probes are used to determine presence of HER2 for breast cancer or for high risk rearrangements for DLBCL (MYC, BCL-2, BCL-6). 

   • Pros: 

     1. Can be run on peripheral blood, marrow, or fixed specimen 

     2. Much faster than karyotype, which is useful when a diagnosis is needed quickly 

   • Cons: 

     1. You need to have an index of suspicion for what you are looking for 

     2. Does not give full analysis of chromosomal changes, therefore you still need the karyotype

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References

1. https://www.nature.com/articles/nrg1692 - Nature review article about overview of cytogenetics 

1. https://www.ashclinicalnews.org/spotlight/demystifying-the-lab/demystifying-lab-cytogenetics/ - ASH overview on Cytogenetics