Cell Surface Markers
These are proteins expressed on the outside of the cell membrane. They reflect the cell’s lineage (what type of cell it is) and its maturation stage. They are detected by flow cytometry using fluorescent antibodies.
- They tell you what the cell looks like immunologically — essentially its identity card
- They are used primarily for diagnosis and classification (e.g., CD5+/CD19+/CD23+ tells you this is a CLL cell, not a normal B cell)
- They also serve as therapeutic targets — CD20 is targeted by rituximab, CD38 by daratumumab, BCMA by CAR-T and bispecifics in myeloma
- They do not tell you why the cell became malignant
Cytogenetics
This looks at the structure and number of entire chromosomes — large-scale changes in the DNA. Detected by conventional karyotype (G-banding), FISH (fluorescence in situ hybridization), or chromosomal microarray.
- Cytogenetics tells you about gross chromosomal rearrangements: translocations (pieces of chromosomes swapping), deletions, gains, or inversions
- These changes usually activate oncogenes or inactivate tumor suppressors at a large structural level — for example, t(9;22) fuses BCR and ABL1 into an abnormal kinase that drives CML
- They are the most powerful prognostic tools in many diseases (e.g., del(17p) in CLL or complex karyotype in AML predict poor outcomes)
- They can also be therapeutic targets — the BCR-ABL1 fusion created by t(9;22) is directly inhibited by imatinib/dasatinib
The key distinction is scale: cytogenetics involves changes visible at the chromosomal level, often affecting millions of base pairs at once.
Gene Mutations
These are point mutations, small insertions, or small deletions within the DNA sequence of a specific gene — changes too small to be seen on a karyotype. Detected by next-generation sequencing (NGS), PCR, or Sanger sequencing.
- Gene mutations tell you about molecular-level alterations in individual genes — a single nucleotide changed, a few bases inserted or deleted, or a gene duplicated at the sequence level
- They can drive oncogenesis (e.g., BRAF V600E in HCL, FLT3-ITD in AML, NOTCH1 in T-ALL), affect prognosis (e.g., TP53 mutation, NPM1), or predict drug resistance (e.g., BTK C481S mutation causing ibrutinib resistance in CLL)
- They are increasingly actionable therapeutically — IDH1 mutations are targeted by ivosidenib, FLT3 by midostaurin/gilteritinib, BRAF V600E by vemurafenib
How They Relate to Each Other
Think of it as three nested levels of the same problem:
| Level | What it examines | Scale | Method |
|---|---|---|---|
| Surface markers | Proteins on the cell membrane | Protein level | Flow cytometry |
| Cytogenetics | Chromosome structure/number | Chromosomal (Mb) | Karyotype / FISH |
| Gene mutations | DNA sequence changes | Gene/nucleotide (bp) | NGS / PCR |
An important nuance: cytogenetic changes and gene mutations are not always separate events. A translocation like t(15;17) in APL creates the PML-RARA fusion gene — so the cytogenetic abnormality and the molecular driver are the same event viewed at different resolutions. Similarly, t(9;22) creates the BCR-ABL1 fusion that can also be detected as a gene-level mutation by PCR. The difference is whether you are detecting the chromosomal rearrangement (cytogenetics) or the resulting abnormal gene/transcript (molecular/mutation testing).