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Cytogenetics

ISCN Nomenclature

The final output of a FISH analysis is a formal report. To ensure that this report is universally understood by geneticists, oncologists, and researchers worldwide, the results must be described using the International System for Human Cytogenomic Nomenclature (ISCN). This standardized “grammar” describes exactly what probe was used, what cells were analyzed, and what pattern was observed

Basic Syntax of a FISH Result

An ISCN string for FISH is built in a specific order: [Location] [Technique] (Probe) [Result]

  1. Technique Code
    • nuc ish: Nuclear In Situ Hybridization (Interphase FISH). This is the most common code for uncultured cells
    • ish: In Situ Hybridization (Metaphase FISH). Used when signals are mapped to chromosomes
  2. Probe Description
    • The probe is defined by the band it targets (e.g., 9q34) and the gene name (e.g., ABL1)
    • Example: (ABL1,BCR)x2 means “The ABL1 probe and the BCR probe were both seen 2 times.”
  3. Signal Pattern (Multiplication Sign)
    • The result is expressed as the number of signals: observed per cell
    • x2: Two signals (Normal diploid)
    • x3: Three signals (Gain/Trisomy)
    • x1: One signal (Loss/Monosomy)

Scenario 1: Normal Interphase Result (Enumeration)

  • Clinical: A prenatal screen for Down Syndrome using a probe for Chromosome 21 (D21S259)
  • Observation: Two signals seen in all cells
  • ISCN: nuc ish(D21S259x2)[400]
    • nuc ish: Interphase analysis
    • (D21S259x2): The D21S259 probe was present in 2 copies
    • [400]: The number of cells scored was 400

Scenario 2: Abnormal Interphase Result (Translocation)

  • Clinical: CML diagnosis using a Dual-Color Dual-Fusion probe for BCR (22q11) and ABL1 (9q34)
  • Observation: 1 Red (ABL1), 1 Green (BCR), and 2 Fusions (BCR:ABL1). This implies a t(9;22)
  • ISCN: nuc ish(ABL1,BCR)x3(ABL1 con BCRx2)[200]
    • (ABL1,BCR)x3: There are 3 “objects” containing probe signals (1 normal ABL1, 1 normal BCR, and… wait)
    • Wait, the ISCN for fusion is tricky.
    • Simplified Modern Usage: Many labs use the explicit fusion notation: nuc ish(ABL1x3,BCRx3)(ABL1 con BCRx2)[200]
      • ABL1 con BCRx2: Two signals showed “Connection” (Fusion) between ABL1 and BCR
      • Note: The total signal count for each color is typically listed first (x3 because 1 single + 2 in fusions = 3 total copies of the gene locus)

Scenario 3: Abnormal Interphase Result (Deletion)

  • Clinical: CLL diagnosis looking for ATM deletion (11q22.3). Probe set includes ATM (Target) and D11Z1 (Control Centromere)
  • Observation: 1 ATM signal, 2 Centromere signals
  • ISCN: nuc ish(D11Z1x2,ATMx1)[200]
    • D11Z1x2: Two copies of the centromere (Disomy 11)
    • ATMx1: Only one copy of the ATM gene (Deletion)
    • [200]: Result seen in 200 cells

Scenario 4: Metaphase FISH (Mapping)

  • Clinical: Characterizing an unknown marker chromosome using a Whole Chromosome Paint (wcp) for Chromosome 12
  • Observation: The marker chromosome “lights up” with the Chromosome 12 paint
  • ISCN: ish der(12)(wcp12+)
    • ish: Metaphase analysis
    • der(12): The abnormal chromosome is a derivative of 12
    • (wcp12+): It is positive (+) for the Whole Chromosome Paint 12

Relative Positioning (Sep vs. Con)

When describing patterns precisely:

  • con (Connected): Signals are overlapping or adjacent (Fusion). Used in translocations
    • Example: (IGH con MYC)
  • sep (Separated): Signals are separated. Used in Break-Apart probes
    • Example: (KMT2A sep) means the 5’ and 3’ ends of the KMT2A gene are separated (rearranged)

Reporting Clones

If a patient has multiple populations (Mosaicism):

  • nuc ish(D21S259x2)[200]/(D21S259x3)[100]
    • Interpretation: 200 cells were normal (x2), and a separate clone of 100 cells showed Trisomy 21 (x3)
    • The slash / separates the clones. The counts in brackets [] indicate the size of each clone