FISH Diagnostic Guidelines

Introduction to FISH Diagnostics

The American College of Medical Genetics recommends that FISH test reports clearly state whether results are normal/negative or abnormal/positive, though terms like "inconclusive," "equivocal," or "borderline" may be used when results are ambiguous 1

FISH identifies chromosomal abnormalities, including microdeletions and microduplications, such as DiGeorge syndrome and Prader-Willi syndrome, where deletions account for ~70% of cases 2, 3
The American College of Medical Genetics suggests that FISH detects microdeletions and microduplications, with detection rates varying by syndrome, such as 70% for Prader-Willi/Angelman syndromes versus 11-12% for Rubinstein-Taybi syndrome 2, 3

In advanced maternal age patients (>35 years), FISH using probes for chromosomes X, Y, 13, 18, and 21 detects approximately 80% of clinically significant abnormalities 4
The American College of Medical Genetics states that the overall detection rate of FISH across all prenatal indications is 65-70% of significant cytogenetic abnormalities 4

FISH provides prognostic information and clarifies diagnoses in hematologic malignancies and solid tumors, with gene amplification thresholds being disease-specific, such as HER2 ratio >2.2 in breast cancer versus MYCN ratio >4 in neuroblastoma 5
The American College of Medical Genetics recommends that when amplification is detected and dividing cells are available, conventional chromosome analysis should be recommended to detect homogeneously staining regions or double minutes 5

FISH confirms or visualizes copy number variants identified by microarray, but requires specific validation considerations, including parental FISH testing by the same laboratory that conducted the initial microarray and proband FISH evaluation 6, 7

Metaphase FISH provides information only about the specific probe locus tested and does not substitute for complete karyotypic analysis, with whole chromosome paints potentially not hybridizing uniformly across small derivative chromosome regions 8, 9

Borderline results require extreme caution and clinical context, with cut-off values being estimates of the upper limit for abnormal patterns in normal populations, and normal FISH results with probes not targeting the critical gene should include disclaimers about potential false negatives from very small deletions or point mutations 8, 9

For probes with limited clinical experience, concurrent normal controls must be run with patient material, and databases for interpreting mosaicism must be established for each probe set, with rare individuals with small numbers of repeated sequence targets potentially yielding false-negative results with repeated sequence probes 6, 7, 9

The American College of Medical Genetics (ACMG) states that a FISH result is considered abnormal when the proportion of cells showing an abnormal signal pattern exceeds the laboratory‑established cut‑off value at a 95 % confidence level【10】.
Most laboratories set cut‑offs for copy‑number probes in the range of 5 %–10 % of cells; a finding of 36 % positive cells therefore surpasses typical thresholds and is classified as definitively abnormal【10】. (Strength of evidence: guideline recommendation based on expert consensus)

The Blood Cancer Journal reports that chromosome 11 centromere probe D11Z1 is routinely employed in multiple myeloma FISH panels to assess centromeric copy number, targeting the centromere rather than the MAML2 locus at 11q21【11】【12】【13】.
Consequently, when a specimen originates from bone‑marrow or other hematologic tissue, the presence of a MAML2‑related signal is likely artifactual and should not be interpreted as evidence of mucoepidermoid carcinoma【11】【12】. (Strength of evidence: observational data from a peer‑reviewed oncology journal)