3.1 Karyotype, FISH & Chromosomal Microarray

Why cytogenetic methods still matter

Domain 3A expects you to choose and counsel cytogenetic technologies with the same rigor you apply to NGS. Families often arrive with a report labeled “chromosome study,” “FISH,” or “microarray” and assume these tests are interchangeable. They are not. Each modality answers a different structural question at a different resolution, with different false-negative classes. Your job is to connect the indication (aneuploidy, microdeletion syndrome, balanced translocation carrier status, unexplained developmental delay) to the right first-line test—and to explain limitations before results return.

Conventional karyotype (G-banded chromosome analysis)

A karyotype examines metaphase chromosomes after culture, harvesting, and banding (typically G-banding with trypsin–Giemsa). Chromosomes are counted and scrutinized for large gains/losses and structural rearrangements.

When karyotype is the right tool

• Suspected aneuploidy with need for structural characterization (e.g., distinguishing free trisomy 21 from translocation Down syndrome for parental recurrence counseling).
• Known or suspected balanced rearrangement in a parent (recurrent pregnancy loss, family history of rearrangement) where microarray alone would be falsely reassuring.
• Characterization of a marker chromosome or complex rearrangement after an abnormal CMA or FISH finding.

Exam trap: Ordering CMA alone when the clinical question is “Is this parent a balanced translocation carrier?” CMA does not answer that question.

FISH (fluorescence in situ hybridization)

FISH hybridizes fluorescent DNA probes to metaphase or interphase nuclei to ask a targeted locus question.

Strengths and blind spots

• Strength: Fast, targeted, excellent when you already know which locus matters.
• Blind spot: FISH does not scan the rest of the genome. A negative 22q11.2 FISH does not exclude other pathogenic CNVs.
• Probe design matters: If a deletion is atypical and lies outside the probe region, FISH can be falsely negative relative to CMA coverage of that interval.

Use FISH as a precision tool, not as a substitute for genome-wide copy-number assessment when the phenotype is nonspecific.

Chromosomal microarray (CMA)

Chromosomal microarray (oligonucleotide array CGH, SNP array, or combined platforms) detects copy-number variants (CNVs) at much finer resolution than karyotype—often in the kilobase to low-megabase range depending on probe density and laboratory thresholds.

The balanced-rearrangement rule (board-critical)

Because CMA measures dosage, a balanced reciprocal translocation or inversion that does not change copy number is typically invisible. A person can be a balanced carrier, have recurrent pregnancy loss or an unbalanced offspring, and still have a normal microarray. Teach this explicitly in pretest counseling whenever reproductive or familial rearrangement risk is on the differential.

SNP array bonuses and caveats

SNP-based arrays can reveal regions of homozygosity, which may suggest identity by descent (consanguinity), uniparental disomy (UPD) suspicion for a chromosome, or other mechanisms—interpretation is clinical and often requires follow-up (methylation testing, UPD studies, or sequencing), not automatic diagnosis from ROH alone.

Mosaicism (note now; prenatal CPM detail later)

Mosaicism—two or more genetically distinct cell lines—can be missed or under-quantified by any modality:

• Karyotype may detect mosaic aneuploidy if the abnormal line grows in culture, but culture can select for or against clones.
• CMA may miss low-level mosaicism below the lab’s detection threshold.
• FISH can quantify mosaicism at a targeted locus in many cells but still misses untargeted changes.

Counsel that a “normal” cytogenetic result reduces but does not always eliminate mosaic disease, especially when phenotype is highly suggestive. Detailed confined placental mosaicism (CPM) counseling belongs with prenatal diagnostic chapters; here, remember that tissue source and mosaicism affect what blood-based cytogenetics can show.

Choosing among karyotype, FISH, and CMA

Common counseling traps

1. Equating “chromosomes normal” on CMA with “no chromosomal problem”—balanced rearrangements and some mosaicism remain possible.
2. Using FISH as a genome-wide screen.
3. Ignoring that variant of uncertain significance (VUS) CNVs on CMA require phenotype correlation, inheritance studies, and careful language—not automatic pathogenicity.
4. Forgetting that culture failure or poor DNA quality can delay or cancel cytogenetic testing—plan sample type accordingly (next section).

Integrating cytogenetics into the testing pathway

Cytogenetics and molecular sequencing are complementary, not competitors. A child with developmental delay may start with CMA; a negative CMA does not exclude sequence-level Mendelian disease (exome/genome). Conversely, an exome that misses a large multi-exon deletion may need CNV-aware analysis or CMA/MLPA. On the CGC exam, stems often turn on whether the missing piece is copy-number, balanced structure, or sequence—and whether the ordered test can see that piece.