Cytogenetic Techniques
Overview
Cytogenetic techniques are laboratory methods used to visualize and analyze chromosomes. This chapter covers the three major cytogenetic platforms used in clinical genetics (karyotype, FISH, and chromosomal microarray (CMA)), each with distinct capabilities, resolution limits, and clinical applications. Knowing when to order each test, what it can and cannot detect, and how to interpret the results is core to clinical practice.
Selecting the right cytogenetic test from a clinical scenario is a routine decision-making framework. The key is the resolution and scope of each technique: karyotype detects large-scale changes (>5-10 Mb), FISH targets specific known regions with rapid turnaround, and CMA provides genome-wide detection of copy number variants at much higher resolution (~50 kb to 5 Mb) but cannot detect balanced rearrangements.
The choice of cytogenetic test depends on the clinical question. A suspected aneuploidy in a prenatal sample may start with FISH for rapid results, followed by karyotype or CMA for comprehensive analysis. A child with developmental delay and dysmorphic features is typically evaluated first with CMA. A couple with recurrent pregnancy loss may need karyotyping to detect balanced translocations. These decision pathways are central to ordering and interpreting cytogenetic studies.
Key Concepts
- Resolution hierarchy: karyotype (>5-10 Mb) vs. CMA (~50 kb) vs. FISH (targeted, ~100 kb probe)
- Balanced vs. unbalanced rearrangements: karyotype detects balanced translocations and inversions; CMA does not
- Copy number variants: CMA is the first-tier test for unexplained developmental delay, intellectual disability, autism, and multiple congenital anomalies
- Turnaround time: FISH provides rapid results (24-48 hours); karyotype requires cell culture (7-14 days); CMA typically 2-4 weeks
- Limitations: no single test detects everything; low-level mosaicism, balanced rearrangements, and point mutations each require different approaches
Conventional Cytogenetics
Karyotype is conventional chromosome analysis using G-banding: specimen requirements, cell culture, banding techniques, and interpretation of numerical and structural abnormalities. It is the only cytogenetic test that visualizes whole chromosomes and can detect balanced rearrangements, making it indispensable for evaluating recurrent pregnancy loss, confirming suspected aneuploidies, and characterizing complex rearrangements.
Copy Number Detection
Chromosomal microarray (CMA) detects copy number gains and losses across the entire genome and has largely replaced karyotype as the first-tier test for children with unexplained developmental delay or congenital anomalies. Both array CGH and SNP array platforms are in clinical use; SNP arrays additionally detect regions of homozygosity (relevant for UPD and consanguinity). Variants of uncertain significance are the principal interpretive challenge.
These three techniques form a complementary toolkit, and knowing how they relate to one another is as important as understanding each one individually.
Molecular Cytogenetics
FISH targets specific chromosome regions with fluorescent probes. The major probe types (locus-specific, centromeric, whole chromosome painting, subtelomeric) each have distinct applications. FISH is most useful when the question is targeted: confirming a suspected microdeletion, rapidly ruling out aneuploidy on uncultured cells, or characterizing a rearrangement identified by another method.