GeneticsTier 1Medical Sciences concept

Cytogenetic testing methods - karyotype, FISH, array CGH, indications

Core concept

Choose the test by the size and type of the abnormality you are looking for
- Whole chromosome / balanced rearrangement -> karyotype
- Known specific locus, or a rapid answer -> FISH
- Unexplained copy number change anywhere in the genome -> array CGH / SNP array
- Single base change -> sequencing (panel, exome, genome)
Resolution ladder: karyotype ~5-10 Mb -> FISH ~100-200 kb -> array ~10-100 kb -> sequencing 1 bp
The single most examined fact: array CGH cannot see a balanced translocation or inversion, because there is no net gain or loss of material

Method	Detects	Misses	Needs dividing cells?
G-banded karyotype	Aneuploidy, balanced and unbalanced translocations, inversions, ring chromosomes, marker chromosomes, mosaicism >~10%	Anything <5-10 Mb; single-gene variants	Yes - cultured, metaphase
FISH	A specific known locus - microdeletion, fusion, amplification; interphase FISH gives a same-day aneuploidy answer	Anything you did not probe for	No (interphase) or yes (metaphase)
Array CGH / SNP array	Copy number variants genome-wide - microdeletions/duplications; SNP arrays also detect UPD, consanguinity and triploidy	Balanced rearrangements, point mutations, low-level mosaicism, repeat expansions	No - DNA only
Sequencing (panel/WES/WGS)	Point mutations, small indels; WGS also structural variants	Repeat expansions (unless targeted), methylation	No
MLPA	Exon-level deletions/duplications in a chosen gene	Balanced changes	No
Optical genome mapping	Structural variants including balanced, at high resolution - increasingly replacing karyotype in haematology	Point mutations	No

Where each is the right answer

Recurrent miscarriage / a couple with a translocation carrier -> karyotype (this is the balanced-rearrangement question)
Suspected Down, Edwards, Patau, Turner, Klinefelter -> karyotype (or rapid FISH/QF-PCR)
22q11.2 deletion (DiGeorge), Williams (7q11.23), Prader-Willi/Angelman (15q11-13) -> FISH or array; PWS/AS also need methylation studies to detect UPD and imprinting defects
Developmental delay, intellectual disability, autism, multiple congenital anomalies -> array CGH is first-line
HER2 amplification, ALK/ROS1 rearrangement, BCR-ABL1, PML-RARA -> FISH
Noonan syndrome -> RAS-MAPK gene sequencing (PTPN11, SOS1, RAF1) - the karyotype is normal; the classic distractor against Turner
Fragile X, myotonic dystrophy, Huntington -> targeted repeat sizing, not array or exome

Balanced translocation carriers are phenotypically normal but produce unbalanced gametes -> recurrent miscarriage, infertility, an affected child
- Robertsonian translocation 14;21 -> translocation Down syndrome with a recurrence risk of ~10-15% if the mother carries it, ~1-2% if the father does - unlike free trisomy 21, this risk is not age-related and mandates parental karyotyping
Variants of uncertain significance are the practical cost of array and exome testing - counsel before the test, and consider parental samples to establish de novo status
Incidental/secondary findings (cancer predisposition genes, consanguinity, non-paternity) - consent must cover them
Mosaicism - a normal blood karyotype does not exclude tissue-limited mosaicism (Pallister-Killian, hypomelanosis of Ito) - sample skin fibroblasts
Non-invasive prenatal testing is a screening test on cell-free fetal DNA; a positive result requires confirmatory CVS or amniocentesis - placental confined mosaicism causes false positives
Haematology: karyotype remains the backbone of AML and MDS risk stratification, with FISH and NGS panels layered on

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