Indications in which the karyotype remains superior to molecular diagnostic techniques:
Typical phenotypic features of a specific chromosomal syndrome (e.g. Down).

Short stature, delayed puberty, amenorrhea, or ambiguous genitalia (to rule out aneuploidies and sex chromosome mosaics).

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1.
Bharath R, Unnikrishnan AG, Thampy MV, Anilkumar A, Nisha B, Praveen VP, et al. Turner syndrome and its variants. Indian J Pediatr [Internet]. 2010 [cited 2022 Sept 24];77(2):193–5. Available from: http://link.springer.com/10.1007/s12098-009-0226-7
Fetal death, neonatal death, and miscarriage (to rule out aneuploidy).

Couples with a history of infertility or recurrent miscarriage (to rule out balanced translocations: reciprocal chromosomal rearrangements o inversions).
Much like reciprocal translocations, most inversions are inherited and are not associated with a clinical phenotype, but carriers are at increased risk of producing abnormal gametes and associated fertility problems as a consequence of crossing over events in meiosis involving the inverted segment.
Family history of chromosomal abnormalities detected by cytogenetic methods (heterochromatin variants, etc.).

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1.
Liehr T. Cytogenetically visible copy number variations (CG-CNVs) in banding and molecular cytogenetics of humans; about heteromorphisms and euchromatic variants. Mol Cytogenet [Internet]. 2016 Jan 22 [cited 2022 Sept 24];9:5. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724132/
When aCGH detects a trisomy of an acrocentric chromosome (particularly of 13 and 21), this may be the result of a free trisomy (which in most cases is sporadic) or a Robertsonian translocation parental (associated with an increased risk of recurrence).

When aCGH detects a deletion and a duplication in the same chromosome.
It may be indicative of a parental pericentric inversion, so a karyotype will have to be performed on the parents.
When we suspect chromosomal structural alterations without copy number alteration.
- Investments.
- Chromosomes in the ring.
- Isodicentric chromosomes (idic15).
Microcephaly and severe short stature, or complex chromosomal rearrangements, to rule out mosaic variegate aneuploidy, Nijmejen syndrome.



