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.
Microcephaly and severe short stature, or complex chromosomal rearrangements, to rule out mosaic variegate aneuploidy, Nijmejen syndrome.
Metaphase 18
Metaphase 30
Metaphase 23