There isn't any difference in the way the cytogenetic analysis has to be performed, whether it is Downs or any other syndrome. You have to follow your routine optimized protocol.
One of the protocol- Rooney and Czepulkowski method:
One milliliter of sodium-heparinized whole blood was collected from each patient and control individual. A blood sample of 0.5 cm3 from each patient and control individual was added to 5 cm3 of a complete media containing Roswell Park Memorial Institute (RPMI) 1640, fetal calf serum (10%), phytohaemoagglutinin (PHA) (10 μg/ml), L-glutamate (2 mM), penicillin (200 unit/ml), and gentamicin (50 μg/ml). After 72 h of incubation at 37°C, colcemid was added (0.2 μg/ml). After 90 min, the cells were harvested by centrifugation (150 × g for 10 min). Then, 5 ml of 0.075 M KCl solution was added and mixed and incubated at 37°C for 90 min. After centrifugation (150 × g for 10 min), hypotonic supernatant was removed. Then, 5 cm3 of cold, fresh fixative solution (3:1 methanol–acetic acid) was added dropwise to the cell pellet. Centrifugation was done afterward, and the supernatant was removed. These last two steps were repeated until a clear pellet was obtained. Finally, cells obtained were dropped on distinct slides. Staining with Giemsa was performed for some of the slides prepared from each patient. Fifty metaphases, each cultured on both the patients and the normal controls, were analyzed.
We performed a similar protocol, but treatment with potassium chloride to hypotonic shock applies only for 20 minutes to obtain satisfactory results. The use of pre-moistened slides with cold methanol promotes quality extensions.