BACKGROUND & OBJECTIVES: Microdeletion syndromes are characterized by small (<5 
Mb) chromosomal deletions in which one or more genes are involved. These are 
frequently associated with multiple congenital anomalies. The phenotype is the 
result of haploinsufficiency of genes in the critical interval. Fluorescence in 
situ hybridization (FISH) technique is commonly used for precise genetic 
diagnosis of microdeletion syndromes. This study was conducted to assess the 
role of FISH in the diagnosis of suspected microdeletion syndrome.
METHODS: FISH was carried out on 301 clinically suspected microdeletion syndrome 
cases for the confirmation of clinical diagnosis using non-commercial probes. Of 
these, 177 cases were referred for 22q11.2 microdeletion, 42 cases were referred 
for William syndrome, 38 cases were referred for Prader Willi/Angelman and 44 
cases were referred for other suspected microdeletion syndromes.
RESULTS: FISH was confirmatory in 23 cases only (7.6%). There were 17 cases of 
22q11.2 microdeletion, four cases of Prader Willi syndrome and two cases of 
William syndrome.
INTERPRETATION & CONCLUSION: We conclude that FISH should not be the method of 
choice for clinically suspected microdeletion syndromes. We propose to follow 
strict clinical criteria for FISH testing or preferably to follow better methods 
(genotype first approach). Whole genome screening may be used as first line of 
test and FISH may be used for confirmation of screening result, screening of 
family members and prenatal diagnosis.