Objective: Congenital anomalies of the kidneys and urinary tract (CAKUT) are frequently associated with malformations of other organ systems. In a high number of cases the aetiology of maldevelopment remains unexplained. Array-based comparative genomic hybridisation (CGH) was tested to determine the detection rate of genomic microimbalances in these patients.

Methods: We analysed DNA samples of 30 unexplained CAKUT patients affected by at least one additional relevant extrarenal symptom using the genome-wide screening technology array CGH. Subsequently, results were verified by fluorescence in situ hybridisation (FISH) analysis in both patients’ and parental samples.

Results: Two of 30 patients presented microimbalances in array CGH analysis, confirmed by FISH analysis. Patient A showed a de novo microdeletion in 3q (3q23–q24), patient B an unbalanced translocation (46,XY, der(1)t(1;16)(q44;q23.3) with partial monosomy of 1q44 and trisomy of bands 16q23.3 to 16q24.3. Clinically, patient A was affected by a multicystic-dysplastic kidney associated with mental retardation, microcephalus, growth retardation and multiple joint contractions. Patient B presented with microhaematuria, hypospadia, eye anomalies, cleft palate, auricular fistula, laryngomalacia, mental retardation and corpus callosum agenesis.

Conclusion: The identification of these microimbalances allowed the restriction of the critical interval harbouring possible causative genes. In total, the results demonstrate that array CGH is a promising approach to identify a genetic origin in a subset of patients affected by congenital complex malformations.