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Background  The overall birth prevalence for congenital malformations of the central nervous system (CNS) among Europeans may be as high as 1 in 100 live births. The etiological factors remain largely unknown. The aim of this study was to detect causative copy number variations (CNVs) in fetuses of terminated pregnancies with prenatally detected isolated brain malformations.    Methods  Array-based molecular karyotyping was performed in a cohort of 35 terminated fetuses with isolated CNS malformations. Identified putative disease-causing CNVs were confirmed using quantitative polymerase chain reaction or multiplex ligation-dependent probe amplification.    Results  Based on their de novo occurrence and/or their established association with congenital brain malformations, we detected five disease-causing CNVs in four fetuses involving chromosomal regions 6p25.1-6p25.3 ( FOXC1 ), 6q27, 16p12.3, Xp22.2-Xp22.32 ( MID1 ), and Xp22.32-Xp22.33. Furthermore, we detected a probably disease-causing CNV involving chromosomal region 3p26.3 in one fetus, and in addition, we detected 12 CNVs in nine fetuses of unknown clinical significance. All CNVs except for two were absent in 1307 healthy in-house controls (frequency <0.0008). Each of the two CNVs present in in-house controls was present only once (frequency = 0.0008). Furthermore, our data suggests the involvement of  CNTN6  and  KLHL15  in the etiology of agenesis of the corpus callosum, the involvement of  RASD1  and  PTPRD  in Dandy-Walker malformation, and the involvement of  ERMARD  in ventriculomegaly.    Conclusions  Our study suggests that CNVs play an important role in the etiology of isolated brain malformations.

Array-based molecular karyotyping in fetuses with isolated brain malformations identifies disease-causing CNVs