Copy number variations in Saudi family with intellectual disability and epilepsy

Abstract

Background: Epilepsy is genetically complex but common brain disorder of the world affecting millions of people with almost of all age groups. Novel Copy number variations (CNVs) are considered as important reason for the numerous neurodevelopmental disorders along with intellectual disability and epilepsy. DNA array based studies contribute to explain a more severe clinical presentation of the disease but interoperation of many detected CNVs are still challenging.

Results: In order to study novel CNVs with epilepsy related genes in Saudi family with six affected and two normal individuals with several forms of epileptic seizures, intellectual disability (ID), and minor dysmorphism, we performed the high density whole genome Agilent sure print G3 Hmn CGH 2x 400 K array-CGH chips analysis. Our results showed de novo deletions, duplications and deletion plus duplication on differential chromosomal regions in the affected individuals that were not shown in the normal fathe and normal kids by using Agilent CytoGenomics 3.0.6.6 softwear. Copy number gain were observed in the chromosome 1, 16 and 22 with LCE3C, HPR, GSTT2, GSTTP2, DDT and DDTL genes respectively whereas the deletions observed in the chromosomal regions 8p23-p21 (4303127-4337759) and the potential gene in this region is CSMD1 (OMIM: 612279). Moreover, the array CGH results deletions and duplication were also validated by using primer design of deleted regions utilizing the flanked SNPs using simple PCR and also by using quantitative real time PCR.

Conclusions: We found some of the de novo deletions and duplication in our study in Saudi family with intellectual disability and epilepsy. Our results suggest that array-CGH should be used as a first line of genetic test for epilepsy except there is a strong indication for a monogenic syndrome. The advanced high through put array-CGH technique used in this study aim to collect the data base and to identify new mechanisms describing epileptic disorder, may help to improve the clinical management of individual cases in decreasing the burden of epilepsy in Saudi Arabia.

Keywords: Array-CGH; CNVs; Epilepsy; Intellectual disability; Saudi population.

Fig. 1

A consanguineous family pedigree from Saudi Arabia with intellectual disability and epilepsy. The available samples for microarray and validation study are marked with asterisks

Fig. 2

Array-CGH profiles analysis using Agilent CytoGenomic Analytics software (V.3.0.6.6) showing the deletion. Zero value indicates equal fluorescence intensity ratio between the sample and reference. Copy number losses shifted the ratio toward left (red), whereas copy number gains towards the right side (blue). CNV deletions observed in the chromosomal regions 8p23-p21 in four affected members of the family starts from 4,303,127 end 4,337,759 and the potential gene in this region is CSMD1 (OMIM: 612279)

Fig. 3

Confirmation of deleted and gained CNVs region by using qPCR analysis. The results have shown CSMD1gene copy number deletions in the mother and three affected member of the family showed significant fold change as compared to the control

Fig. 4

a Array-CGH profiles analysis using Agilent CytoGenomic Analytics software (V.3.0.6.6). Zero value indicates equal fluorescence intensity ratio between the sample and reference. Copy number losses shifted the ratio toward left (red) whereas copy number gains towards the right side (blue). CNVs gain at chromosome 1 starts from 150,819,879–150,819,938 cytoband 1q21.3 in the four affected members of the family and the potential gene in this region is LCE3C. b Our results showed the gain at chromosome 16 that starts from 70,647,078–70,669,681 cytoband 16q22.2 in our all four affected members of the family and the potential gene in this region is HPR gene. c Our results showed gain at chromosome 22 starts 22,686,690–22,735,300 cytoband 22q11.23 and the potential gene cluster in this region are GSTT1, GSTTP2, GSTT2B, GSTT2, DDT, and DDTL in all affected members of the family

Fig. 5

a, b, c Confirmation of CNVs by qPCR have shown a significant fold increase in a LCE3C, b HPR, and c GSTT2 gene copy number in the patients of the family member as compared to the healthy individuals