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BMC Genomics

Open Access

Microarray based comparative genome hybridization detects genomic imbalances deletions and duplications in different epileptic patients of Saudi Arabia

  • Muhammad Imran Naseer1Email author,
  • Muhammad Faheem2,
  • Maha Mohsin Al-Quaiti1,
  • Adeel G. Chaudhary1,
  • Nobutaka Hirokawa3 and
  • Mohammed H. Al-Qahtani1
BMC Genomics201415(Suppl 2):P49

Published: 2 April 2014


Chromosomal RegionCopy Number VariantChromosomal AberrationComparative Genome HybridizationEpileptic Patient


Epilepsy is genetically complex neurological disorder affecting millions of people of different age groups varying in its type and severity. Copy number variants (CNVs) are the key players in the genetic etiology of numerous neurodevelopmental disorders and prior findings also revealed that chromosomal aberrations are more susceptible against the pathogenesis of epilepsy [1].

Materials and methods

We performed genome wide study of CNVs in epileptic patients by using high density array comparative genome hybridization (CGH) technology for the identification of novel chromosomal aberrations. For this purpose, a cohort of 60 patients suffering with epileptic disorders was recruited. Investigation by array CGH was done for the detection of their chromosomal aberrations. The attained results were analyzed by microarray data analysis software PARTEK and the novelty of CNVs was checked by using Database of Genomic Variants (DGV). Furthermore, array CGH results amplification and deletions were confirmed by quantitative real time PCR.


Our results showed CNVs including the amplifications, deletions and amplifications plus deletions in different chromosomal regions in the patients. Amplifications were observed in the chromosomal regions 1p21.3, 2p21, 5p14.3, 5q23.2, 6p12.1, 7p15.2, 19p13.13 respectively whereas the deletions were observed in the chromosomal regions 5p14.3, 7q32.3, 19p13.13 respectively. Amplifications plus deletions were observed in 5p14.3, 19p13.13. Moreover, the array CGH results were also validated by quantitative real time PCR.


Finally, we found some of novel genes in our study for the first time in Saudi population. Further analysis of the observed deleted and duplicated genes by array CGH were confirmed by using quantitative real time PCR. Hence, it is recommended that array CGH as well as quantitative real time PCR can be used for screening of novel epileptic genes. These advanced approaches used in this study for the first time aims to identify novel mechanisms underlying epileptic disorder, which can help to improve the clinical management of individual cases in lowering the burden of epilepsy in Saudi Arabia.

Authors’ Affiliations

Center of Excellence In Genomic Medicine and Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
Department of Cell Biology and Anatomy, and Molecular Structure and Dynamics, University of Tokyo, Japan


  1. Hye SK, Sung VY, Kyung HJ, Long TZ, Young HK, Kweon HL, Seung YC, Hyoung KR: Altered DNA copy number in patients with different seizure disorder type By array-CGH. Brain Dev. 2007, 29: 639-643.View ArticleGoogle Scholar


© Naseer et al; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.