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Infantile spasms (IS) is the most common form of catastrophic childhood epilepsies. Above 300 factors are associated with West syndrome, according to the etiology, this syndrome is now classified into two groups, symptomatic and cryptogenic. The aim of this study is to investigate underlying factors in cryptogenic patients with IS. Among 170 IS patients, etiology of 55 cases remain unknown. Array-comparative genomic hybridization (CGH) analysis (G-scanning) was performed on these 55 patients. The array CGH chip data were analyzed using the chromofluor image analysis system (Array Analysis; Macrogen, South Korea). The slides contained 1440 human BAC clones including specific loci of more than 40 chromosomal disorders and 356 cell growth related genes from BAC libraries at a resolution average of 2.3 Mb for the entire genome. Whole-genome array CGH analysis revealed duplications of 2p22p24 and 4q31q32 in two patients, the positive rate is 3.64%. To our knowledge, it’s the first report of these chromosomal abnormalities in IS. Previous study showed that duplication of the 2p23-2pter region is associated with neural tube development, while multiple doses of band 4q32.1 are relatively well-tolerated. The role of duplications of 2p22p24 and 4q31q32 in pathogenesis of IS deserves further study.