AB151. CHD7 variants identified by next-generation sequencing

Background: CHARGE syndrome is a genetic disorder with clinical features including ocular coloboma, heart defects, choanal atresia, retardation or developmental delay, genital hypoplasia, ear anomalies and deafness. Mutations in chromodomain helicase DNA binding protein 7 (CHD7) regulatory gene have been associated with this syndrome. CHD7 gene mutations accounted for more than half of patients with CHARGE syndrome. Advancement of next-generation sequencing technologies like the introduction of bench-top next-generation sequencers has enabled cost-effective and accurate detection of mutations in large genes or disorders which are difficult to diagnose clinically. Molecular diagnosis based solely on Sanger sequencing is time consuming and less efficient. The aim of this study was to test the ability of a targeted gene panel and bench-top sequencing to molecularly diagnose patients with CHARGE syndrome.

Methods: Patients with some clinical characteristics of CHARGE syndrome were sequenced using the Haloplex ICCG targeted panel (containing 180 genes including CHD7) on the Ion Torrent PGM. Sequences were mapped to the human reference genome (hg19). Variants were called using the Torrent Variant Caller and annotated using the web-based GeneTalk software (GmbH, Berlin, Germany). Candidate variants that are potentially pathogenic with population frequencies less than 1% were filtered and prioritized for confirmation by Sanger sequencing.

Results: Sanger sequencing confirmed two truncating and three missense heterozygous CDH7 variants in five children. The R2631X and Q201X pathogenic variants have been previously reported in other patients with CHARGE syndrome. Of the missense variants, the G1504E and T1910 variants are novel but the T894A variant has a population frequency of 0.004%. Parental testing and correlation with clinical phenotypes will be helpful in assessing the pathogenicity of these missense CHD7 variants.

Conclusions: Our results indicate that the use of targeted gene panels like the HaloPlex ICCG panel combined with a bench-top sequencer is useful as a cost-effective and rapid screening tool for molecular diagnosis of clinically heterogeneous disorders like CHARGE syndrome.

Keywords: CHARGE syndrome; CHD7; targeted gene sequencing; Haloplex ICCG targeted panel; Ion Torrent PGM