Discovery of a novel CHD7 CHARGE syndrome variant by integrated omics analyses

Abstract

Chromodomain helicase DNA-binding protein 7 (CHD7) pathogenic variants are identified in more than 90% of infants and children with CHARGE (Coloboma of the iris, retina, and/or optic disk; congenital Heart defects, choanal Atresia, Retardation of growth and development, Genital hypoplasia, and characteristic outer and inner Ear anomalies and deafness) syndrome. Approximately, 10% of cases have no known genetic cause identified. We report a male child with clinical features of CHARGE syndrome and nondiagnostic genetic testing that included chromosomal microarray, CHD7 sequencing and deletion/duplication analysis, SEMA3E sequencing, and trio exome and whole-genome sequencing (WGS). We used a comprehensive clinical assessment, genome-wide methylation analysis (GMA), reanalysis of WGS data, and CHD7 RNA studies to discover a novel variant that causes CHD7 haploinsufficiency. The 7-year-old Hispanic male proband has typical phenotypic features of CHARGE syndrome. GMA revealed a CHD7-associated epigenetic signature. Reanalysis of the WGS data with focused bioinformatic analysis of CHD7 detected a novel, de novo 15 base pair deletion in Intron 4 of CHD7 (c.2239-20_2239-6delGTCTTGGGTTTTTGT [NM_017780.3]). Using proband RNA, we confirmed that this novel deletion causes CHD7 haploinsufficiency by disrupting the canonical 3' splice site and introducing a premature stop codon. Integrated genomic, epigenomic, and transcriptome analyses discovered a novel CHD7 variant that causes CHARGE syndrome.

Keywords: CHARGE syndrome; CHD7; epigenetics; exome sequencing; genome sequencing.

Figure 1.

Photograph of the patient. Note low anterior hairline, squared face, low-set CHARGE-like ears, downslanting palpebral fissures, prominent nose.

Figure 2.

Methylation analysis and transcriptional consequence of our patient’s CHD7 variant. (A) Heatmap comparing the genome-wide methylation patterns of controls (green) Vs patients with confirmed CHARGE syndrome (red). The current patient is indicated with a blue arrow. (B) Effect of our patient’s variant in CHD7 splicing. The upper section shows the localization of the intronic deletion (red circle). The middle section details the effects of the deletion as predicted by Alamut and confirmed by RNA studies. The lower section is a schematic representation of the resulting alternative transcript with retained intron 4 sequence and generation of a premature stop codon (red pentagon)