407 Next generation sequencing approaches identify a novel Alu recombination-mediated large intronic deletion in CDH3 in a family with hypotrichosis with juvenile macular dystrophy (HJMD)

Abstract

HJMD is an autosomal recessive disorder characterized by abnormal growth of scalp hair and late-onset macular degeneration leading to blindness. In this study, we have explored the genetic basis of HJMD in a large consanguineous family. In 10 affected patients, 1-76 years of age, the diagnosis was confirmed by eye examination that established macular degeneration and late-onset loss of visual acuity. We first applied genome-wide homozygosity mapping to 10 affected individuals for linkage analysis to identify the genomic region of the defective gene. All affected individuals shared a 7.2 Mb region of homozygosity (ROH) on chromosome 16q21-22.3, which harbored 298 genes, including CDH3, the gene previously associated with HJMD. However, whole exome sequencing failed to identify the causative mutation in CDH3. Further investigation revealed a missense variant in a closely linked gene (1.4 Mb distance: FHOD1: c.1306A→G, p.Arg436Gly). This variant was homozygous in all affected individuals and was heterozygous in 18 out of 19 obligate carriers. While this variant was found by bioinformatics predictions to be likely pathogenic, a knock-in mouse for this variant, made by the CRISPR/Cas, showed no disease phenotype. Subsequently, whole transcriptome profiling by RNA-Seq of the expression level of all 298 genes within the 7.2 Mb ROH revealed that CDH3 gene expression level was significantly reduced. Using whole genome sequencing, we were able to identify a novel Alu recombination-mediated deletion in CDH3:c.del161-811_246+1044. In conclusion, whole genome and whole transcriptome sequencing techniques were able to identify a deep intronic genomic deletion mutation, which was not detected by whole exome sequencing.