Genetic diagnosis of sibling cases initiated by identification of outlier gene expression using transcriptome analysis of urine-derived cells.

Transcriptome analysis can improve the diagnostic yield for neurodevelopmental disorders. We applied RNA-seq using urine-derived cells (UDCs) to a family with two affected brothers with a muscular dystrophy-dystroglycanopathy and dilated cardiomyopathy. Exome sequencing identified a maternally inherited heterozygous B3GALNT2 splice-site variant (NM_152490.5:c.261-2A>G) but no second pathogenic allele. UDCs RNA-seq with OUTRIDER detected markedly decreased expression of B3GALNT2 in the proband and a milder decrease in the father, suggesting a paternally inherited non-coding variant. Genome sequencing revealed a 357-bp heterozygous deletion encompassing the B3GALNT2 promoter and transcription start site, which segregated with the phenotype. RNA-seq supported aberrant splicing from the splice-site allele and reduction of transcripts from the deletion allele. These findings provide proof of concept that UDCs RNA-seq-guided outlier-expression analysis can identify non-coding second hits and support genetic diagnosis, and they suggest that cardiac surveillance may be warranted in B3GALNT2-related disorder as they age.