Gonadal mosaicism of large terminal de novo duplication and deletion in siblings with variable intellectual disability phenotypes

Abstract

Background: Intellectual disability (ID) is a complex condition that can impact multiple domains of development. The genetic contribution to ID's etiology is significant, with more than 100 implicated genes and loci currently identified. The majority of such variants are rare and de novo genetic mutations.

Methods: We have applied whole-genome microarray to identify large, rare, clinically relevant copy number variants (CNVs). We have applied well-established algorithms for variants call. Quantitative polymerase chain reaction (qPCR) was applied to validate the variants using three technical replicates for each family member. To assess whether the copy number variation was due to balanced translocation or mosaicism, we further conducted droplet digital PCR (ddPCR) on the whole family. We have, as well, applied "critical-exon" mapping, human developmental brain transcriptome, and a database of known associated neurodevelopmental disorder variants to identify candidate genes.

Results: Here we present two siblings who are both impacted by a large terminal duplication and a deletion. Whole-genome microarray revealed an 18.82 megabase (MB) duplication at terminal locus (7q34-q36.3) of chromosome 7 and a 3.90 MB deletion impacting the terminal locus (15q26.3) of chromosome 15. qPCR and ddPCR experiments confirmed the de novo origin of the variants and the co-occurrence of these two de novo events among the siblings, but their absence in both parents, implicates an unbalanced translocation that could have mal-segregated among the siblings or a possible germline mosaicism. These terminal events impact IGF1R, CNTNAP2, and DPP6, shown to be strongly associated with neurodevelopmental disorders. Detailed clinical examination of the siblings revealed the presence of both shared and distinct phenotypic features.

Conclusions: This study identified two large rare terminal de novo events impacting two siblings. Further phenotypic investigation highlights that even in the presence of identical large high penetrant variants, spectrum of clinical features can be different between the siblings.

Keywords: copy number variation; gonadal mosaicism; intellectual disability.

Figure 1

(a) The family pedigree with two affected siblings carrying the terminal de novo deletion and duplication. (b) Physical characteristic showing hypotonia and facial dysmorphism. (c) The probe intensities (−log2 ratio) of the 18.82 megabase (MB) subtelomeric duplication at 7q34‐q36.3 loci and the 3.9 MB deletion at 15q26.3 locus. (d) ddPCR results confirming de novo origin of the two variants. Two probes (targeting MEF2A and CNTNAP2) were used and tested in two technical replicates where label refers as F‐father, P‐proband, S‐affected sibling, M‐mother

Figure 2

(a) The chromosomal location of the candidate genes within the deletion and duplication breakpoint. (b) The boxplot refers to human developmental brain expression (RPKM from RNA‐seq) level of 15 candidate genes. The blue line refers to the average expression level of all genes impacted by the two de novo copy number variants