The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation

BackgroundThe multiplede novocopy number variant (MdnCNV) phenotype is described by having four or more constitutionalde novoCNVs (dnCNVs) arising independently throughout the human genome within one generation. It is a rare peri-zygotic mutational event, previously reported to be seen once in every 12,000 individuals referred for genome-wide chromosomal microarray analysis due to congenital abnormalities. These rare families provide a unique opportunity to understand the genetic factors of peri-zygotic genome instability and the impact ofdnCNV on human diseases.MethodsChromosomal microarray analysis (CMA), array-based comparative genomic hybridization, short- and long-read genome sequencing (GS) were performed on the newly identified MdnCNV family to identifyde novomutations includingdnCNVs,de novosingle-nucleotide variants (dnSNVs), and indels. Short-read GS was performed on four previously published MdnCNV families fordnSNV analysis. Trio-based rare variant analysis was performed on the newly identified individual and four previously published MdnCNV families to identify potential genetic etiologies contributing to the peri-zygotic genomic instability. Lin semantic similarity scores informed quantitative human phenotype ontology analysis on three MdnCNV families to identify gene(s) driving or contributing to the clinical phenotype.ResultsIn the newly identified MdnCNV case, we revealed eightde novotandem duplications, each ~ 1 Mb, with microhomology at 6/8 breakpoint junctions. Enrichment ofde novosingle-nucleotide variants (SNV; 6/79) andde novoindels (1/12) was found within 4 Mb of thednCNV genomic regions. An elevated post-zygotic SNV mutation rate was observed in MdnCNV families. Maternal rare variant analyses identified three genes in distinct families that may contribute to the MdnCNV phenomenon. Phenotype analysis suggests that gene(s) withindnCNV regions contribute to the observed proband phenotype in 3/3 cases. CNVs in two cases, a contiguous gene duplication encompassingPMP22andRAI1and another duplication affectingNSD1andSMARCC2, contribute to the clinically observed phenotypic manifestations.ConclusionsCharacteristic features ofdnCNVs reported here are consistent with a microhomology-mediated break-induced replication (MMBIR)-driven mechanism during the peri-zygotic period. Maternal genetic variants in DNA repair genes potentially contribute to peri-zygotic genomic instability. Variable phenotypic features were observed across a cohort of three MdnCNV probands, and computational quantitative phenotyping revealed that two out of three had evidence for the contribution of more than one genetic locus to the proband’s phenotype supporting the hypothesis ofde novomultilocus pathogenic variation (MPV) in those families.