Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome

Abstract

Background Intrachromosomal triplications (TRP) can contribute to disease etiology via gene dosage effects, gene disruption, position effects, or fusion gene formation. Recently, post-zygotic de novo triplications adjacent to copy-number neutral genomic intervals with runs of homozygosity (ROH) have been shown to result in uniparental isodisomy (UPD). The genomic structure of these complex genomic rearrangements (CGRs) shows a consistent pattern of an inverted triplication flanked by duplications (DUP-TRP/INV-DUP) formed by an iterative DNA replisome template-switching mechanism during replicative repair of a single-ended, double-stranded DNA (seDNA), the ROH results from an interhomolog or nonsister chromatid template switch. It has been postulated that these CGRs may lead to genetic abnormalities in carriers due to dosage-sensitive genes mapping within the copy-number variant regions, homozygosity for alleles at a locus causing an autosomal recessive (AR) disease trait within the ROH region, or imprinting-associated diseases. Methods Here, we report a family wherein the affected subject carries a de novo 2.2-Mb TRP followed by 42.2 Mb of ROH and manifests clinical features overlapping with those observed in association with chromosome 14 maternal UPD (UPD(14)mat). UPD(14)mat can cause clinical phenotypic features enabling a diagnosis of Temple syndrome. This CGR was then molecularly characterized by high-density custom aCGH, genome-wide single-nucleotide polymorphism (SNP) and methylation arrays, exome sequencing (ES), and the Oxford Nanopore long-read sequencing technology. Results We confirmed the postulated DUP-TRP/INV-DUP structure by multiple orthogonal genomic technologies in the proband. The methylation status of known differentially methylated regions (DMRs) on chromosome 14 revealed that the subject shows the typical methylation pattern of UPD(14)mat. Consistent with these molecular findings, the clinical features overlap with those observed in Temple syndrome, including speech delay. Conclusions These data provide experimental evidence that, in humans, triplication can lead to segmental UPD and imprinting disease. Importantly, genotype/phenotype analyses further reveal how a post-zygotically generated complex structural variant, resulting from a replication-based mutational mechanism, contributes to expanding the clinical phenotype of known genetic syndromes. Mechanistically, such events can distort transmission genetics resulting in homozygosity at a locus for which only one parent is a carrier as well as cause imprinting diseases. Electronic supplementary material The online version of this article (10.1186/s13073-019-0633-y) contains supplementary material, which is available to authorized users.

Centers for Mendelian Genomics: A decade of facilitating gene discovery

“…Examples include utilizing genome sequencing to identify pathogenic SVs missed by exome, such as the homozygous inversion in QDPR detected in a patient with dihydropteridine reductase deficiency; 52 applying RNA sequencing to identify genes with aberrant expression and or splicing, including an intronic variant in trans with a missense in muscle disease gene DES that resulted in a pseudo-exon insertion and allelic imbalance; 53 using bisulfite sequencing to identify gene silencing epivariation, such as the characterization of aberrant hypermethylation associated with a pathogenic repeat expansion in the XYLT1 promoter region; 54 and the application of long-read sequencing to characterize a complex genomic rearrangement involving an inverted triplication flanked by duplications in a proband with Temple syndrome. 55 The challenges with interpreting rare variation in the genome is a major barrier for achieving genetic diagnoses. To this end, CMGs investigators have built resources and tools to improve variant interpretation.…”

DNA Methylation in the Diagnosis of Monogenic Diseases

“…These lesions lead to overexpression of the paternally expressed genes and expression loss of DLK1 [58]. Recently, intrachromosomal triplications with runs of homozygosity (rare, postzygotic events, with undetectable mosaicism rate) have been reported as a potential mechanism causing segmental uniparental disomy in TS [59]. Mosaicisms occur in about 50% of cases.…”

Cytogenetically visible inversions are formed by multiple molecular mechanisms

“…In the cytogenetic world, inversions are classically defined as a balanced chromosomal rearrangements, that is, no gain or loss of genomic material is assumed to accompany their generation (Figure 1, left). However, smaller inversions, both unique and nonunique, forming together with kb or Mb size genomic amplifications and deletions can constitute 20%-30% of SVs in certain disease loci, challenging the copy-number neutral inversion model (Beck et al, 2015;Brand et al, 2015;Carvalho et al, 2019Carvalho et al, , 2013Carvalho et al, , 2015Carvalho et al, , 2011Figure 1, right). Supporting the observation in disease cohorts, population studies using NGS revealed that truly balanced inversions constitute a smaller fraction of the total inversions detected.…”