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

TitleInterchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome.
Publication TypeJournal Article
Year of Publication2019
AuthorsCarvalho, CMB, Coban-Akdemir, Z, Hijazi, H, Yuan, B, Pendleton, M, Harrington, E, Beaulaurier, J, Juul, S, Turner, DJ, Kanchi, RS, Jhangiani, SN, Muzny, DM, Gibbs, RA, Stankiewicz, P, Belmont, JW, Shaw, CA, Cheung, SWai, Hanchard, NA, V Sutton, R, Bader, PI, Lupski, JR
Corporate AuthorsBaylor-Hopkins Center for Mendelian Genomics
JournalGenome Med
Date Published2019 Apr 23
KeywordsChromosome Aberrations, Chromosome Disorders, Chromosomes, Human, Pair 14, DNA Methylation, DNA Replication, Genomic Imprinting, Humans, Male, Pedigree, Phenotype, Polymorphism, Single Nucleotide, Young Adult

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.

Alternate JournalGenome Med
PubMed ID31014393
PubMed Central IDPMC6480824
Grant ListR03 HD092569 / HD / NICHD NIH HHS / United States
R35 NS105078 / NS / NINDS NIH HHS / United States
U54 HD083092 / HD / NICHD NIH HHS / United States
UM1 HG006542 / HG / NHGRI NIH HHS / United States

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