Concurrent triplication and uniparental isodisomy: evidence for microhomology-mediated break-induced replication model for genomic rearrangements

Abstract

Whole-genome oligonucleotide single-nucleotide polymorphism (oligo-SNP) arrays enable simultaneous interrogation of copy number variations (CNVs), copy neutral regions of homozygosity (ROH) and uniparental disomy (UPD). Structural variation in the human genome contributes significantly to genetic variation, and often has deleterious effects leading to disease causation. Co-occurrence of CNV and regions of allelic homozygosity in tandem involving the same chromosomal arm are extremely rare. Replication-based mechanisms such as microhomology-mediated break-induced replication (MMBIR) are recent models predicted to induce structural rearrangements and gene dosage aberrations; however, supportive evidence in humans for oneended DNA break repair coupled with MMBIR giving rise to interstitial copy number gains and distal loss of heterozygosity has not been documented. We report on the identification and characterization of two cases with interstitial triplication followed by uniparental isodisomy (isoUPD) for remainder of the chromosomal arm. Case 1 has a triplication at 9q21.11-q21.33 and segmental paternal isoUPD for 9q21.33-qter, and presented with citrullinemia with a homozygous mutation in the argininosuccinate synthetase gene (ASS1 at 9q34.1). Case 2 has a triplication at 22q12.1-q12.2 and segmental maternal isoUPD 22q12.2-qter, and presented with hearing loss, mild dysmorphic features and bilateral iris coloboma. Interstitial triplication coupled with distal segmental isoUPD is a novel finding that provides human evidence for one-ended DNA break and replication-mediated repair. Both copy number gains and isoUPD may contribute to the phenotype. Significantly, these cases represent the first detailed genomic analysis that provides support for a MMBIR mechanism inducing copy number gains and segmental isoUPD in tandem.

Mechanisms underlying structural variant formation in genomic disorders

“…The emerging picture is a perplexing fractal: large genomic-scale structural variants, that is, alterations involving megabases of DNA, can be associated with additional complexities, such as other structural variants that are generated in a one-off event (chromoanasynthesis and chromothripsis-like events (FIG. 5a)) 8,9 or a CGR accompanied by AOH 11,12 . Further alterations might be revealed when these structural variants are scrutinized down to the base-pair sequence level owing to the presence of small-scale changes that can act as mutational signatures, for example, insertions or deletions of short DNA segments and/or de novo point mutations that are present adjacent to the junction of a structural variant 10,106,128,143 (FIG.…”

“…For example, CNVs and SNVs can be generated concomitantly 10 , and SNVs created during mutagenic repair can potentially affect the function of genes that do not map within the CNV. Also, CNVs can be followed by extended regions of absence of heterozygosity (AOH) 11,12 . If the AOH that is generated from template switching between homologues versus sister chromatids occurs at an imprinted locus, disease can result.…”

Absence of Heterozygosity Due to Template Switching during Replicative Rearrangements

“…Occurrence of complex genomic rearrangements (CGRs) associated with an extended segment of UPD has been recently reported, [7][8][9] but the underlying molecular mechanism has remained elusive. We speculate that the previous lack of such CGR þ AOH observations is due to the absence of genomic visualization of such potential events prior to the recent introduction of high-resolution microarrays with genome-wide coverage and the capacity to resolve CNVs and genotype SNPs in the same experimental assay.…”

Concurrent Loss of Heterozygosity and Mosaic Deletion of 12p13.32pter

“…The main steps of this model include invasion of a single segment of the broken double strand in a sister chromatid replication fork or a homologous chromosome chromatid. The invasion and hybridization in the homologous chromosome, instead of the sister chromatid, may result in LOH [Sahoo et al, 2015]. Many deletion cases associated with extensive LOH were reported in cells of patients with acute lymphoblastic leukemia [Mullighan et al, 2007].…”

“…Many deletion cases associated with extensive LOH were reported in cells of patients with acute lymphoblastic leukemia [Mullighan et al, 2007]. Sahoo et al [2015] identified and characterized 2 cases of interstitial triplication followed by LOH, the first detailed genomic analysis providing support for an MMBIR mechanism, inducing gains in copy number with tandem uniparental isodisomy. Zhang et al [2009] also proposed that the DNA FoSTeS/MMBIR replication mechanism is capable of producing complex rearrangements.…”