A case with concurrent duplication, triplication, and uniparental isodisomy at 1q42.12-qter supporting microhomology-mediated break-induced replication model for replicative rearrangements

Abstract

Background: Complex genomic rearrangements (CGRs) consisting of interstitial triplications in conjunction with uniparental isodisomy (isoUPD) have rarely been reported in patients with multiple congenital anomalies (MCA)/intellectual disability (ID). One-ended DNA break repair coupled with microhomology-mediated break-induced replication (MMBIR) has been recently proposed as a possible mechanism giving rise to interstitial copy number gains and distal isoUPD, although only a few cases providing supportive evidence in human congenital diseases with MCA have been documented.

Case presentation: Here, we report on the chromosomal microarray (CMA)-based identification of the first known case with concurrent interstitial duplication at 1q42.12-q42.2 and triplication at 1q42.2-q43 followed by isoUPD for the remainder of chromosome 1q (at 1q43-qter). In distal 1q duplication/triplication overlapping with 1q42.12-q43, variable clinical features have been reported, and our 25-year-old patient with MCA/ID presented with some of these frequently described features. Further analyses including the precise mapping of breakpoint junctions within the CGR in a sequence level suggested that the CGR found in association with isoUPD in our case is a triplication with flanking duplications, characterized as a triplication with a particularly long duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) structure. Because microhomology was observed in both junctions between the triplicated region and the flanking duplicated regions, our case provides supportive evidence for recently proposed replication-based mechanisms, such as MMBIR, underlying the formation of CGRs + isoUPD implicated in chromosomal disorders.

Conclusions: To the best of our knowledge, this is the first case of CGRs + isoUPD observed in 1q and having DUP-TRP/INV-DUP structure with a long proximal duplication, which supports MMBIR-based model for genomic rearrangements. Molecular cytogenetic analyses using CMA containing single-nucleotide polymorphism probes with further analyses of the breakpoint junctions are recommended in cases suspected of having complex chromosomal abnormalities based on discrepancies between clinical and conventional cytogenetic findings.

Keywords: 1q; Breakpoint junction sequence; Chromosomal microarray; Complex genomic rearrangement; DUP-TRP/INV-DUP structure; Microhomology-mediated break-induced replication model; Template switching; Uniparental isodisomy.

Fig. 1

a Chromosome Analysis Suite (ChAS) graphic results of Affymetrix CytoScan HD analysis for the 1q region that presented duplication (DUP), triplication (TRP), or isoUPD in the patient. Detection of CGR and isoUPD were performed using an Affymetrix CytoScan HD CMA platform (Affymetrix), which provides 906,600 polymorphic (SNP) and 946,000 non-polymorphic (CNV) markers, according to the manufacturer’s recommendations. In addition, we used Chromosome Analysis Suite software (ChAS, Affymetrix) to process the raw data, and the output data were interpreted with the UCSC Genome Browser (http://genome.ucsc.edu; GRCh37/hg19 assembly). Top, copy number log2 ratio; bottom, allele peaks. CN, copy number. Possible genotype calls based on the allele dosage normalization algorithm are shown using A and B. The location of each BAC used for FISH analysis is shown. b Images of two-color FISH mapping using six BAC clones and the scheme of distal 1q CGR based on FISH data. Metaphase FISH images with high-magnification images of the distal 1q. BAC clones labeled with either FITC (green) or rhodamine (red) were hybridized to 4’,6-diamidino-2-phenylindole (DAPI)-stained chromosomes of the patient. The location and detailed information of each BAC are shown in Fig. 1a and Additional file 1: Table S1, respectively. In the scheme, arrows indicate the direction of chromosomal fragments I, II (II’, II”), and III, which presented duplication, triplication, and isoUPD, respectively, in CMA. Two junctions (jct 1 and jct2) between fragments II and II’ and between I and II” are also shown. c Color-matched sequence alignment of breakpoint junctions in rearrangements. Top, jct1 (breakpoint junction 1 between segments II and II’); bottom, jct2 (breakpoint junction 2 between segments I and II”) (see Fig. 1b). Microhomology at the junctions is represented by underlined letters. Frequent mismatch sequences were only observed near jct2 within long-range PCR products (data not shown). Thick arrows indicate the possible orientation of chromosomal fragments. Various types of repeat elements observed around junctions are shown

Fig. 2

Replication-based mechanism model for the generation of DUP-TRP/INV-DUP rearrangement followed by isoUPD detected in the present case. a The event probably occurred involving parental homolog chromosomes, P1 and P2. The first template switch (template switch 1) have been triggered by a stalled or collapsed replication fork (fork collapse 1), and used a complementary strand to resume replication through using microhomology in the complementary strand at the annealing site (jct1, Fig. 1c) to prime DNA synthesis, resulting in the production of a segment with the inverse orientation compared with the reference genome. Two putative jct1 sites, jct1 between c and d_c (left) and jct1 between d and c_c, (right) are predicted, because the same sequence result can be obtained in both cases (see Fig. 1c). Then, a new fork stalling or collapsing event (fork collapse 2) have released a free 3’ end that can be resolved by the second template switching (template switch 2) through using the microhomology in the homologous chromosome at the annealing site (jct2, Fig. 1c) to prime and resume DNA synthesis, resulting in the generation of jct2 as well as isoUPD. a–d, representative chromosome alleles in P1 chromosome; a_c–e_c, complementary chromosome alleles in P1 chromosome; A–E: corresponding homologous chromosome alleles in the P2 chromosome. b Top: different genomic structures are predicted to be generated depending on the location of the selected annealing site (jct1) to prime DNA synthesis in the first template switch event. isoUPD will result if the unidirectional replication fork continues until the telomere. Bottom: predicted segmental CNV in a simulated CMA. Note that the small size of the telomeric duplication between fork collapse 1 and jct1 led to the evasion of CMA detection (Fig. 1a), because the region was too small to be detected by Affymetrix Cytoscan HD array