A familial inverted duplication/deletion of 2p25.1-25.3 provides new clues on the genesis of inverted duplications

Abstract

We studied a family in which the same 10 Mb inverted duplication of 2p25.3-p25.1 segregates in two children and their father, all showing a trisomy phenotype. As FISH analysis demonstrated that the duplication was inverted, we suspected that a contiguous terminal deletion was also present, according to the classical inv dup del type of rearrangements. Although FISH with 2p and 2q subtelomeric probes gave normal results, 100 kb resolution array-C/GH (aCGH) showed that, beside the duplication, a 273 kb deletion was also present. The presence of a single-copy region between the deleted and duplicated regions was further suspected through high-resolution aCGH analysis (approximately 20 kb), although only one informative spot having a normal log ratio was detected. The precise structure of the rearrangement was re-defined by real-time PCR and breakpoint cloning, demonstrating the presence of a 2680 bp single-copy sequence between deleted and duplicated regions and the involvement of a simple repeat with the potential for forming a non-B DNA structure. The rearrangement was not mediated by segmental duplications or short inverted repeats, and the double-strand break might have been repaired by non-homologous end joining or microhomology-mediated intrastrand repair. These data highlight the fact that concomitant deletions associated with inverted duplications are very likely to be more frequent than classical cytogenetic methods alone have been able to demonstrate. The phenotypic effects of the trisomy and of the terminal 2p deletion are discussed.

Figure 1

Overview of molecular data from Case 2. Identical results were obtained on Case 1 and Case 3. (a) Cytogenetics and FISH results. (from left) cut-out of the normal and abnormal chromosomes 2 in G-banding at a resolution of 550 bands. Ideogram of normal and inverted duplicated chromosomes 2p: th 2p25.3 and 2p25.1 bands are depicted in green and red, respectively. The dots represent BAC clones RP11-90H11 (2p25.3, green dot) and RP11-1B18 (2p25.1, red dot). Double-colour FISH with BACs RP11-90H11 (green signal) and RP11-1B18 (red signal): the normal chromosome 2 (arrow) has two signals. The order of red and green signals in the dup(2) (arrowhead) demonstrates that the duplication is inverted (a.1). FISH with subtelomeric 2p probe (green signal) and 2q (red signal) (Vysis) showed hybridization signals on both normal (arrow) and invdup (arrowhed) chromosome 2 (a.2). (b) Array-CGH (aCGH) analysis. aCGH profile of chromosome 2 showing the deletion/duplication at 2p25.3–25.1. Enlargement of the deleted and duplicated regions (b.2). On the right, detailed view of deletion/duplication boundary. The arrow points to a single probe with a log ratio of +0.2 located between the deleted and duplicated regions (b.3). (c) Detail of the breakpoint region on chromosome 2p. The deletion is shown in red, the duplication in green, the single-copy region in blue. The locations of the breakpoints (black triangles), aCGH (circles) and real-time (vertical arrows) probes, and long-range PCR primers (horizontal arrows) are indicated. The positions of the LOC285016 gene and of a CpG island (gray box) containing several repetitive elements (dark gray boxes) are also shown. (d) Real-time PCR results. Average Relative Quantification (RQ) by real-time PCR of Cases 1–3 (P) and three normal controls (c). (e) Sequence of the breakpoints. The CG dinucleotide representing the only homology between the two breakpoints is highlighted in bold.

Figure 2

(a) Schematic representation of the deleted/duplicated region in our patients. Screenshot obtained from http://genome.ucsc.edu, UCSC Genome Browser on Human May 2004 Assembly. The upper part of the figure shows the idiogram of chromosome 2, in which the aberrant region is indicated by a grey square^*. The deletion of 273 kb is indicated by the two vertical grey lines^** and pointed by a black arrowhead. The duplicated region of 10 Mb is shown by a black square. (b) Structure of the rearrangement and comparison with other recently described 2p rearrangements. Deleted regions are indicated by lines, duplicated regions by boxes. ^*Red square in the html version, ^**green lines in the html version.