22q11.2 distal deletion: a recurrent genomic disorder distinct from DiGeorge syndrome and velocardiofacial syndrome

Abstract

Microdeletions within chromosome 22q11.2 cause a variable phenotype, including DiGeorge syndrome (DGS) and velocardiofacial syndrome (VCFS). About 97% of patients with DGS/VCFS have either a common recurrent approximately 3 Mb deletion or a smaller, less common, approximately 1.5 Mb nested deletion. Both deletions apparently occur as a result of homologous recombination between nonallelic flanking low-copy repeat (LCR) sequences located in 22q11.2. Interestingly, although eight different LCRs are located in proximal 22q, only a few cases of atypical deletions utilizing alternative LCRs have been described. Using array-based comparative genomic hybridization (CGH) analysis, we have detected six unrelated cases of deletions that are within 22q11.2 and are located distal to the approximately 3 Mb common deletion region. Further analyses revealed that the rearrangements had clustered breakpoints and either a approximately 1.4 Mb or approximately 2.1 Mb recurrent deletion flanked proximally by LCR22-4 and distally by either LCR22-5 or LCR22-6, respectively. Parental fluorescence in situ hybridization (FISH) analyses revealed that none of the available parents (11 out of 12 were available) had the deletion, indicating de novo events. All patients presented with characteristic facial dysmorphic features. A history of prematurity, prenatal and postnatal growth delay, developmental delay, and mild skeletal abnormalities was prevalent among the patients. Two patients were found to have a cardiovascular malformation, one had truncus arteriosus, and another had a bicuspid aortic valve. A single patient had a cleft palate. We conclude that distal deletions of chromosome 22q11.2 between LCR22-4 and LCR22-6, although they share some characteristic features with DGS/VCFS, represent a novel genomic disorder distinct genomically and clinically from the well-known DGS/VCF deletion syndromes.

Figure 1

Schematic Overview of the 22q11.2 Region Numbers below the schematic represent distance (million base units) from the 22p telomere according to NCBI human genome build 36 (2006). LCRs are depicted as gray boxes and labeled according to their number. LCR22-7 and LCR22-8 are located telomeric to the scheme and are not shown. The BAC clones that are included in the array-based CGH are depicted as horizontal black lines. Boxes below the map depict the typical deletions in DGS/VCFS and the different distal deletions reported in patients by this study and in previous reports (ref.). Note that exact deletion borders are sometimes only estimated in previously reported cases as well as in patient 3.

Figure 2

Array-CGH and FISH Findings among Patients and Their Parents (A) Representative array-CGH output. The mean normalized log2(Cy3/Cy5) ratio of each BAC is plotted on the x axis as dots with error bars and arranged along the vertical axis from chromosome 1 at the top to chromosomes X and Y at the bottom. Decreased copy number was identified for two BAC clones, RP11-36N5 and 296H20 (marked by a red ellipse to the left of the vertical axis), which map between LCR22-4 and LCR22-5 on chromosome 22q11.2, just distal to the telomeric end of the common DGS/VCFS ∼3 Mb deletion. (B) Representative FISH analysis of deletion case. The two red fluorescence signals represent hybridization using a subtelomeric chromosome 22q FISH probe, and the single green signal represents the hybridization of the RP11-36N5 clone to the normal (nondeleted) chromosome 22. Deletions were confirmed by FISH analyses in all the cases. (C and D) Representative FISH analyses of normal parents. Metaphase FISH analysis using the same probes detected two normal copies of the distal 22q11.2 probe among the parents.

Figure 3

Facial Appearance of Patients with 22q11.2 Distal Deletions Shared facial dysmorphic features include arched eyebrows, flattened midface, smooth philtrum, and thin upper lip. (A) Patient 1, whose ∼2.1 Mb deletion extends from LCR22-4 through LCR22-6. Note the arched eyebrows and the smooth philtrum. This patient also has sex-chromosome aneuploidy with 47,XYY karyotype. (B and C) Patient 2, with ∼2.1 Mb deletion. Note the low-set, cuboidal ears, hypoplastic browridges, broad nasal bridge, smooth philtrum, and pointed chin. (D) Patient 5, whose ∼1.4 Mb deletion extends from LCR 22-4 through LCR22-5. Note the pointed chin in addition to partial ptosis. (E and F) Patient 6, with ∼1.4 Mb deletion. Note the arched eyebrows, hypoplastic browridges, smooth philtrum, and flat retracted midface.

Figure 4

Analysis of 22q11.2-Distal-Deletion Breakpoints by High-Resolution Oligonucleotide Microarray Analysis Results of Agilent 244K array-based oligonucleotide CGH performed on DNA samples from patients 1, 2, and 5 and 6 revealed similar proximal breakpoints in all of the cases. Red arrows represent the known LCR22s in the region. Black horizontal lines represent the different breakpoints, and the numbers represent genomic distance of the different breakpoints (Megabase units) from 22p telomere according to NCBI human genome build 36 (2006). Note that the proximal breakpoint is common in all of the cases, and the distal breakpoints also coincide for patients 1 and 2 and patients 5 and 6, respectively. The breakpoints are located in the known LCR22s, implying NAHR-based recombination mechanism.