Introduction

Diagnostic implementation of oligoarray-based copy number variant (CNV) profiling in patients with intellectual disability and/or developmental delay has identified genomic regions that are recurrently prone to copy number change, as well as sporadic (ie, ‘patient-unique’) gains and losses.1 Recurrent CNVs may be caused by non-allelic homologous recombination (NAHR). NAHR is driven by breakpoint-flanking low copy repeats (LCRs), which comprise 5–6% of the human genome and which can misalign in meiosis due to their sequence homology.2, 3 Genotype–phenotype relationships for such recurrent NAHR-mediated rearrangements have led to the definition of recurrent and syndromic genomic disorders, that is, microdeletion and duplication syndromes.4, 5, 6

Here, we report rare, recurrent 9.4-Mbp deletions occurring de novo in the proximal short arm of chromosome 2. These 2p11.2-2p12 deletion patients show a relatively mild phenotype, despite the large deletion size, with mild-to-moderate intellectual disability, a happy disposition, speech delay and delayed motor development as main features.

Materials and methods

Patients

Patient 1 was clinically evaluated at the age of 15 years and 8 months. He was born preterm after an uncomplicated pregnancy as a dizygotic twin, with a birth weight of 2080 g. The sole clinical phenotype apparent at time of birth was clubfeet. In his early youth, he showed developmental delay with moderate intellectual disability, normal growth parameters and a tendency to obesity. Cognitive assessment showed a verbal IQ of 49 and a performance IQ of 52 at age 9 years. He has a broad nasal bridge, relatively big nose, low set ears and broad dental ridges but no overt facial dysmorphic features. He has hyperreflexia of the lower limbs and a hypotonic habitus as well as a varus deformity of both feet with toeing in and he is incontinent. The boy is of a very friendly disposition. His height at clinical evaluation was 175 cm (∼50th percentile) and his weight was 75 kg (∼80th percentile) and he has a slight tendency to overweight. Patient 2 was evaluated at the age of 5 years and 4 months. He was born after an uncomplicated pregnancy and developmental delay was noticed at 1.5 years of age, with delayed fine motor skills, language impairment and an IQ of 80. He is an easy-going, very friendly child. There were no overt facial dysmorphic features and no growth delay. He was hypermobile with his hands. His height was 114 cm (∼60th percentile) and his weight was 21.9 kg (∼75th percentile).

Cytogenetic investigations and in silico analyses

Genome-wide copy number profiling was done using high-resolution CytoScan HD arrays with 2.7 million markers, according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA, USA). CNVs were called using Chromosome Analysis Suite 1.2.2 Software (Affymetrix). Microarray nomenclature was designated according to HGVS.7 Nucleotide positions were derived from the Genome Reference Consortium build GRCh37 (Ensembl release 68, July 2012). Genomic architecture of LCRs was analysed with the Human Genome Segmental Duplication Database (http://humanparalogy.gs.washington.edu/) based on human genome build 37 (February 2009) and as described previously.8

Results

Microarray analysis of DNA isolated from peripheral blood of both patients 1 and 2 showed a diminished signal for 7368 markers in the proximal short arm of chromosome 2. Thus, they have an identical 9.4-Mbp deletion: chr2.hg19:g.(77,907,115_77,916,761)_(87,322,042_87,330,965)del (Figure 1). Karyotyping of both parents of patient 1 showed that the deletion had occurred de novo. Analysis of informative SNP genotypes in the 2p11.2-2p12 region showed that the deletion had occurred de novo on the maternal chromosome in patient 2 (ie, only the paternal haplotype was present). Finally, metaphase FISH on the available parental blood samples, using probe RP11-301O19 specific for band 2p11.2, excluded balanced insertional translocations.

Figure 1
figure 1

Interstitial deletion 2p11.2→2p12 in patients 1 and 2 as identified by high-resolution Cytoscan HD array. The log2ratio of the hybridisation signal of patient vs references (1.1 and 2.1 for patients 1 and 2, respectively) shows a diminished signal in bands 2p11.2 and 2p12. The ‘allele peak’ analysis track (1.2 and 2.2 for patients 1 and 2, respectively) shows absence of heterozygous calls in the deleted region, whereas three ‘bands’ are seen outside of the deletion, representing homozygous calls (top and bottom bands) and heterozygous calls (middle band).

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The breakpoints of the deletions are flanked by two paired blocks of homologous LCRs, which are in direct orientation relative to each other. The first LCR at the distal breakpoint in band 2p12 (position chr2: 77,894,189–77,901,295) is 7106 bp in size and has 99.50% sequence identity to an LCR block at the proximal breakpoint in 2p11.2, sized 7435 bp (position chr2: 87,338,168–87,345,604). The second LCR block in band 2p12 (chr2: 77,901,296–77,916,981) has 99.23% sequence identity to a 16 114 bp region near the proximal breakpoint of the deletion in band 2p12 (chr2: 87,322,054–87,338,168). Figure 2 gives a schematic representation of the genomic architecture of the LCRs at both breakpoint regions and the genomic localisation of the deletions.

Figure 2
figure 2

Genomic organisation of segmental duplications (Seg dups) flanking the deletion breakpoints in chromosome bands 2p11.2 and 2p12, their orientation and sequence identity. Figure is based on data obtained from UCSC human genome built 37 and from http://humanparalogy.gs.washington.edu/.

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Discussion

We identified identical, recurrent 9.4-Mbp deletions at chromosome bands 2p11.2-2p12, which occurred de novo in two unrelated patients. A very similar deletion was reported recently,9 which has an identical proximal breakpoint (Figure 2). The distal breakpoints differ by a mere 5 kbp, which is within experimental variation of the array. Both breakpoints are directly flanked by two LCR blocks, which have >99% sequence identity and are in same orientation (Figure 2). Such genomic architecture is consistent with an NAHR-mediated rearrangement.2, 3, 4, 5 Owing to their high sequence identity, LCRs can be substrates for meiotic misalignment, in an inter- or intrachromosome or intrachromatid manner, leading to either deletion or duplication of the intervening region.

The clinical phenotype matches with that of other patients with overlapping deletions in proximal 2p (incl. MIM 613564).9, 10, 11, 12 All show mild-to-moderate intellectual disability, a very happy disposition, speech delay, delayed motor development and minor facial anomalies such as high forehead, broad nasal bridge and large low set ears (Table 1). Despite the very large size of the del(2)(p11.2p12), the clinical phenotype is relatively mild when compared generally with similar-sized deletions reported in literature. This fits with previous observations that deletion of the major part of chromosome band 2p12, a gene-poor G-dark band, has minimal phenotypic impact.12 On the basis of the striking phenotypic resemblance of patients, the identical, non-random breakpoints and the presence of highly identical LCR blocks at both breakpoints, we propose here a previously unrecognised, recurrent 2p11.2-2p12 deletion syndrome.

Table 1 Clinical findings in patients with 2p11.2→2p12 deletions presented in this report and in literature
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The deletion includes the REEP1 gene in band 2p11.2. Nonsense variants in REEP1 causing haploinsufficiency/loss of function are responsible for autosomal dominant hereditary spastic paraplegia (HSP)-type SPG31 (OMIM 610250).13, 14 HSP-related features were seen in patient 1, the previous patient with the 9.4-Mbp deletion2 and other patients with REEP1 deletions.10, 11 The age distribution for SPG31 shows a bimodal pattern of <20 and >30 years of age13, 14 leaving a possibility that HSP is not yet manifest in patient 1. Furthermore, most patients with 2p11.2p12 deletion exhibit feet deformities (Table 1), which is also described in patients with REEP1 variants/SPG31.13

Candidate genes for the intellectual disability phenotype are LRRTM1 and CTNNA2. The LRRTM1 protein is part of a trans-synaptic adhesion network involved in axon guidance, synapse formation, synaptic strength regulation and stabilisation of neuronal circuits. LRRTMs have been implicated in neuropsychiatric disorders such as autism and schizophrenia.15, 16, 17 CTNNA2 is a neuronal-specific αN-catenin expressed in the prefrontal cortex. It functions in stabilising synaptic contacts and is a schizophrenia candidate gene.18, 19, 20 Moreover, mouse CTNNA2 knock-outs show defective neuron migration and nuclear organisation.21

Recurrent deletion 2p11.2-2p12 is exceedingly rare, given the very limited literature on this aberration to date.9 Its scarcity may be related to the very large intervening segment that is flanked by the LCRs (Figure 2) as the physical proximity of LCRs may be positively related to the chance of non-allelic synapsis in meiosis.22, 23 The percentage identity of the two misaligning LCRs determines NAHR chance and for the 2p11.2 and 2p12 breakpoint-flanking LCRs this is extremely high (>99% identity). However, the size of the segmentally duplicated LCR sequences is just over 20 kbp in total, which is comparable to LCRs flanking other rare microdeletion syndromes, for example, that at 17q23.1q23.2. However, this is much smaller than the size of LCRs mediating more frequent microdeletion syndromes such as the 22q11 DiGeorge deletion.22, 24 A 2p11.2p12 duplication reciprocal to the deletion is expectable, in similarity with other opposite microdeletions/microduplications.4, 22 Still, 2p11.2-2p12 duplication has not been identified to date in literature or ISCA or DECIPHER databases. Like the deletion presented here, it may be extremely rare.