A recurrent deletion on chromosome 2q13 is associated with developmental delay and mild facial dysmorphisms
- Eva Hladilkova†1, 2,
- Tuva Barøy†1,
- Madeleine Fannemel1,
- Vladimira Vallova2, 3,
- Doriana Misceo1,
- Vesna Bryn4,
- Iva Slamova3, 5,
- Sarka Prasilova2,
- Petr Kuglik2, 3Email author and
- Eirik Frengen1Email author
© Hladilkova et al. 2015
Received: 26 February 2015
Accepted: 5 July 2015
Published: 31 July 2015
We report two unrelated patients with overlapping chromosome 2q13 deletions (patient 1 in chr2:111415137-113194067 bp and patient 2 in chr2:110980342-113007823 bp, hg 19). Patient 1 presents with developmental delay, microcephaly and mild dysmorphic facial features, and patient 2 with autism spectrum disorder, borderline cognitive abilities, deficits in attention and executive functions and mild dysmorphic facial features. The mother and maternal grandmother of patient 1 were healthy carriers of the deletion. Previously, 2q13 deletions were reported in 27 patients, and the interpretation of its clinical significance varied. Our findings support that the 2q13 deletion is associated with a developmental delay syndrome manifesting with variable expressivity and reduced penetrance which poses a challenge for genetic counselling as well as the clinical recognition of 2q13 deletion patients.
Genome-wide analyses performed on large numbers of patients have led to the discovery of a multitude of copy-number variations (CNVs). Segmental duplications predispose genomic regions to recurrent duplication and deletion by non-allelic homologous recombination (NAHR) events, some of which cause clinically recognizable core phenotypes, e.g., Angelman, Prader-Willi, Smith-Magenis and Williams-Beuren syndromes (reviewed by ). Other imbalances, such as deletions in chromosome 1q21, 15q11, 15q13 and 16p11, present with significant clinical variability . For example the chromosome 1q21.1 deletion is found in patients manifesting one of several features including intellectual disability (ID), autism spectrum disorders (ASDs), schizophrenia, microcephaly, cataracts and congenital heart defects, and it is also detected in healthy carriers [3, 4]. Similarly the chromosome 16p11.2 deletion is detected in patients presenting with a variable combination of clinical features including ID, ASDs, cardiac defects, speech delay, obesity and dysmorphic features, as well as in healthy carriers [5–7].
Recurrent genomic imbalances involving the chromosome 2q13 (chr2:110-114 Mb) are less described. So far 27 patients carrying a 2q13 deletion have been reported [8–15]. The patients present with an apparently unspecific and variable clinical phenotype, including developmental delay (DD), ASDs, attention deficits hyperactivity disorder (ADHD), heart defects and craniofacial abnormalities, and several healthy carriers have been identified [8, 9, 11, 15]. Still, the clinical significance of the 2q13 deletion is not fully determined.
We describe two additional, unrelated patients carrying a deletion in 2q13. Patient 1 presents with DD, microcephaly and mild dysmorphic features, and patient 2 with ASD, borderline cognitive ability, attention and executive function deficits and mild dysmorphic features. The reduced penetrance associated with this deletion syndrome is supported by the identification of two generations of healthy carriers in one of the families.
Patient 2, a boy, was the only child to a healthy, non-consanguineous Norwegian couple. He was delivered at term by an unplanned caesarean section due to his large size. Birth weight was 4600 g (97th centile), length 56 cm (>97th centile), and OFC was not recorded. Norwegian consensus anthropometric measures were used for this patient . He gained weight adequately, and walked at 16 months. Lack of interest in the surrounding was noticed by the kindergarten staff. He had impaired hearing due to recurrent middle ear infections, which normalized after he received drainage tubes bilaterally at 4 years of age. Cognitive testing at age 7, using Wechsler Intelligence Scale for Children - third edition 1991 (WISC-III), indicated global developmental delay. Neuropsychological testing with an extensive panel of tests performed at age 8.5 years showed an overall score in the lower normal range. He showed deficits in attention and executive functions. Cerebral MRI and EEG examinations were normal. At the clinical examination at age 9, his height was 125.5 cm (3rd centile), weight 25.7 kg (10th centile) and OFC 52 cm (10th centile). He had delayed fine motor skills, and impaired balance and coordination. He received special tutoring at school. He had mild facial dysmorphisms, including mild hypertelorism, high and broad nasal bridge, low-set ears with thick, upper helixes and hypoplastic cruz superior, full lips, retrognathia, crowded teeth and an open mouth appearance (Fig. 1b-d). He also had mild divergent strabismus and hypermetropia. At age 12 he was diagnosed with pervasive developmental disorder not otherwise specified (PDD-NOS), and found to have borderline cognitive functioning. Testing for fragile X syndrome was negative. Metabolic screening of urine was normal.
G-banded karyotyping at 550 band resolution was performed on metaphases from peripheral blood. Array Comparative Genome Hybridization (aCGH) analysis was performed using the Human Genome CGH Microarray 44 K or 244A (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol. Samples were sex-matched with Human Genomic DNA (Promega, Madison, WI). aCGH slides were scanned with the Agilent Microarray Scanner, data obtained using Feature Extraction software (v. 6.1.1) and visualized by Agilent Workbench (v. 3.5.14). CNVs were detected by using the ADM-2 algorithm with three neighboring oligos with aberrant intensity ratios of 0.4 as cut off. All genomic positions were based on the February 2009 human reference sequence (GRCh37/hg19) produced by the Genome Reference Consortium.
Quantitative Real-time PCR (qPCR)
Quantitative Real-time PCR (qPCR) was performed using the SYBR Green Jump-Start Taq ReadyMix PCR kit (Sigma, Saint Louis, MO). Reactions were run on the ABI PRIMS 7900 HT Sequence Detection System (Life Technologies Corporation, Carlsbad, CA) according to the manufacturer’s recommendations. Amplification levels were calculated using the ∆∆Ct method . Primer sequences are supplied in Additional file 1: Table S1.
Fluorescence in situ hybridization (FISH) analysis was performed on chromosomal metaphase spreads from peripheral blood of the maternal grandmother of patient 1, using the BAC clone RP11-41806 (chr2:111631068-111793024 bp) as probe. An Olympus BX 61 fluorescence microscope (Olympus optical company, Tokyo, Japan) with a 1300D CCD camera (Vds Vosskühler, Osnabrück, Germany) was used for image acquisition. Image analysis was performed using the LUCIA-KARYO/FISH software (Laboratory Imaging, Prague, Czech Republic).
The cytogenetic band 2q13 is enriched in clusters of segmental duplications (SDs), which may facilitate NAHR resulting in deletions and duplications with variable size and borders in the region chr2:110-114 Mb. These deletions are associated with a developmental syndrome, manifesting with heterogeneous phenotype and incomplete penetrance, which is referred to as 2q13 deletion syndrome. The high prevalence of the 2q13 deletion in patients ascertained for intellectual disability or developmental delay (12 out of 15767) compared to controls (1 out of 8329) reported by Cooper et al. indicates that this deletion is not a benign variant , but more research is needed to establish its pathogenicity.
Of the 29 patients so far described, two had a verified de novo 2q13 deletion (patients 9887950 and 9893017 from ). In 11 the deletion was inherited from a healthy parent, and the inheritance was unknown in 14 patients. In the two remaining cases (cases 3 and 4 from ), the 2q13 deletion was inherited from parents reported to have a history of developmental delay. However, these parents were not included in the total 29 patients with 2q13 deletions due to the limited information available. In the family of patient 1 in the present report, the 2q13 deletion was identified in two generations of unaffected female carriers.
In the first two described patients carrying the 2q13 deletion and presenting a pathological phenotype, the imbalance was inherited from their healthy mother and therefore concluded to be a benign familial variant . The hypothesis that the 2q13 deletion was pathogenic, but manifesting with high phenotypic variability and incomplete penetrance, was suggested after the detection of the imbalance in three additional patients . Those were part of a cohort of 2419 patients ascertained for developmental delay, ASDs or birth defects and investigated by aCGH analysis. Cooper et al. identified 12 patients with 2q13 deletions among 15767 patients (overall 73 % of cases suffer from ID/DD and/or ASD), and one 2q13 deletion among 8329 controls, supporting the pathogenicity of the 2q13 deletion .
There could be several explanations for the variable expressivity and reduced penetrance observed for the 2q13 deletion, such as differences in gene content due to variable deletion break points. It could also be due to differences in genetic background , or a recessive allele unmasked by the deletion . According to the “two hit” model, the 2q13 deletion could be a risk factor representing the “first hit”, while the “second hit” could be an additional genomic imbalance, a single mutation in a gene functionally related to a gene in the deletion, or an environmental factor influencing the phenotype . In support of the “two hit” model, three of the 29 patients with a 2q13 deletion patients were reported to carry an additional genomic imbalance (case 1 and 3 from ; patient #7 from ). In the attempt to detect an unmasked recessive allele, FBLN7 and TMEM87B were sequenced in two 2q13 deletion patients presenting with cardiac defects, but mutations were not found in the remaining alleles . Thus the heterogeneous presentation and the incomplete penetrance of the 2q13 deletion syndrome remain to be elucidated.
Russell et al. depleted the expression of six genes within the 2q13 region, FBLN7, ANAPC1, TMEM87B, MERTK, ZC3H8 and ZC3H6, in zebrafish in search for the genes responsible for cardiac defects and craniofacial abnormalities associated with the deletion syndrome . Cardiac hypoplasia were seen in animals depleted of TMEM87B or FBLN7, in addition to craniofacial abnormalities in the latter, while no such abnormalities were monitored in the zebrafish depleted of the four remaining genes . This suggests that heterozygous loss of FBLN7 and TMEM87B contributes to cardiac defects and craniofacial abnormalities associated with 2q13 deletion syndrome. In addition, one or both of these genes could be responsible for additional phenotypes that are not easily monitored in zebrafish, such as developmental delay, or other genes within the region could contribute to some of the remaining phenotypes. For example BCL2L11, encoding a Bcl2-like antiapoptotic protein with a role in neuronal apoptosis, has been found down regulated in individuals with ASDs [22–24], a diagnosis given to three of the 29 patients with 2q13 deletion.
Due to limited number of patients reported with smaller, atypical deletions, and limited functional information about several of the genes included in the deletion, it is challenging to establish genotype-phenotype correlations. However, FBLN7 and TMEM87B likely contribute to the cardiac defects and craniofacial dysmorphisms . Another gene of interest is BCL2L11, suggested to play a role in the development of ASDs [22–24]. Despite several 2q13 deletion patients described and functional studies performed, the understanding of the genotype-phenotype correlations and of the mechanisms underlying the heterogeneous presentation and incomplete penetrance in this syndrome is limited. Further functional studies of the 2q13 genes, additional reports of patients with smaller, atypical deletions as well as the identification of mutations in single genes are needed to establish the pathogenicity of the deletion and improve the understanding of the 2q13 deletion syndrome.
Written informed consent was obtained from the patient for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.
We are grateful to the patients and their families for participating in this study. This work was supported by the Ministry of Health (Czech Republic) for conceptual development of research organization 65269705 (University Hospital, Brno, Czech Republic) and by OP VK (CZ.1.07/2.3.00/20.0183); by the Research Council of Norway through the Yggdrasil mobility program (Grant 202752); by European Science Foundation (ESF) 'Frontiers of Functional Genomics' (Grant 3419); by the Southeastern Regional Health Authorities (project no 2011071). TB was supported by “Legatet til Henrik Homans Minde”, and DM was supported by “Anders Jahres fond til vitenskapens fremme”.
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