Developmental delay (DD) and intellectual disability (ID) represent common conditions affecting 1 to 3% of the general population and it has been estimated that one-half of the cases are due to genetic factors [1–4]. With a prevalence of 5 to 16% and 1 to 2% of cases respectively, trisomy 21 and Fragile X syndrome are the most common genetic causes of ID [5].

Routine cytogenetic analysis detects chromosomal aberrations involving at least 3–5 megabases (Mb) of DNA, in concordance with the technique resolution power. Fluorescent in situ hybridisation (FISH) overcomes this limitation allowing to investigate specific loci or subtelomeric regions for cryptic aberrations that are responsible of roughly 5 to 7% of all DD/ID cases [6, 7]. These anomalies represent one of the most common causes of idiopathic DD/ID [8–11], being identified in 6.3% to 10.2% of moderate to severe DD/ID and in a significantly lower rate, less than 1%, in mildly retarded patients [12]. Major malformations and/or dysmorphisms, pre and post-natal growth retardation, and/or positive family history can be observed in the majority of patients with moderate to severe DD/ID related to criptic chromosomal imbalances [9, 13–15]. As a matter of fact, clinical pre-selection of DD/ID patients improves the detection rate. It has been suggested for this purpose the use of specific check-list, such as the five item of De Vries et al. [16]. In recent years the study of genotype-phenotype correlations of these anomalies has allowed the definition of new emerging chromosomal phenotypes [15, 17, 18]. The recent introduction of the technology of array comparative genomic hybridization (CGH), that allows the detection of submicroscopic copy number variations in the whole genome, represents the next step forward in this effort.

We performed subtelomeric FISH analysis in 76 unrelated children affected by various degree of DD/ID, congenital malformations (CM) and facial dysmorphisms (FD), with normal standard karyotype. Ten subtelomeric anomalies have been identified (13.16%), underlying the role of cryptic subtelomeric anomalies in the pathogenesis of complex clinical presentation associated with DD/ID.

Chromosomal subtelomeric anomalies are a relevant cause of DD/ID and birth defects [14, 20, 21]. Here we present the results of a subtelomeric analysis performed on 76 paediatric patients, aged from 3 days to 14 years, presenting with a complex clinical phenotype associated with DD/ID. Ten cryptic chromosomal anomalies have been identified in the cohort, with a detection rate of 13.16%: 3 de novo deletions, 4 unbalanced translocations of parental origin, and 3 de novo unbalanced translocations. Interestingly we have observed relevant differences in the detection rate among the 3 groups identified on clinical features. In particular, the detection rate was 25% in the first group of patients (DD/ID, CM and FD), percentage reduced to 11,11% in the second one (DD/ID and FD), while no anomalies were identified in the third group (DD/ID and CM). This gradient in the detection rate reflects the probability that a chromosomal imbalance is responsible for complex developmental disturbances and leads to relevant facial dysmorphisms.

Some frequent cryptic telomeric anomalies are characterized by a specific phenotype and are emerging as recognizable subtelomeric syndromes, such as 1p terminal deletion (Patients 1–2). The phenotype is characterized by neurodevelopmental disability and a recognizable pattern of malformation associated with specific facial dysmorphisms, straight eyebrows, deep set eyes and frontal bossing that may direct towards the correct clinical diagnosis [10, 17, 18, 22, 23]. Also terminal 9q deletion (Patient 3) is a new emerging recognizable phenotype, described in about 30 patients [24], being characterized by severe ID, hypotonia, brachycephaly or microcephaly, flat face with hypertelorism, synophrys, anteverted nares, a distinctive mouth with macroglossia and a thickened lower lip, and congenital hearth defects. Moreover, sleep disturbances, autistic features and obesity due to food seeking behaviour have been reported in those patients [24–26]. Agenesis of corpus callosum associated with diaphragmatic hernia characterized Patient 4, suggesting the diagnosis of Donnai-Barrow syndrome (OMIM 222448). Subsequently an unbalanced t(9;16)(9qter;16q24.3qter)pat with partial monosomy 9q34-qter and partial trisomy 16q24-qter has been identified suggesting the hypothesis that 9q terminal deletion can cause Donnai-Barrow syndrome [19]. Patient 5 carried an unbalanced paternally derived der(20) t(16;20)(q24;q13.3), with partial 16q trisomy and 20q monosomy. Trisomy 16q24 is a clinical recognizable phenotype characterized by periorbital oedema in the neonatal period, generalized hypotonia, failure to thrive, severe DD/ID and a distinctive facies with a high forehead and bitemporal narrowing, associated with a variable genital and anal abnormalities [27, 28]. This patient presented basopenienal hypospadia, supporting the hypothesis that one or more genes involved in uro-genital development are located in this chromosomal region [29, 30]. Deletion of 20q13 is a very rare anomaly and it is associated with severe malformations of the limbs, short neck, flat occiput, midfacial dysmorphism, and failure to thrive [31–33]. Patient 6 carried a maternally derived unbalanced translocation, consisting with 6p trisomy and 1q monosomy. He presented a complex craniosynostosis, renal hypoplasia, hystologically characterized by membranous glomerulonephritis, leading to progressive renal failure. Interestingly, Pierpoint et al described a patient carrying a 6p terminal trisomy, who presented a striking overlapping facial phenotype associated with progressive renal failure [34]. These observations allow the hypothesis that a gene locus for syndromic renal failure maps to 6p22.3-pter. Moreover, we propose 6p terminal deletion as a new chromosomal syndrome, characterized by a peculiar facial appearance, renal failure and DD/ID. Interestingly the patient we described reached a good cognitive development and school performance after the surgical correction of the craniosynostosis, the kidney transplantation and an intensive rehabilitation program. Chromosome 1q terminal deletion [16, 35–37] is emerging as a new specific chromosomal phenotype characterized by DD/ID, pre-postnatal growth retardation, microcephaly, seizures, bow shaped eyebrows, hand – foot anomalies and midline defects, including corpus callosum hypoplasia [36, 38], and may probably contribute to the pathogenesis of the complex phenotype of this patient. The clinical presentation of Patient 7 confirms the role of genes mapping to terminal region of 7q in caudal regression pathogenesis [39]. Moreover, the peculiar facial traits, such as microcephaly, hypertelorism, epicanthus, coloboma/cataract, blepharoptosis/phimosis, broad nasal bridge with bulbous nasal tip, ear anomalies, short neck, and abnormal genitalia could be considered a specific phenotype for 7q34-qter deletion, as argued by Lukusa et al. [40]. Partial terminal 12q duplication is a rare event described in about 35 cases with mild phenotypical effects [41, 42]. In Patient 8 facial dysmorphisms, characterized by hypertelorism and a striking external ear malformation, short neck associated with early motor developmental delay led to the clinical suspicion of 6p terminal deletion subsequently confirmed by subtelomeric FISH analysis. She is now 6 years old and she displays normal cognitive development at periodic clinical evaluation. This patient confirms that criptic chromosomal aberrations do not always result in DD/ID, suggesting caution in the definition of prognosis, particularly in prenatal genetic counselling. More extensive reports about the size of subtelomeric imbalances in normally neurodeveloped patients are needed in order to investigate which subtelomeric loci are implicated in syndromic DD/ID [43]. In Patient 9, IUGR, severe hypotonia associated with flat facies, hypertelorism, down-slanting palpebral fissures, and toes syndactyly first suggested us the clinical hypothesis of Smith-Lemli-Opitz syndrome (OMIM 270400). Subtelomeric FISH analysis revealed a partial monosomy 5p associated with trisomy 10q, already described in a single patient with an overlapping phenotype, characterized by hands and feet anomalies and facial dysmorphisms [44]. Patient 10 carried a partial monosomy 13q31.1 and partial trisomy 1p32.2. Eight patients with pure monosomy 13q33 have been previously reported, delineating a well-recognized syndrome, characterized by growth and psychomotor retardation, microcephaly and deficiency of coagulation factors VII and X [44, 45]. Partial duplication of chromosome 1p has been described in 10 patients: major characteristics are abnormal genitalia in males, congenital heart defects, craniofacial and hand anomalies [46].

Our report illustrates the relevance of careful dysmorphologic evaluation of patients with DD/ID variably associated with CM and/or FD as an useful tool for pre-selection for genomic analysis. This is particularly noteworthy in respect of the recent availability in the clinical setting of new technologies, such as array genomic hybridization, that allow whole-genome screening for sub-microscopic genomic anomalies, not previously detectable by conventional methods. Literature reports of patients affected by subtelomeric imbalances are very helpful in increasing clinicians awareness of subtle chromosomal phenotypes, and in revealing genomic candidate region for specific developmental defect. Paediatricians and clinical geneticists might improve their expertise in correlating new specific patterns of congenital anomalies with specific chromosomal imbalances, in order to optimize, both in terms of time and cost, the yield of chromosomal studies.