We describe herein the phenotypic and molecular findings in 27 subjects with either deletion or duplication of the apparently identical genomic region within chromosome 16p11.2. Submicroscopic 16p11.2 chromosomal rearrangements are increasingly recognised as one of the most common genomic disorders, and were found in 0.6% of samples that were submitted to the diagnostic laboratory at BCM for various indications. Although initial reports described an association of 16p11.2 chromosomal rearrangements with autism, we observed a broad spectrum of clinical manifestations, and the autism phenotype was observed in only one fifth of the deletion cases. The most common clinical manifestations in our cohort were language delay and MR. The role of this genomic interval in speech/language development was also suggested in a study of Icelandic samples in which the deletion frequency was ~0.1% among patients with a psychiatric or language disorder, as compared to 0.01% in the general population.25
Other less common phenotypes in our cohort included motor delay, seizures, behavioural problems (especially ADHD), and congenital anomalies.
The increased incidence of congenital anomalies in individuals with the 16p11.2 deletion or duplication is intriguing. Of special interest is the apparently high incidence of pyloric stenosis among patients with the 16p11.2 deletion. In addition to patient 2-DEL in our cohort, Bijlsma et al
reported two patients with the same finding.26
In our cohort, we identified a high incidence of structural brain abnormalities among patients with deletions, a fact that has implications for establishing the diagnostic and surveillance guidelines for patients with the 16p11.2 rearrangements. The dysmorphic features were not emphasised in previous reports but careful physical examination revealed a high prevalence in our cohort of these abnormal findings that were more severe in individuals with the duplication. The broad forehead, macrocephaly, and flat midface render a distinct facial gestalt to the deletion patients ().
We found differences in the rate of the clinical manifestations between the deletion and duplication cases (, ). However, because of the small sample size of the duplication none of these differences reach statistical significance. In addition to the variable expressivity in the 16p11.2 rearrangements, we observed incomplete penetrance for the entire phenotype (mother of 9-DEL) or for the cognitive phenotype (3-DUP). The deletion cases were referred for testing 1.5-fold more frequently than the duplication cases (27 vs 18), suggesting a potential lower penetrance and/or milder expressivity of the duplications. However, this over representation of the deletions can be biologically based on the 2:1 deletion to duplication ratio underlying many known genomic disorders associated with NAHR events.33
Unexpectedly, the male to female ratio in our cohort was 3.2:1 and 1.5:1 among patients with deletion or duplication, respectively. This higher preponderance of males was also observed in all previous 16p11.2 studies (reviewed in reference 26
), and is a recognised bias in classic autism.
Clinical and demographic findings in patients with 16p11.2 deletions and duplications
The microcephaly in duplication patients and macrocephaly in deletion patients, as well as the higher incidence of ADHD in the duplication patients and the presence of autism in the deletion patients, support the model of behavioural phenotypes in genomic sister disorders suggested by Crespi et al
According to this model, diametric copy number alterations can generate contrasting phenotypes associated with autistic spectrum and psychotic spectrum conditions that may represent evolution of the social brain.35, 36
We observed opposing phenotypes for head circumference—that is, macrocephaly for 16p11.2 deletion and microcephaly for 16p11.2 duplication that are reciprocal to those observed for 1q21.1 rearrangements. Interestingly, at the 1q21.1 deletion/duplication locus the deletion is associated with microcephaly whereas the duplication is associated with macrocephaly.23
Deletion of 1q21.1 is also associated with schizophrenia.18, 19
However, we do not observe other opposing phenotypes for duplication versus deletion patients ().
The differences in the mean head sizes in patients with the 16p11.2 deletion and duplication as compared to controls were striking. The mean head sizes of deletion patients were above normal, and 2/3 of them had absolute or relative macrocephaly (). The duplication patients had small mean head sizes with 6/10 having microcephaly (). Interestingly, macrocephaly is found in a high frequency in patients with autism spectrum disorders, and small head sizes are overrepresented in psychotic spectrum conditions.35
These observations raise intriguing questions regarding the evolutionary aspects of the human cognitive architecture and the development of the social brain in humans.
The analysis of the genomic structure of the rearranged 16p11.2 chromosomal region revealed two major LCR families (147 kb and 72 kb repeats) that contribute to the complexity in this region (). These repeats are most likely responsible for generating the observed recurrent deletions/duplications by NAHR in our cohort. However, further studies to refine the recombination hotspots are required to determine precisely which LCRs are involved in these chromosomal rearrangements. We also performed in silico analyses to investigate potential structural variation polymorphisms in this region and identified a deletion polymorphism that might affect an individual’s susceptibility to rearrangements in the disease locus ().
In the three previous 16p11.2 studies the great majority of deletions were de novo.5, 23, 24
A more recent study reported six familial cases among 14 index patients.26
In this study, the transmitting parent had developmental problems in half of the familial case.26
In our cohort, the chromosomal rearrangements were de novo in most of the deletion cases in which parental studies were available, but inherited and de novo patterns were observed in the subjects with duplications. The reduced penetrance and variable expressivity in these studies on the 16p11.2 rearrangements are important findings for genetic counselling of newly diagnosed patients and for antenatal diagnoses. Variability in the phenotype has also been observed in other genomic disorders such as the Smith Magenis microdeletion syndrome (MIM 182290) despite a common sized genomic imbalance.37
Some variability may relate to SNPs or CNVs on the remaining hemizygous allele.38
Perhaps mosaicism for this frequent rearrangement might potentially contribute to both penetrance and variable expressivity, but additional patients need to be evaluated and further molecular studies are required to clarify this point. No imprinted genes have been identified so far within the rearranged region (according to the http://geneimprint.com/
website, October 2009), suggesting that imprinting is unlikely to modify the phenotype or contribute to the phenotypic variability of these individuals.
Our study clearly demonstrates a dosage effect of 16p11.2 copy number on the various clinical findings, and suggests the presence of dosage sensitive genes within the rearranged interval. It is important to note that, in addition to causing autosomal dominant phenotypes, the deletion of genes can occasionally unmask a mutation in the second allele, resulting in an autosomal recessive phenotype, or could cause an imprinting disorder due to deletion of imprinted genes.39
This clinical scenario has been recently described in a patient with severe combined immunodeficiency due to Coronin-1A (MIM 605000) mutation and a 16p11.2 deletion.40
The rearranged 16p11.2 interval contains 27 annotated genes (), and some are promising candidates for the different phenotypes in patients with these syndromes. MAPK3 (MIM 601795) is a synaptic signalling component necessary for several forms of learning. Mapk3
−/− null mice showed a dramatic enhancement of striatum dependent long term memory.41
(MIM 602427) gene encodes a transcriptional regulator involved in developmental processes and can play a role in the congenital anomalies that were observed in our patients. SEZ6L2
is an apparent seizure related gene with high central nervous system (CNS) specific levels of expression. Recently, a sequence variation was identified in SEZ6L2
that may represent a novel genetic risk factor for autism.42
(MIM 606248) encodes quinolinate phosphoribosyltransferase, a key enzyme in catabolism of a potent endogenous exitotoxin to neurons called quinolinate. Elevation of quinolinate levels in the brain due to decreased activity of this enzyme has been linked to the pathogenesis of epilepsy in humans.43
(MIM 604567) encodes a protein predominantly expressed in brain and is possibly involved in calcium dependent neurotransmitter release and in dynein dependent intracellular vesicle transport.44
The protein serine/threonine phosphatase 4 encoded by PPP4C
(602035) interacts with the survival of motor neurons complex45
and is regulated by histone deacetylase 3.46
gene (MIM 600999), expressed in human embryonic brain and in mouse brain, encodes the transcription factor MYC associated zinc finger protein which enhances the NMDA receptor subunit type 1 (MIM 138249) activity during neuronal differentiation.47
In addition, overexpression of MAZ can inhibit cell cycle proliferation in rabbit synoviocyte cells.48
In conclusion, our results expand the spectrum of phenotypic abnormalities observed in patients with the 16p11.2 deletion or duplication and reveal specific objective clinical features (eg, microcephaly or macrocephaly) associated with copy number imbalances at this locus. These deletion/duplication genomic disorders are highly associated with speech/language delay, cognitive impairment, and abnormal head size. Motor delay, neuropsychiatric abnormalities, congenital anomalies, and seizures are also frequent phenotypic findings. The incomplete penetrance and variable expressivity of clinical findings in patients with these rearrangements complicates both the clinical interpretation of the molecular data and the genetic counselling. The phenotypic variability may be related to other genetic or genomic variants, but further molecular analysis is essential to enable robust genomotype/phenotype correlations.