Recurrent reciprocal 16p11.2 rearrangements associated with global developmental delay, behavioural problems, dysmorphism, epilepsy, and abnormal head size

Abstract

Background: Deletion and the reciprocal duplication in 16p11.2 were recently associated with autism and developmental delay.

Method: We indentified 27 deletions and 18 duplications of 16p11.2 were identified in 0.6% of all samples submitted for clinical array-CGH (comparative genomic hybridisation) analysis. Detailed molecular and phenotypic characterisations were performed on 17 deletion subjects and ten subjects with the duplication.

Results: The most common clinical manifestations in 17 deletion and 10 duplication subjects were speech/language delay and cognitive impairment. Other phenotypes in the deletion patients included motor delay (50%), seizures ( approximately 40%), behavioural problems ( approximately 40%), congenital anomalies ( approximately 30%), and autism ( approximately 20%). The phenotypes among duplication patients included motor delay (6/10), behavioural problems (especially attention deficit hyperactivity disorder (ADHD)) (6/10), congenital anomalies (5/10), and seizures (3/10). Patients with the 16p11.2 deletion had statistically significant macrocephaly (p<0.0017) and 6 of the 10 patients with the duplication had microcephaly. One subject with the deletion was asymptomatic and another with the duplication had a normal cognitive and behavioural phenotype. Genomic analyses revealed additional complexity to the 16p11.2 region with mechanistic implications. The chromosomal rearrangement was de novo in all but 2 of the 10 deletion cases in which parental studies were available. Additionally, 2 de novo cases were apparently mosaic for the deletion in the analysed blood sample. Three de novo and 2 inherited cases were observed in the 5 of 10 duplication patients where data were available.

Conclusions: Recurrent reciprocal 16p11.2 deletion and duplication are characterised by a spectrum of primarily neurocognitive phenotypes that are subject to incomplete penetrance and variable expressivity. The autism and macrocephaly observed with deletion and ADHD and microcephaly seen in duplication patients support a diametric model of autism spectrum and psychotic spectrum behavioural phenotypes in genomic sister disorders.

Figure 1

Distribution of clinical indications at the time of referral to array comparative genomic hybridisation (aCGH) testing among patients with 16p11.2 deletion and duplication. DYSMOR, dysmorphism; FTT, failure to thrive; MCA, congenital anomalies; MR/DD, mental retardation/developmental delay; SZ, seizures.

Figure 2

Representative Agilent 8X15K oligoarray comparative genomic hybridisation (CGH) results for heterozygous deletion, heterozygous duplication, and mosaic deletion of the proximal 16p11.2 region. Shown above is the genomic region harbouring the recurrent duplication/deletion. Red and blue bars depict low copy repeats (LCRs) flanking the recurrent rearrangement region. The representative array data below are drawn to the scale of the above region. Log₂ ratio values for all oligos are plotted as a function of their chromosomal position. Probes with Log₂ ratio greater than 0.25 are shown in red points, less than −0.25 are shown as green points, between −0.25 and 0.25 are shown as black points. The horizontal line for each array CGH represents an ~10 kb moving average. The upper two arrays show a moving average of close to −1 and 0.5 in the disease locus, respectively, and therefore interpreted as heterozygous deletion and duplication. The bottom array shows a patient whose array CGH on genomic DNA from blood that reveals a moving average below, but very close to zero, therefore interpreted as mosaic deletion.

Figure 3

Clinical phenotypes in 16 patients with the 16p11.2 deletions and 10 patients with the 16p11.2 duplication. (see figure 2 legend for abbreviations).

Figure 4

Facial features of individuals with 16p11.2 deletion. a: case 1; b: case 2; c: case 3; d: case 4; e: case 5; f: cases 6; g: case 7; h: case 8; i: case 9; j: case 10; k: case 11; l: case 12; m: case 13; n: case 14; o: case 16. All patients with deletion showed a broad forehead and flat midface. Hypertelorism and micrognathia appear to be common findings in the 16p11.2 deletions.

Figure 5

Facial features of individuals with 16p11.2 duplications. a: case 1; b: case 2; c: case 3; d: case 4; e: case 5; f: cases 6; g: case 7; h: case 8; i: case 9.

Figure 6

Deletions and duplications of 16p11.2 are associated with an abnormal head size. (A) The Z score of the head circumference among deletion (circles) and duplication (squares) patients. (B) The head size (HC) adjusted to height (Hgt). The mean of zHC-zHgt is depicted among deletion cases. All measurements are plotted as age and sex matched Z scores. Bars indicate mean and 95% CIs. Age and sex matched HC and Hgt centiles were obtained using Abase, a PalmOS-based calculator, and converted into Z scores.

Figure 7

Schematic representation of the proximal 16p11.2 region based on the March 2006 freeze of the reference human genome sequence (NCBI build 36.1) and summary of genomic structure analyses. (a) Genes within this region are represented by grey bars, drawn to scale. (b) There are two major low copy repeat (LCR) families in this region. The blue arrows, termed 147A and 147B, represent the two ~147 kb LCRs. They are in direct orientation and share 99.6% identity. The red arrows, termed 72A, 72B, and 72C, represent the three ~72 kb LCRs. They are all in direct orientation and share ~98.6% identity. (c) Structural variation in this region based on fosmid sequencing data from Kidd et al Fos1, Fos2, and Fos3 represent three groups of discordant fosmids, whose mapping is too large relative to the reference genome. The black bars at the ends indicate mapping positions of sequenced fosmid ends in the reference genome. The exact sites of structural variations are unknown because most of these fosmids are only sequenced at the ends. ABC12-J13 represents the deletion structural variation found in the fosmid ABC12-46789100J13. The green bar indicates the region deleted from this fosmid relative to the reference genome.