We identified 5 exon-affecting rare CNVs that are either de novo (CNV 5 in ) or recurrent (CNV 1–4 in ) in the TS population in 10 out of 111 patients with TS. We found that genes/loci in 3 out of the 5 CNVs have been implicated by other studies in closely related neurodevelopmental disorders, notably in schizophrenia, autism, and ADHD. In addition, while not recurrent, a large 1q21 deletion in a pair of identical twins (both with TS) was reported previously in association with autism, schizophrenia, and mental retardation.
We identified several CNVs containing genes that are highly expressed in brain and play a prominent role in cell–cell interaction and synaptic connectivity and function. Several of these genes encode cell adhesion molecules (NRXN1, CTTNBP2
, and CTNNA3
belongs to the neurexin family of proteins. In humans, alterations in genes encoding neurexins or neuroligins have recently been implicated in autism, schizophrenia, and other neurodevelopmental diseases, linking synaptic cell adhesion to cognition and its disorders.10,17
Familial deletion within the X-linked neuroligin 4 (NLGN4
) gene has been associated with autism and TS with affected individuals represented by an autistic boy with a motor tic, his brother with TS and ADHD, and their carrier mother with learning disorder, anxiety, and depression.18
A common genetic basis for autism and schizophrenia has been noted previously.19–21
Rare recurrent exonic CNVs affecting NRXN1, NLGN3, NLGN4
, and CNTNAP2
have been previously implicated in autism, schizophrenia, and ADHD.9,10
Many patients with TS have ADHD as a comorbid condition. The same genes involved in different neurodevelopmental disorders suggests that additional modifying factors play an important role in determining whether a given subject develops TS, autism spectrum disorder, or schizophrenia. However, we have not used any formal diagnostic instrument in all cases to evaluate for comorbid conditions such as autism, ADHD, and schizophrenia. Hence, we cannot differentiate between true pleiotropy and a missed comorbidity.
There are some limitations to the present study. No significant difference in rare CNV burden was found between cases and controls. The rare CNV burden could be potentially used to assess germline chromosome instability. However, the small sample size did not allow us to infer about the importance of germline chromosome instability in this group.
This study also showed that there were 2 exonic CNVs that were present in 2 or more controls but in none of the cases. These included genes LIN28B, BVES, SRPK2, and PUS7 that have never been implicated in any neurodevelopmental disorders and may represent some rare nondisease phenotypes unique to these individuals. In addition, asymptomatic parents of 2 patients with TS (patients 6 and 7 in ) harbored the CNV. This may perhaps be due to reduced penetrance of the CNV.
As seen in figure e-4, there were batch/population stratification effects in our raw data. We checked 6 principal components determined based on elbow of scree plot (figure e-9) and binary segmentation of eigenvalues and corrected for these components that account for batch and population stratification effects. Only the PCA-corrected data were used for identifying the CNVs reported in and hence these are unlikely to be due to batch/stratification effects.
A Fisher exact test to determine the probability of finding 9 instances of recurrent CNVs out of 111 cases vs 4 instances of recurrent CNVs out of 73 controls revealed no significant difference. Considering recurrent CNV at a specific locus, the Fisher exact test comparing 2/111 vs 0/73 also did not show any significant difference. This is perhaps due to the smaller sample size of the study. Future studies with larger sample size will further clarify the role of identified CNVs in the pathogenesis of TS.