De Novo Coding Variants Are Strongly Associated with Tourette Syndrome

Abstract

Based on the contribution of de novo coding variants to other neurodevelopmental disorders, and their utility for hypothesis-naive gene discovery, we whole-exome sequenced 325 Tourette syndrome trios (311 passed quality control) from the TIC Genetics consortium, and identified de novo sequence variants. We observed a strong association for de novo likely gene disrupting (LGD; insertion of premature stop codon, disruption of canonical splice site, or frameshift insertion/deletion) variants as well as de novo damaging variants (LGD + probably damaging missense [Mis3]) variants. We replicated these findings in 186 TS trios (173 after quality control) from the TSAICG Consortium, and performed a combined analysis strongly associating de novo LGD (RR 2.32, 95% CI 1.37-3.93, p = 0.002) and damaging (RR 1.37, 95% CI 1.11-1.69, p = 0.003) variants with TS risk. We estimate that de novo damaging variants in approximately 12% of patients contribute risk through the perturbation of approximately 400 risk genes. Finally, we leveraged recurrent de novo damaging variants and the TADA algorithm to identify one high confidence (false discovery rate (FDR) < 0.10) TS risk gene: WWC1 (WW and C2 Domain Containing 1); and three probable (FDR < 0.30) TS risk genes: CELSR3 (Cadherin EGF LAG Seven-Pass G-Type Receptor 3); NIPBL (Nipped-B-Like); and FN1 (Fibronectin 1). These findings establish the contribution of de novo variants to TS risk and highlight that de novo based gene discovery is a viable path forward for this disorder.