Table 4.

Nominally significant SNP findings from our transmission disequilibrium tests with corresponding P values from the TS GWAS of the Tourette Syndrome Association International Consortium for Genetics of the previously implicated TS candidate SNPs or tSNPS from previously implicated candidate genes

SNP	CHR	BP	Gene	Minor/major allele	MAF	Over-transmitted allele	T:U	ORa	95% CIa	χ 2 b	P value nominalc	P value adjusted (FDR)d	OR TS GWASe	P value TS GWASe
Nominally significant candidate SNPs previously implicated in TS
rs3744161	17	80828057	TBCD	G/C	0.49	Minor	123:91	1.35	1.03–1.77	5.45	0.03	0.64	0.97	0.31
rs4565946	12	72336769	TPH2	T/C	0.49	Minor	205:163	1.26	1.02–1.55	6.01	0.02	0.57	1.01	0.81
Nominally significant tSNPs from candidate genes previously implicated in TS or OCD
rs17812372	9	4519989	SLC1A1	G/C	0.04	Minor	49:24	2.04	1.25–3.33	11.23	0.0006	0.11	1.06	0.29
rs1042098f	5	1394815	SLC6A3/DAT1	G/A	0.29	Minor	159:118	1.35	1.06–1.71	4.96	0.03	0.71	1.00	0.98
rs11615016f	12	72415994	TPH2	G/A	0.03	Minor	42:28	1.5	0.93–2.42	7.35	0.006	0.57	0.97	0.63
rs4760813f	12	72322894	TPH2	C/G	0.30	Major	58:39	1.49	0.99–2.23	4.24	0.04	0.71	1.01	0.85
rs7969998f	12	72328745	TPH2	C/T	0.05	Major	57:41	1.39	0.93–2.08	7.38	0.01	0.57	0.95	0.29
Nominally significant SNPs from TS GWAS studies
rs11603305	11	10997949	Intergenic	G/A	0.32	Minor	125:92	1.36	1.04–1.78	6.11	0.02	0.24
rs621942	11	85783738	PICALM	A/C	0.24	Minor	121:84	1.44	1.09–1.90	7.08	0.01	0.24

SNP, single nucleotide polymorphism; CHR, chromosome; BP, base pair position (Build GRCh37); MAF, minor allele frequency (based on 1000 genomes); T:U, transmitted:untransmitted count; OR, odds ratio; FDR; false discovery rate; SLC1A1, solute carrier family 1 member 1, glutamate transporter; SLC6A3, solute carrier family 6, dopamine transporter; DAT1, Dopamine Transporter 1; TBCD, Tubulin Folding Cofactor; TPH2, tryptophan hydroxylase 2

^aThe odds ratios and 95% confidence intervals presented are based on the standard transmission disequilibrium test in PLINK

^bThe χ ² test statistic is derived from the Parent-TDT option in plink

^cEmpirical P value for the gene based on 10,000 permutations

^d P value adjusted for multiple comparisons using the FDR for all SNPs that passed quality control checks

^eBased on case–control comparisons from the TSAICG cohort [6]. Note that uncorrected P values are reported

^fThe gene-based analysis showed no evidence of association, however, this particular SNP did show nominal significance when separately analyzed