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. 2017 May 29;268(3):301–316. doi: 10.1007/s00406-017-0808-8

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