Table 1.
Genetic association results for the eight previously reported and seven novel putative Parkinson’s disease STR risk loci
| STR position | Nearest gene | Effect allele | MAFnew | ORIPDGC | P IPDGC | ORnew | P new | ORmeta | P meta | Directions | Indep. signal | P meQTL | H4 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| (a) Replication evidence for previously reported primary STR loci | |||||||||||||
| 3:122 146 661 | LOC102723582 | [A]12C[A]6 | 0.13 | 1.12 | 6.52E−07 | 1.05 | 3.85E−01 | 1.11 | 6.87E−07 | −−−− | STR | 7.71E−04 | 0.4500 |
| 4:189 000 404 | TRIML2 | TT[A]12 | 0.05 | 1.31 | 1.44E−07 | 0.87 | 1.67E−01 | 1.20 | 5.66E−05 | +++− | STR | 9.73E−03 | 0.0101 |
| 5:60 437 492 | NDUFAF2 | AA[TGAA]6 | 0.43 | 0.77 | 6.94E−08 | 0.95 | 1.85E−01 | 0.87 | 6.32E−06 | ++−+ | STR | 7.63E−07 | 0.0340 |
| 7:127 793 488 | MIR129-1 | [T]14G | 0.25 | 0.86 | 2.79E−07 | 1.05 | 2.78E−01 | 0.91 | 1.73E−04 | +−−+ | STR | 3.83E−13 | 0.9045 |
| 8:11 696 990 | FDFT1 | TCTACT[A]13 | 0.25 | 0.89 | 1.96E−09 | 1.01 | 7.68E−01 | 0.91 | 3.62E−08 | −−++ | STR | 1.23E−07 | 0.9866 |
| 8:22 464 976 | CCAR2 | TAGGG[T]20GATG | 0.34 | 0.91 | 6.91E−07 | 0.92 | 6.76E−02 | 0.91 | 1.28E−07 | −+++ | STR | 1.23E−31 | 0.9790 |
| 12:46 452 915 | SCAF11 | AAGCAAGCA | 0.42 | 0.92 | 5.19E−06 | 0.97 | 5.29E−01 | 0.93 | 8.91E−06 | −+−+ | STR | 3.35E−04 | 0.1409 |
| 17:15 941 750 | NCOR1 | [T]10 | 0.46 | 0.93 | 3.77E−06 | 0.95 | 2.35E−01 | 0.93 | 2.10E−06 | ++++ | STR | 7.42E−11 | 0.8356 |
| (b) Novel suggestive primary STR associations (P < 5.3E−6) | |||||||||||||
| 3:24 310 875 | THRB | [CA]2[CG]6[CA]18[T]3[A]2G | 0.04 | - | - | 0.60 | 2.43E−06 | 0.60 | 2.43E−06 | +++? | STR | 2.94E−04 | 0.1642 |
| 5:120 435 533 | PRR16 | CTC[A]19T | 0.08 | - | - | 0.70 | 4.45E−06 | 0.70 | 4.45E−06 | −−−? | STR | 2.02E−02 | 0.0580 |
| 6:27 666 933 | LINC01012 | [A]9G[A]8 | 0.09 | 0.87 | 7.26E−06 | 0.90 | 1.68E−01 | 0.87 | 3.05E−06 | ++++ | ? | 6.62E−09 | 0.8284 |
| 9:34 054 301 | UBAP2 | [T]13 | 0.39 | 1.07 | 8.96E−06 | 1.06 | 2.04E−01 | 1.10 | 4.15E−06 | −−−− | ? | 4.07E−03 | 0.3404 |
| 16:1 977 617 | TCRBV20S1 | [A]12 | 0.29 | 0.91 | 1.26E−05 | 0.93 | 1.11E−01 | 0.91 | 3.71E−06 | ++−+ | ? | 9.59E−09 | 0.0711 |
| 17:77 019 776 | C1QTNF1 | [GC]6G[CA]18 | 0.04 | - | - | 1.68 | 2.16E−06 | 1.68 | 2.16E−06 | +++? | STR | 7.50E−07 | 0.2577 |
| 19:46 243 112 | MEIOSIN | [T]11 | 0.69 | 1.09 | 6.67E−05 | 1.11 | 1.94E−02 | 1.10 | 4.15E−06 | −−−− | STR | 1.77E−19 | 0.1722 |
This table displays all signals from the IPDGC that are due to independent STR signals (upper part of the table) and all study-wide suggestive primary STR signals from the updated meta-analyses combining the IPDGC data with our newly generated STR data. Bold gene names highlight the STR-based signals for which the updated meta-analysis results improved in significance. Bolded meta-analysis P-values indicate at least study-wide suggestive evidence for association (α = 5.3E−6).
STR position, position for the first nucleotide of the STR (hg19); MAF, minor allele frequency; OR, odds ratio; new, the newly generated STR data independent of the IPDGC data (datasets: PEG, PASIDA, GHC); P, P-value; meta, results of fixed-effect meta-analysis; direction, directions of effect in the individual datasets included in the meta-analysis provided in the following study order: PEG, PASIDA, GHC, IPDGC (see Material and Methods for details on these datasets); Indep. signal, result of the ‘conditional and joint association’ (COJO) and/or conditional analyses assessing whether STR signal is independent from single-nucleotide polymorphisms (‘STR’ denotes independence and ‘?’ analyses could not be performed); meQTL, methylation quantitative trait locus.