Analysis steps and inclusion thresholds | Selected SNPs | Copaxone-treated patients | ||||
---|---|---|---|---|---|---|
GALA DB | FORTE DB | |||||
Gene | SNP rsID | Odds ratio | P value | Odds ratio | P value | |
Step 1. Replicated variants from 35 prioritized candidate variants. Inclusion threshold: p value <0.05 GALA, p value <0.05 FORTE | HLA-DRB1*1501 | rs3135391 | 0.66 | 0.040 | 0.64 | 0.0499 |
Step 2. Priority list of 4012 variants in 30 genes. Inclusion threshold: p value <0.05 GALA, p value <0.05 FORTE | HLA-DQB2/DOB | rs28724893 | 0.53 | 0.00060 | 0.46 | 0.00037 |
HLA-DOB/TAP2 | rs1894408 | 1.72 | 0.0030 | 1.82 | 0.0093 | |
MBP | rs1789084 | 0.70 | 0.036 | 0.57 | 0.01 | |
Step 3. Broad genome-wide analysis. Inclusion threshold: p value <0.01 GALA, p value <0.05 FORTE | PTPRT | rs117602254 | 0.21 | 0.0037 | 0.28 | 0.016 |
ALOX5AP | rs10162089 | 1.56 | 0.0078 | 1.58 | 0.032 | |
MAGI2 | rs16886004 | 2.15 | 0.0023 | 5.56 | 3.3E-05 | |
ZAK(CDCA7) | rs139890339 | 0.05 | 3.4E-05 | 0.14 | 0.011 | |
SLC5A4(RFPL3) | rs73166319 | * | 0.0060 | * | 0.015 | |
Step 4. Secondary genome-wide screen in patients with highest Copaxone response (relapse-free with no new T2 lesions). Inclusion threshold: p value <0.01 GALA, p value <0.05 FORTE | UVRAG | rs80191572 | 0.20 | 0.0024 | 0.12 | 3.4E-05 |
SLC1A4 | rs759458 | 3.31 | 4.4E-05 | 1.86 | 0.049 |