Table 1.
Test statistics for the top 11 suggestively associated variants (p < 1e–5) from Harroud et al. (2023) in 1813 longitudinally phenotyped patients from Jokubaitis et al. (2023) – binary outcome measure.
| Variant (tagging variant) | Chr | Position (bp) | Gene | Minor allele | MAF | Harroud (2023) a | Jokubaitis (2023) | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Binary outcomes | |||||||||||||||||||
| l-ARMSS | l-MSSS | l-ARMSS (collider bias tested) | l-MSSS (collider bias tested) | ||||||||||||||||
| β | p | OR | p b | Power c | OR | p d | Power | OR | p e | Power | OR | p f | Power | ||||||
| rs10191329 | 2 | 71676999 | DYSF-ZNF638 | A | 0.167 | 0.09 | 9.69x10-9 | 1.04 | 0.80 | 0.84 | 1.04 | 0.81 | 0.85 | 1.03 | 0.82 | 0.76 | 1.03 | 0.80 | 0.76 |
| rs149097173 | 1 | 172370873 | DNM3-PIGC | T | 0.001 | 0.26 | 4.07x10-6 | 0.46 | 0.15 | 0.01 | 0.46 | 0.14 | 0.01 | 0.44 | 0.18 | 0.01 | 0.53 | 0.13 | 0.01 |
| rs2876767 | 13 | 82044107 | - | C | 0.05 | -0.14 | 8.76x10-8 | 0.98 | 0.94 | 0.01 | 1.04 | 0.83 | 0.03 | 0.95 | 0.82 | 0.01 | 1.04 | 0.87 | 0.03 |
| rs181310516 | 1 | 200217158 | - | T | NA | -0.35 | 1.55x10-7 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| rs147933117 | 3 | 24926166 | RARB | A | 0.01 | 0.23 | 3.40x10-6 | 0.62 | 0.34 | 0.04 | 0.62 | 0.41 | 0.04 | 0.58 | 0.27 | 0.05 | 0.68 | 0.39 | 0.03 |
| rs194722 | 14 | 69320947 | - | T | 0.20 | -0.07 | 1.39x10-6 | 0.84 | 0.18 | 0.14 | 0.71 | 0.42 | 0.80 | 0.85 | 0.19 | 0.12 | 0.91 | 0.45 | 0.04 |
| rs12494504 | 3 | 2831218 | CNTN4 | A | 0.01 | 0.21 | 1.37x10-6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| rs112663015 (rs55787257 g ) | 7 | 37640233 (37818628) | - | A (C) | NA (0.01) | -0.22 | 4.24x10-6 | NA (1.29) | NA (0.65) | NA (0.02) | NA (0.72) | NA (0.51) | NA (0.02) | NA (1.15) | NA (0.80) | NA (0.01) | NA (0.69) | NA (0.45) | NA (0.03) |
| rs9397000 | 6 | 170164053 | ERMARD | T | 0.05 | -0.13 | 2.10x10-6 | 1.85 | 0.01 | 0.95 | 1.85 | 0.17 | 0.98 | 1.83 | 0.01 | 0.94 | 1.32 | 0.18 | 0.28 |
| rs61215450 | 6 | 148550897 | - | A | 0.09 | 0.09 | 2.45x10-6 | 1.34 | 0.09 | 0.60 | 1.34 | 0.54 | 0.72 | 1.33 | 0.09 | 0.58 | 1.10 | 0.55 | 0.20 |
| rs4251626 | 14 | 54875607 | CDKN3 | G | 0.22 | -0.07 | 3.52x10-6 | 0.95 | 0.71 | 0.01 | 1.02 | 0.89 | 0.86 | 0.95 | 0.70 | 0.01 | 1.02 | 0.86 | 0.86 |
| rs115687581 | 5 | 169785565 | KCNIP1 | A | 0.03 | -0.16 | 2.94x10-6 | 1.42 | 0.25 | 0.17 | 1.42 | 0.52 | 0.23 | 1.38 | 0.22 | 0.14 | 1.19 | 0.51 | 0.18 |
ARMSS: age-related MS severity score; bp: base pair; b: beta; Chr: chromosome; IMSGC: International MS Genetics Consortium; MAF: minor allele frequency; MSSS: MS severity score; NA: not applicable; OR: odds ratio.
Discovery cohort statistics.
Adjusted for: principal components 1–5, % time on therapy since disease onset, weighted genetic risk score, number of DRB1*1501 alleles and imbalanced variables: follow-up time in MSBase (years), symptom duration (years), annualised relapse rate.
rs10191329 power tested using alpha of 0.05. For suggestive variants, power tested using alpha 0.05/9 (0.006) for binary outcomes.
Adjusted for: principal components 1–5, % time on therapy since disease onset, weighted genetic risk score, number of DRB1*1501 alleles and imbalanced variables: symptom duration (years), age at most recent visit, number of EDSS scores assessed.
Adjusted for: principal components 1–5, weighted genetic risk score, number of DRB1*1501 alleles and imbalanced variables: follow-up time in MSBase (years), symptom duration (years), annualised relapse rate.
Adjusted for: principal components 1–5, weighted genetic risk score, number of DRB1*1501 alleles and imbalanced variables: symptom duration (years), age at most recent visit, number of EDSS scores assessed.
r2 = 0.557.