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Table 2 Summary of statistical analysis of selected SNPs in the discovery and validation cohorts

From: Exome sequencing study in patients with multiple sclerosis reveals variants associated with disease course

Selected variants Discovery cohort (n = 20) First validation cohort (n = 194) Second validation cohort (n = 257) Meta-analysis
SNP Gene Minor allele MAF, Benign (n = 10) MAF, Aggressive (n = 10) p value MAF, Benign (n = 107) MAF, Aggressive (n = 87) MAF, Benign (n = 224) MAF, Aggressive (n = 33) Joint p value OR (95% CI)
rs17844444 PCDHB6 A 0.10 0.40 0.03 0.15 0.15 0.18 0.14 0.52  
rs17082236 SYNE1 A 0.00 0.35 0.003 0.09 0.1 0.05 0.07 0.54  
rs10279499 SAMD9 A 0.45 0.00 0.0006 0.12 0.12 0.10 0.04 0.29  
rs10488532 SAMD9L T 0.45 0.00 0.0006 0.12 0.14 0.12 0.06 0.79  
rs2374639 VPS50 C 0.60 0.06 0.003 0.27 0.31 0.27 0.15 (*)  
rs17552167 EZH2 T 0.30 0.00 0.007 0.07 0.06 0.08 0.12 0.63  
rs28469012 CPXM2 T 0.05 0.45 0.003 0.04 0.10 0.10 0.12 0.04 1.81 [1.03–3.18]
rs10894768 IGSF9B G 0.50 0.05 0.001 0.35 0.28 0.36 0.27 0.04 0.70 [0.49–0.99]
rs60252902 DHX37 A 0.30 0.00 0.007 0.11 0.11 0.09 0.07 0.76  
rs3742130 GPR18 A 0.55 0.05 0.0005 0.26 0.27 0.23 0.19 0.80  
rs9919887 SYNE3 G 0.05 0.45 0.003 0.20 0.16 0.20 0.19 0.43  
rs2230434 ITGAL T 0.00 0.25 0.01 0.11 0.09 0.09 0.07 0.32  
rs2070896 ITGAX C 0.56 0.05 0.0006 0.37 0.38 0.33 0.32 0.85  
rs35299026 HSD17B14 A 0.25 0.00 0.01 0.05 0.07 0.05 0.06 0.31  
rs10423927 NLRP9 G 0.25 0.00 0.01 0.11 0.06 0.08 0.06 0.09 0.58 [0.31–1.09]
rs2254562 SYNJ1 C 0.05 0.45 0.003 0.30 0.29 0.29 0.35 0.65  
  1. The minor allele frequencies (MAF) and uncorrected p values for each SNP selected from the discovery cohort are presented. For validation, heterogeneity tests and subsequent meta-analysis was performed in the two replication cohorts whenever possible. MAF and joint p values (calculated with Mantel-Haenszel test) are depicted for each SNP. In addition, odds ratio (OR) with their corresponding 95% confidence intervals (95% CI) are presented for SNPs with statistically significant results. *For SNP rs2374639, validation cohorts cannot be meta-analyzed due to high heterogeneity (I2 = 80%, p = 0.03). On a separate analysis, the first validation cohort shows replication of the effect observed in the discovery cohort, with a lower frequency of the minor allele in aggressive MS compared to benign MS [p = 0.04, OR = 0.47 (0.23–0.95)]. The second validation cohort shows an increased frequency of the minor allele in aggressive MS that is not statistically significant [p = 0.39, OR = 1.22 (0.77–1.94)]