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Using the trend test for association, 22 SNPs (6.5%) were significant at the 5% level, and 5 SNPs (1.5%) were significant at the 1% level.
The MAF for each SNP is reported for cases and controls in the merged dataset as well as the strength of association using the trend test (Table S3).
Using the trend test in the discovery dataset, a total of 501 SNPs in Class I, II and III regions showed statistically significant association with MS susceptibility; most of these associations were likely due to LD within extended haplotypes, particularly the one anchored by the HLA-DRB1*15:01 allele (Figure1A).
Genotype frequencies were compared between patients with RA and controls using the trend test.
Genotype frequencies were compared between cases and controls using the trend test implemented in PLINK.
Genotype frequencies were compared between RA cases and controls using the trend test implemented in STATA (StataCorp LP, Texas, USA).
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To identify significant interaction, we used the trend test assessing relative risks across categories of micronutrient intake.
Consistent with the results of the main analysis, rs10995190 in ZNF365 and rs1011970 near CDKN2A/CDKN2B provided marginal evidence of association using the trend-test statistic (P-trend = 0.05 for both) and SNPs rs865686 was associated with breast cancer risk under the genotype specific model (2df -P = 0.03).
For bivariate analysis, we computed odds ratios and confidence intervals using the trend chi squared test.
Logistic regression modeling was also used for the trend test [ 25, 26].
The logistic regression model was also used for the trend test of the genotypes with different number of the minor alleles.
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