“nominally significant”

If the primary endpoint is not significantly different between groups, we will consider all analyses comparing secondary endpoints with p < 0.05 as nominally significant.

Thus, when we analyzed the results, many of the variants found had a much lower alpha that became nominally significant at smaller sample sizes.

28 Variants with a nominally significant pleiotropy were used to perform a gene-based analysis with the Versatile Gene-based Association Study 2 tool. 29 The test uses information from a set of markers while accounting for linkage disequilibrium.

Nominally significant association was seen for the rs10513025 and rs4307059 SNPs in this subset [ Table S6 in File S1 ].

A nominally significant association was found with plasma insulin and HOMA-IR and ADIPOQ variant rs17300539 after adjustment for plasma adiponectin.

Single coding variant association test We identified 3 nominally significant variants, clustering in genes involved in Aβ catabolism ( TTR [p.T139M], ACE [p.T916M]) and APP cleavage ( APH1B [p.T27I]).

Nevertheless, as can be observed in Figure 3 , there were situations involving small interaction effects explaining less than 0.4% of the variance for which a nominally significant Levene's test was more powerful than linear regression testing (after multiple hypothesis correction).

Associations with raw p < 0.05 but FDR-adjusted p ≥ 0.05 were considered nominally significant before multiple-testing correction, but were not interpreted as statistically significant after FDR adjustment. 2.9.

Eight of the 22 CpGs remained significant in the longitudinal EWAS using LMM in model 1 after Bonferroni correction, and were also nominally significant in the meta-analyses in cross-sectional EWAS at baseline and at follow-up (Table 4 ).

Interestingly, haplotype comparison between patients and healthy controls revealed five haplotypes with nominally significant differences between schizophrenic patients and controls, namely, A-T-T-T (haplotype frequencies in patients vs controls: 13% vs 19%, OR = 0.57, 95%CI: 0.40-0.81, p nominal = 0.02, p corrected = 0.32), A-G-T-T (4% vs 11%, OR = 0.41, 95%CI: 0.23-0.74, p nominal = 0.002, p corrected = 0.03), A-G-G-T (

Forty-seven of 78 associations presented a nominally significant summary effect and 21 associations remained statistically significant at P < 1 × 10 −6 .

To adjust for multiple testing, a Bonferroni-corrected value of p was set as 0.05/8, meanwhile value of p < 0.05 was regarded as nominally significant.

Several SNPs showed nominally significant associations with SSc in the discovery cohort (Table 2 ).

For all other analyses, 2-sided P values <0.05 were considered nominally significant.

Finally, we observed nominally significant associations between higher CD5L and increased dementia risk, but these did not achieve FDR≤0.1.

All lead SNPs in these 12 loci are nominally significant in both original studies as well as consistent in effect direction between them, providing solid evidence of replication.

Another possibility is that if the relationship between FTO sequence variation and diabetes is at least partially mediated by BMI, the nominally significant p-value found for the association of rs1421085 with obesity and the absence of association for the remaining variants in African-Americans may make an increase in diabetes susceptibility more difficult to detect.

We also identified several nominally significant genetic correlations including a positive genetic correlation between TSH levels and ER‐positive breast cancer risk and a negative genetic correlation between FT4 levels and ER‐positive breast cancer risk, which both had consistent directionality with previous observational studies [ 48 , 49 ].

Whilst there is no established methodology for correcting for such correlated polygenic tests we did confirm nominally significant results with permutation.

At the aggregated MOA level, 9 of 43 evaluable MOA classes were nominally significant in CellPaintSSL and OpenPhenom, corresponding to 20.9% of evaluable MOA classes, whereas 8 of 43 were nominally significant in uniDINO, corresponding to 18.6%.

We elected, a priori, to report and focus on uncorrected p values < 0.05 as nominally significant.

ALIGATOR requires the user to specify a nominally significant threshold value, and particularly when the sample size is low, this choice can significantly affect the membership of the list of significant pathways.

Comparing control subjects and subjects with DM-ESRD revealed two SNPS (rs12763743 and rs3897983) that were nominally significant (0.041 and 0.037, respectively).

Finally, two additional and related limitations of our study were our limited evidence for GC causality, as association testing resulted in nominally significant values for a handful of genes ( ATM , BRCA2 , MLH1 , RAD51D , and TP53 ; see Supplementary Table S8 ), and the possibility that these variants may be associated with other cancer types that are more common in HBOC or Lynch Syndrome.

Nominally significant differences between TMPRSS2:ERG positive and negative cases were present for four variants.