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The results of our study differed from these other studies due most likely to differences in the minor allele frequency range of the SNPs utilized.
In addition to differences in the minor haplotype patterns between the two sets of HEK samples, the relative frequencies of the two most common haplotypes, H1 and H2, differ (Table 1).
Thus, the difference in the association cannot be explained by differences in the minor allele frequencies.
Proposed explanations for this include environmental interactions, genetic heterogeneity, inadequate statistical power and population differences, i.e. inter-population differences in the minor allele frequencies (MAF).
The significance of differences in the minor allele frequency between RA patients and controls, and stratified patients, was assessed using the chi-square goodness-of-fit test.
Interestingly, this cannot be attributed to differences in the minor allele frequencies between CB A (average MAF = 26.0%) and CB B (average MAF = 25.2%).
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There was no difference in the minor allele (C) frequency for this tp53 variant for cases (25.1%) and controls (27.0%; P = 0.56).
There was no difference in the minor allele (T) frequency between cases (10.5%) and controls (10.4%) for this PTPN22 variant (P = 0.96).
This further underlines the remarkable effect of the minor differences in the amino acid sequences of the Fab fragments to their binding characteristics.
There were ethnic differences in the estimated minor allele frequency (MAF) of rs10235235 (Q = 7317.1, two degrees of freedom; P for heterogeneity (Phet) = 0).
Other differences in the topology were minor rearrangements of apical genera.
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