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Table 3 Tests of association between ENPP1 polymorphisms and osteoarthritis (OA) of hand joints

From: Association of ENPP1gene polymorphisms with hand osteoarthritis in a Chuvasha population

Marker Allele/haplotype Freq. P values of TDT Combined P values for 3 testsa Bonferroni correction n inf. n test Pedigree-based disequilibrium test
    FBAT QTDTb EOT A B A B    P Δ (years)
M06NR1A 4Fc 0.27 0.0001 1.0e-5 0.0009 <1.0e-6 <5.0e-5 <4.0e-6 <2.0e-5 84 4 0.0002 -3.5
K173Q 1 0.11 0.0129 0.0347 0.0403 0.0020 0.0104 0.0020 0.0104 48 1 0.0196 1.9
_XXXd _221 0.66 0.0147 0.0174 0.0043 0.0002 0.0033 0.0006 0.0099 88 3 0.3430 -1.3
_XXX _211 0.10 0.0148 0.0373 0.0096 0.0007 0.0074 0.0021 0.0220 39 3 0.0110 2.3
_XX_ _22_ 0.67 0.0046 0.0050 0.0030 1.8e-5 0.0006 0.0001 0.0018 89 3 0.1827 -1.7
_XX_ _21_ 0.10 0.0114 0.0378 0.0091 0.0005 0.0062 0.0016 0.0185 40 3 0.0114 2.3
__XX __11 0.12 0.0426 0.0509 0.0426 0.0074 0.0177 0.0147 0.0351 47 2 0.0278 2.1
__XX __21 0.85 0.0362 0.0515 0.0576 0.0082 0.0205 0.0164 0.0406 58 2 0.1574 -1.6
  1. Osteoarthritis scores were measured by the Kellgren–Lawrence method [19]. K–L scores of 28 joints on both hands, which were used as primary phenotype. The primary phenotype was subjected to principal component analysis resulting in first factor scores (FS1-OAs). After being adjusted for age, FS1-OA was used as a quantitative trait for the association tests. aCombined P value using χ2 (A) and simulated three-dimensional null distribution (B). bColumn presents orthogonal test, which uses parent trait values as covariates. cF is an artificial 'allele' combining all rare alleles but not the three most frequent ones. dXXXX is the haplotype of the four SNPs (rs1800949, rs858342, K173Q, and R774C). The minor allele frequencies of the four individual SNPs in the study population are 0.24 for the T-allele (2) of rs1800949, 0.21 for the G-allele (1) of rs858342, 0.11 for the C-allele (1) of K173Q, and 0.03 for the T-allele (2) of R774C. Δ, mean difference between the allele carriers and other individuals in age at onset of the disorder; EOT = extreme offspring design t-test; FBAT, family-based association test; Freq., frequency; n inf., number of informative families for TDT in the sample; n test, number of tests performed for the marker (alleles with n inf. >40); QTDT, quantitative transmission disequilibrium test; TDT, transmission disequilibrium test.