Table 55: Validation of top signals by Sequenom MassARRAY iPLEX Gold assay. amvnam, hip OA with axial/medial joint space narrowing vs. hip OA with non-axial/medial joint space narrowing; avna, hip OA with atrophic bone response vs. hip OA with non-atrophic response. Concordance between Sequenom summary statistics GWAS summary statistics Sequenom and GWAS Imputation % Genotype % Minor N OR EAF EAF OR EAF EAF SNP EA Stratum P P score concordance allele case/control [95%CI] cases controls [95%CI] cases controls concordance 1.43 1.42 rs754106 T amvnam 413/1366 0.393 0.479 1.37x10-5 0.393 0.478 1 100 100 [1.21-1.68] [1.21-1.67] 2.05 2.11 rs16869403 G avna 262/1517 0.170 0.092 2.36x10-7 0.164 0.088 0.97 99 97 [1.57-2.68] [1.61-2.77]
Table 55: Validation of top signals by Sequenom MassARRAY iPLEX Gold assay. amvnam, hip OA with axial/medial joint space narrowing vs. hip OA with non-axial/medial joint space narrowing; avna, hip OA with atrophic bone response vs. hip OA with non-atrophic response. Sequenom summary statistics GWAS summary statistics Concordance between Sequenom and GWAS SNP EA Stratum N case/control OR [95%CI] P EAF cases EAF controls OR [95%CI] P EAF cases EAF controls Imputation score % Genotype concordance % Minor allele concordance rs754106 T amvnam 413/1366 1.43 [1.21-1.68] 0.393 0.479 1.42 [1.21-1.67] 1.37x10-5 0.393 0.478 1 100 100 rs16869403 G avna 262/1517 2.05 [1.57-2.68] 0.170 0.092 2.11 [1.61-2.77] 2.36x10-7 0.164 0.088 0.97 99 97
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