Cindy Boer

Hand osteoarthritis and Matrix-Gla Protein | 121 3.1 Results GWAS of KL sum score We conducted a GWAS of a semiquantitative measure of hand OA, a bilateral summed score of KL scores,[20] which grades radiographic OA severity, across all hand joints (KL sum score, range of 0–120). The discovery set consisted of three Rotterdam Study cohorts (RSI, RSII and RSIII) and included 8,743 participants with KL sum scores. Repli- cation was done in another 4011 individuals from three different cohorts; LS, Framing- ham Heart Study and Twins UK (TUK). General characteristics of the discovery cohorts and replication cohorts can be found in Supplementary Table 3 and Supplementary Text 1 . The discovery analysis yielded two novel independent genome-wide significant loci (p-value≤5*10 −8 ) on chromosome 12, an intergenic region between matrix Gla pro- tein (MGP) and ERP27 and an intronic region in CCDC91 . We also identified seven oth- er novel loci with suggestive significance (p-value<5x10 −06 ) ( Figure 1 ). In total, nine loci were selected for replication in 4,011 individuals from three different cohorts (LS, FHS and TUK). Using a Bonferroni corrected p-value <5.56x10 −03 , we significantly repli- cated one of nine loci, rs4764133 (Beta meta =0.83, SE meta =0.10, p-value replication =3.4x10 −07 , p-value meta =1.8x10 −15 ) with the same direction of effect as identified in the discovery analysis ( Table 1 and Supplementary Figure 1 ). This locus maintained genome-wide significance and another locus near ENPP3 reached near genome-wide significance (chr6: 132063842:D, Beta meta =0.58, SE meta =0.11, p-value meta =3.8x10 −07 ) in the combined discovery and replication joint meta-analysis ( Table 1 ). Since the KL sum score has a skewed distribution, the top hit was also reanalysed in the discovery set using a Poisson regression (rs4764133, Beta poisson =0.12, SE poisson =0.02, p-value poisson =1.98*10 −11 ). Our top replicated and genome-wide significant finding, rs4764133 [T] (p-val- ue meta =1.80*10 −15 , Beta=0.83, MAF=0.39) is located in a non-coding intergenic region between MGP and endoplasmic reticulum protein 27  ( ERP27 ). However, variants in high LD with rs4764133 (r 2 ≥0.8) span a ~80Kb region encompassing multiple genes, in- cluding MGP and an open-reading frame C12orf60 ( Figure 2a ). Moreover, several of these variants are located in an mRNA transcript, including a non-synonymous variant in MGP, and variants in 3 ′ and 5 ′ UTR of MGP and C12orf60 ( Table 2, Figure 2b ). The non-synonymous variant in MGP , rs4236, is predicted to be non-damaging (STIFT=1, tolerated; polyPhen=0, benign) causing a threonine to alanine amino acid substitution. Two variants are located in predicted active promoter region of MGP (rs1800801) and C12orf60 (rs9668569) in chondrogenic cells and primary osteoblasts ( Table 2 ).