Cindy Boer

Genetics of Osteoarthritis Consortium GWAS Meta-Analyses | 187 4.1 Mouse and human musculoskeletal phenotype We investigated if any of the genes within 1Mb (upstream and downstream) of the 100 SNVs had a musculoskeletal phenotype in mouse knockouts using information from the Mouse Gene expression database (GDX) of the Mouse Genome Informatics (MGI) da- tabase[96]. Mouse orthologues of the all the genes within 1 MB (upstream and down- stream) of the 100 osteoarthritis associated SNVs, were extracted from Ensemble Ge- nomes, using biomarkt (GRCh37, Version 69)[97]. The MGI Batch Query was used to extract all mouse knockout phenotypes from the GDX. We also investigated if any genes had a musculokeletal phenotype in mouse knockouts using information from www.bo- neandcartilage.com . Genes which had a mouse musculoskeletal phenotype were report- ed ( Supplementary Table 8 ). We also investigated human skeletal genetic disorders. We used the Nosology and classification of genetic skeletal disorders[98] to identify genes within 1Mb (upstream or downstream) of the 100 SNVs that had links to human musculosketal phenotypes. Tissue specificity We selected all independent genome-wide significant SNVs across osteoarthritis GWAS (n=100). For each signal we investigated the lead SNV and all fine mapped SNVs (95% posterior probability) (n=542) to see if they colocalized with active enhancer histone marks as defined by the ROADMAP epigenomics project[26]. All tissue and cell types available in the ROADMAP epigenomics and ENCODE project were used (n=127)[26]. For each lead SNV and their Fine-Mapped SNVs, the percentage of SNVs located in ac- tive enhancer marks was calculated. For the enrichment analysis a background value was calculated (1000 permutations) using 100 random SNVs selected from 1000 Ge- nomes Project[99](MAF>0.05). For these 100 random SNVs and all SNV in high LD (r 2 =0.8, LD based on 1000 Genomes Project) their percentage of colocalization with enhancer histone marks was calculated. Once all background permutations were done, an average of all results was taken as the final background values. Enrichment was calculated for each osteoarthritis phenotype and investigated cell type separately, by using the two-proportions Z-test to test if. The significance for enrichment was set to genome-wide significance (p-value<1.3x10 -08 ). As the analysis is highly dependent on the amount of variants included (power) significance was only based on enrichment analysis including all 100 independent SNVs across osteoarthritis phenotypes. For the eQTL colocalization using GTEx tissues, we considered the following GTEx tissues as possible osteoarthritis target tissues, based on the tissue specificity analysis: Adipose, Brain, Heart, Lung, Muscle, Nerve, Ovary, Placenta, Skin, Stomach, Cultured fibroblasts, Adrenal gland, and Breast tissue.