Further analyses were performed for the SNPs carried forward for replication. Each of these analyses is described in detail in the “
Supplementary Note”. In brief, we performed: 1) a conditional genome-wide association analysis to examine whether any of the 82 BMD loci harbored additional independent signals; 2) tested gene-by-gene pair-wise interactions between these BMD loci; 3) assessed within the independent setting of the PERF study (for details on study design see
Supplementary Tables 20A, 20B & 20C) the predictive ability derived from the cumulative effect of the 63 genome-wide significant autosomal BMD SNPs in relation to BMD levels and osteoporosis risk; and that of the 16 BMD SNPs also associated with fracture risk in relation to fracture risk; 4) identified SNPs having r
2 ≥ 0.80 with the lead SNP that were potentially functional (nonsense, nonconservative non-synonymous, synonymous, exonic splicing, transcription factor binding sites, etc) using regional imputation with the 1000 Genomes data (June 2010 release); 5) tested the relationship between gene expression profiles from a) trans-iliacal bone biopsies and BMD in 84 unrelated postmenopausal women
49 (link) and b) also examined cis- associations between each of the 55 significant BMD SNPs and expression of nearby genes in different tissues including lymphoblastoid cell lines
50 (link)–52 (link), primary human fibroblasts and osteoblasts
53 (link), adipose tissue
54 (link), whole blood
54 (link) and circulating monocytes
55 (link); and finally 6) evaluated the connectivity and relationships between identified loci using the literature-based annotation with Gene Relationships across Implicated Loci (GRAIL
19 (link)) statistical strategy.
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