Coding and non-coding genetic variants as the basis for early-onset osteoporosis

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Whole genome sequencing offers the opportunity for a comprehensive detection of variants in an individual. However, the interpretation of variants in regard to their potential pathogenicity remains a challenge in particular in the non-coding genome. We propose to study the genetics of early-onset osteoporosis (EOOP), a condition with phenotypic overlap to common disease. Sequencing of a panel containing known disease genes revealed causal mutations in about 20% of more than 400 EOOP patients, showing that this condition has a strong genetic component. We here propose a genome-wide analysis of additional 200 EOOP patients in which mutations in genes for known bone fragility disorders have been excluded. Whole genome sequencing (WGS) data will be analysed with in-house pipelines to generate a comprehensive list of single nucleotide variants (SNVs) and structural variants (SVs). In a large part of these patients we expect non-coding alterations influencing gene regulation as the basis of the phenotype, possibly in an oligogenic manner. To identify the regions of the genome that are involved in gene regulation of osteoblasts and osteoclasts (bone regulome), we will use chromatin profiling, ATAC-seq, and RNA-seq in mesenchymal stromal cells (MSCs), MSC-derived osteoblasts and in osteoclasts from healthy donors. In addition, we will perform chromosome conformation capture (HiC) in these cells to generate genome-wide interaction profiles. The combination of RNA-, ATAC- and ChIP-seq for histone marks and HiC will enable us to reliably predict the entirety of non-coding gene regulatory elements and their interaction domains. This combined approach will shed light onto the missing inheritance observed in osteoporosis GWAS studies and enable stratification and individualized treatment of EOOP patients.