Bone mineral density exhibits strong heritability in family and twin-based studies. This has been the focus of large-scale international genome-wide association studies (GWAS) that have identified genetic loci associated with bone mass but only explain a small proportion (<10%) of the heritability, suggesting that new approaches to identifying the genes that control skeletal mass are required.

We hypothesised that whole genome sequencing (WGS) in families with heritable high bone mass will identify novel rare variants of large effect size for bone mass providing insight into bone biology and targets for anabolic therapies.

In our large, extended families with high bone mass (heritable as a dominant trait) in the Dubbo Osteoporosis Epidemiology cohort, we have applied WGS followed by selection based on osteocyte-specific transcriptome and large-scale international bone GWAS data to identify informative gene variants.

In a 5-member sub-unit of one of the large families, WGS identified >7 million variants. These were narrowed to 1.2 million rare (<1%) coding and non-coding genetic variants and then to 513 genes based on projected high functional impact and then to 167 genes based on family-segregation criteria. Of these, 8 genes showed consistent osteocyte-specific expression and two are close to GWAS peaks in the GEFOS international bone genetics consortium. One of these genes has been reported to have a high bone mass phenotype in knockout mice. The variants in these two genes, that encode major amino acid changes expected to materially change protein function and/or folding, are in regions and encoded proteins are highly conserved from human to lamprey. These are being examined by gene editing in mouse and zebrafish.

These initial studies are ‘proof-of-principle’ that the WGS strategy in Mendelian families can identify rare genetic variants as major contributors to high bone mass/density within families and novel genes and pathways in bone biology.