Targeted sequencing of genome wide significant loci associated with bone mineral density (BMD) reveals significant novel and rare variants: the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) targeted sequencing study

Abstract

Background Bone mineral density (BMD) is a heritable phenotype that predicts fracture risk. We performed fine-mapping by targeted sequencing at WLS, MEF2C, ARHGAP1/F2 and JAG1 loci prioritized by eQTL and bioinformatic approaches among 56 BMD loci from our previous GWAS meta-analysis. Methods and Results Targeted sequencing was conducted in 1,291 Caucasians from the Framingham Heart Study (n = 925) and Cardiovascular Health Study (n = 366), including 206 women and men with extreme low femoral neck (FN) BMD. A total of 4,964 sequence variants (SNVs) were observed and 80% were rare with MAF <1%. The associations between previously identified SNPs in these loci and BMD, while nominally significant in sequenced participants, were no longer significant after multiple testing corrections. Conditional analyses did not find protein-coding variants that may be responsible for GWAS signals. On the other hand, in the sequenced subjects, we identified novel associations in WLS, ARHGAP1, and 5′ of MEF2C (P-values < 8×10−5; false discovery rate (FDR) q-values < 0.01) that were much more strongly associated with BMD compared to the GWAS SNPs. These associated SNVs are less-common; independent from previous GWAS signals in the same loci; and located in gene regulatory elements. Conclusions Our findings suggest that protein-coding variants in selected GWAS loci did not contribute to GWAS signals. By performing targeted sequencing in GWAS loci, we identified less-common and rare non-coding SNVs associated with BMD independently from GWAS common SNPs, suggesting both common and less-common variants may associate with disease risks and phenotypes in the same loci.

Conditional Loss of MEF2C Expression in Osteoclasts Leads to a Sex-Specific Osteopenic Phenotype

“…Mef2c ’s role in multiple cell types has been well studied [ 12 , 13 ]. SNPs associated with the Mef2c locus are associated with osteoporosis and osteoporotic fractures [ 14 , 15 , 16 ]. Mef2c has been shown to regulate chondrocytes and osteoblast differentiation in mouse models [ 17 ]; however, its role in osteoclast differentiation has not been well studied.…”

Assessing the Relationship Between Gut Microbiota and Bone Mineral Density

“…For example, genome-wide association studies (GWAS) have identified more than 65 novel genomewide significant loci for BMD and detected 14 risk loci for fracture (Estrada et al, 2012). In a targeted sequencing of genome-wide significant loci for BMD, WLS, ARHGAP1, and 5′ of MEF2C were identified much more strongly associated with BMD compared to the GWAS SNPs (Hsu et al, 2016). However, the full genetic mechanism of BMD remains elusive now.…”

A multi-ethnic meta-analysis confirms the association of rs6570507 with adolescent idiopathic scoliosis

“…Recently, numerous sequencing studies of candidate genes in GWAS loci identified rare large-effect variants 20 – 22 . To assess the potential contribution of rare variants at the chromosome 6q24.1 locus to AIS, we carried out targeted sequencing.…”