Whole-genome Sequencing Identifies EN1 as a Determinant of Bone Density and Fracture

Nature. 2015 Oct 1;526(7571):112-7. doi: 10.1038/nature14878. Epub 2015 Sep 14.

Abstract

The extent to which low-frequency (minor allele frequency (MAF) between 1-5%) and rare (MAF ≤ 1%) variants contribute to complex traits and disease in the general population is mainly unknown. Bone mineral density (BMD) is highly heritable, a major predictor of osteoporotic fractures, and has been previously associated with common genetic variants, as well as rare, population-specific, coding variants. Here we identify novel non-coding genetic variants with large effects on BMD (ntotal = 53,236) and fracture (ntotal = 508,253) in individuals of European ancestry from the general population. Associations for BMD were derived from whole-genome sequencing (n = 2,882 from UK10K (ref. 10); a population-based genome sequencing consortium), whole-exome sequencing (n = 3,549), deep imputation of genotyped samples using a combined UK10K/1000 Genomes reference panel (n = 26,534), and de novo replication genotyping (n = 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size fourfold larger than the mean of previously reported common variants for lumbar spine BMD (rs11692564(T), MAF = 1.6%, replication effect size = +0.20 s.d., Pmeta = 2 × 10(-14)), which was also associated with a decreased risk of fracture (odds ratio = 0.85; P = 2 × 10(-11); ncases = 98,742 and ncontrols = 409,511). Using an En1(cre/flox) mouse model, we observed that conditional loss of En1 results in low bone mass, probably as a consequence of high bone turnover. We also identified a novel low-frequency non-coding variant with large effects on BMD near WNT16 (rs148771817(T), MAF = 1.2%, replication effect size = +0.41 s.d., Pmeta = 1 × 10(-11)). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population.

MeSH terms

  • Animals
  • Bone Density / genetics*
  • Bone and Bones / metabolism
  • Disease Models, Animal
  • Europe / ethnology
  • European Continental Ancestry Group / genetics
  • Exome / genetics
  • Female
  • Fractures, Bone / genetics*
  • Gene Frequency / genetics
  • Genetic Predisposition to Disease / genetics
  • Genetic Variation / genetics
  • Genome, Human / genetics*
  • Genomics
  • Genotype
  • Homeodomain Proteins / genetics*
  • Humans
  • Mice
  • Sequence Analysis, DNA
  • Wnt Proteins / genetics

Substances

  • EN1 protein, human
  • En1 protein, mouse
  • Homeodomain Proteins
  • WNT16 protein, human
  • Wnt Proteins

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