Genome-wide Haplotype Association Mapping (HAM) in mice leads to an identification of a genetic variant in CER1 associated with bone mineral density in premenopausal women

Abstract

Bone Mineral Density (BMD) is a complex trait likely determined by multiple genes. We attempted to identify the quantitative trait loci (QTL) for BMD in mouse genome and to replicate the findings in human. Information on single nucleotide polymorphisms (SNPs) (1) and whole body BMD of 18 weeks female mice (2) were gathered from 30 mouse strains. The Haplotype Association Mapping (HAM) program which utilized a sliding window of 3 SNPs in the grouping of a haplotype block was applied (1). A modified F-test was used to query for the existence of some haplotypes structure that can partition mice with high BMD and low BMD. The positional candidate gene was then replicated in 1,083 young southern Chinese women aged 20-40 years having extreme high (BMD Z score > +1 at either the spine or hip) and low BMD (Z score=< -1.28, equivalent to the lowest 10th percentile of the population). The association was examined using binary logistic regression with adjustment of age, height and weight. 22 blocks in the female mice genome were identified to contain genes for BMD variation. Chromosome 4, 82.2-87.9 Mb and Chromosome 12, 26.9-28.6 Mb had two peaks in close proximity. No genes can be found in the gap in Chromosome 12, 26.9-28.6 Mb. 27 genes were found in that of Chromosome 4, 82.2-87.9 Mb. Examination of the gene list identified Cer1 as a positional candidate gene in chromosome 4 QTL. Cer1 is a homolog of Cerberus in Xenopus, which belongs to a cystine knot superfamily containing a cystine knot motif in a C-terminal cysteine-rich region. Genotyping of 10 SNPs in human CER1 gene in 1,083 high and low BMD subjects revealed a non-synonymous SNP (rs3747532) was associated with an increased risk of low BMD in premenopausal women (odds ratio 2.2; 95% confidence interval: 1.0 - 4.6; p < 0.05). Our successful identification of an association of CER1 with BMD variation in both young mature female mice and humans suggested that CER1 is one of the genes associated with peak bone mass. Our study highlights the utility of publicly available databases for rapidly surveying the genome for QTL. References: 1. Pletcher, M. T., McClurg, P., Batalov, S., Su, A. I., Barnes, S. W., Lagler, E., et al. (2004). Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse. PLoS Biol 2:e393 2. http://www.jax.org/phenome