Common variants in a novel gene, FONG on chromosome 2q33.1 confer risk of osteoporosis in Japanese

Abstract

Osteoporosis is a common disease characterized by low bone mass, decreased bone quality and increased predisposition to fracture. Genetic factors have been implicated in its etiology; however, the specific genes related to susceptibility to osteoporosis are not entirely known. To detect susceptibility genes for osteoporosis, we conducted a genome-wide association study in Japanese using ∼270,000 SNPs in 1,747 subjects (190 cases and 1,557 controls) followed by multiple levels of replication of the association using a total of ∼5,000 subjects (2,092 cases and 3,114 controls). Through these staged association studies followed by resequencing and linkage disequilibrium mapping, we identified a single nucleotide polymorphism (SNP), rs7605378 associated with osteoporosis. (combined P = 1.51×10(-8), odds ratio = 1.25). This SNP is in a previously unknown gene on chromosome 2q33.1, FONG. FONG is predicted to encode a 147 amino-acid protein with a formiminotransferase domain in its N-terminal (FTCD_N domain) and is ubiquitously expressed in various tissues including bone. Our findings would give a new insight into osteoporosis etiology and pathogenesis.

Figure 1. Evaluation of population stratification for the GWAS.

(A) Principal component analysis. Samples in the GWAS and in HapMap database are analyzed by a program, Smartpca , and plotted for the first (X axis) and the second (Y axis) principal components (PCs), respectively. Our case and control samples are plotted in a single cluster of Japanese. (B) Quantile-quantile (Q-Q) plots of allelic association using Fisher's exact (allelic) test in Discovery 2. Under the null hypothesis of no association at any locus, the points would be expected to follow the slope line (light green). Deviations of the points (red dots) from the line correspond to loci that deviate from the null hypothesis. The genetic inflation factor lambda is 1.04.

Figure 2. Association signals around rs7605378 on chromosome 2 in the GWAS stage.

(A) LD plot for the studied region based on the r ² statistic. The intensity of shading is proportional to r ². (B) Genomic structure around the FONG region. (C) Results of GWAS for osteoporosis in a Japanese population. The log10-transformed P values are plotted on the y axis.

Figure 3. Nucleotide and deduced amino acid sequences of FONG.

A domain homologous to the FTCD_N domain is underlined. A stop codon is indicated by an asterisk, and the putative poly-A addition signal is enclosed in an open box. Multiple transcription start sites (TSSs) were identified by 5′-RACE, but only the major TSS is shown.

Figure 4. Tissue expression of FONG.

(A) Northern blotting in human tissues. Lane 1, kidney; lane 2, skeletal muscle; lane 3, liver; lane 4, bone. (B) Quantitative real-time PCR in various human tissues. FONG is highly expressed in liver, skeletal muscle, and moderately expressed in bone. Data represent the mean ratios of FONG mRNA to β-actin (ACTB) mRNA ± s.e.m. of two independent experiments.