Pleiotropy and heterogeneity in the expression of bone strength-related phenotypes in extended pedigrees

BMP7 gene polymorphisms are not associated with bone mineral density or osteoporotic fractures in postmenopausal Chinese women

AIM

A previous study shows that bone morphogenetic protein 7 (BMP7) gene polymorphisms are associated with bone mineral density (BMD) in 920 European Americans. To determine the association of BMP7 polymorphisms and BMD and osteoporotic fracture susceptibility, we performed a case-control association study in postmenopausal Chinese women with or without osteoporotic fracture.

METHODS

A total of 3815 unrelated postmenopausal Chinese women (1238 with osteoporotic fracture and 2577 healthy controls) were recruited. BMDs of the lumbar spine 1-4 (L1-4) and proximal femur (including total hip and femoral neck) were measured using dual-energy X-ray absorptiometry. Eight tagging single nucleotide polymorphisms (SNPs) in BMP7 gene, including rs11086598, rs4811822, rs12481628, rs6025447, rs230205, rs17404303, rs162316 and rs6127980, were genotyped.

RESULTS

Among the 8 SNPs, rs6025447 and rs230205 were associated with total hip BMD (P=0.013 and 0.045, respectively). However, the associations became statistically insignificant after adjusting for age, height and weight. The TGTG haplotype of BMP7 gene was associated with total hip BMD (P=0.032), even after adjusting for age, height and weight (P=0.048); but the association was insignificant after performing the Bonferroni multiple-significance-test correction. Moreover, the 8 SNPs and 9 haplotypes of BMP7 gene were not associated with L1-4 or femoral neck BMD or osteoporotic fracture.

CONCLUSION

This large-sample case-control association study suggests that the common genetic polymorphisms of BMP7 gene are not major contributors to variations in BMD or osteoporotic fracture in postmenopausal Chinese women.

Weak Epistasis Generally Stabilizes Phenotypes in a Mouse Intercross

The extent and strength of epistasis is commonly unresolved in genetic studies, and observed epistasis is often difficult to interpret in terms of biological consequences or overall genetic architecture. We investigated the prevalence and consequences of epistasis by analyzing four body composition phenotypes—body weight, body fat percentage, femoral density, and femoral circumference—in a large F2 intercross of B6-lit/lit and C3.B6-lit/lit mice. We used Combined Analysis of Pleiotropy and Epistasis (CAPE) to examine interactions for the four phenotypes simultaneously, which revealed an extensive directed network of genetic loci interacting with each other, circulating IGF1, and sex to influence these phenotypes. The majority of epistatic interactions had small effects relative to additive effects of individual loci, and tended to stabilize phenotypes towards the mean of the population rather than extremes. Interactive effects of two alleles inherited from one parental strain commonly resulted in phenotypes closer to the population mean than the additive effects from the two loci, and often much closer to the mean than either single-locus model. Alternatively, combinations of alleles inherited from different parent strains contribute to more extreme phenotypes not observed in either parental strain. This class of phenotype-stabilizing interactions has effects that are close to additive and are thus difficult to detect except in very large intercrosses. Nevertheless, we found these interactions to be useful in generating hypotheses for functional relationships between genetic loci. Our findings suggest that while epistasis is often weak and unlikely to account for a large proportion of heritable variance, even small-effect genetic interactions can facilitate hypotheses of underlying biology in well-powered studies.

The role of statistical epistasis in the genetic architecture of complex traits has been of great interest to the genetics community since Fisher introduced the concept in 1918. However, assessing epistasis in human and model organism populations has been impeded by limited statistical power. To mitigate this limitation, we analyzed bone and body composition traits in an unusually large mouse intercross population of over 2000 mice, paired with a recently-developed computational approach that leverages information to detect interactions across multiple phenotypes. We discovered a large network of highly significant genetic interactions between variants that influence complex body composition traits. Although epistasis was abundant, the interaction network was dominated by epistasis that stabilizes phenotypes by reducing phenotypic deviation from the parent strains. Nevertheless, the observed network provides an overview of genetic architecture and specific hypotheses of how QTL combine to affect phenotypes. These findings suggest that epistatic effects are generally of lesser magnitude than main QTL effects, and therefore are unlikely to account for major components of variance, but also reinforce genetic interaction analysis as a potent tool for dissecting the biology of complex traits.

Genetic analysis of vertebral trabecular bone density and cross-sectional area in older men

We investigated 383 bone candidate genes for associations between single nucleotide polymorphisms and vertebral trabecular volumetric bone mineral density (vBMD) and cross-sectional area (CSA) in 2,018 Caucasian men aged ≥ 65 years. SNPs in TGFBR3, SOST, KL, CALCR, LEP, CSF1R, PTN, GNRH2, FGFR2, and MEPE were associated with vBMD and SNPs in CYP11B1, DVL2, DLX5, WNT4, and PAX7 were associated with CSA in independent study samples (p < 0.005).

INRODUCTION

Vertebral bone mineral density and cross-sectional area are important determinants of vertebral bone strength. Little is known about the specific genetic variants that influence these phenotypes in humans.

METHODS

We investigated the potential genetic variants associated with vertebral trabecular volumetric BMD and CSA measured by quantitative computed tomography. We initially tested for association between these phenotypes and 4608 tagging and potentially functional single nucleotide polymorphisms (SNPs) in 383 candidate genes in 862 community-dwelling Caucasian men aged ≥ 65 years in the Osteoporotic Fractures in Men Study.

RESULTS

SNP associations were then validated by genotyping an additional 1,156 randomly sampled men from the same cohort. We identified 11 SNPs in 10 genes (TGFBR3, SOST, KL, CALCR, LEP, CSF1R, PTN, GNRH2, FGFR2, and MEPE) that were consistently associated with trabecular vBMD and five SNPs in five genes (CYP11B1, DVL2, DLX5, WNT4, and PAX7) that were consistently associated with CSA in both samples (p < 0.005).

CONCLUSION

None of the SNPs associated with trabecular vBMD were associated with CSA. Our findings raise the possibility that at least some of the loci for vertebral trabecular BMD and bone size may be distinct.

Candidate gene analysis of femoral neck trabecular and cortical volumetric bone mineral density in older men

In contrast to conventional dual-energy X-ray absorptiometry, quantitative computed tomography separately measures trabecular and cortical volumetric bone mineral density (vBMD). Little is known about the genetic variants associated with trabecular and cortical vBMD in humans, although both may be important for determining bone strength and osteoporotic risk. In the current analysis, we tested the hypothesis that there are genetic variants associated with trabecular and cortical vBMD at the femoral neck by genotyping 4608 tagging and potentially functional single-nucleotide polymorphisms (SNPs) in 383 bone metabolism candidate genes in 822 Caucasian men aged 65 years or older from the Osteoporotic Fractures in Men Study (MrOS). Promising SNP associations then were tested for replication in an additional 1155 men from the same study. We identified SNPs in five genes (IFNAR2, NFATC1, SMAD1, HOXA, and KLF10) that were robustly associated with cortical vBMD and SNPs in nine genes (APC, ATF2, BMP3, BMP7, FGF18, FLT1, TGFB3, THRB, and RUNX1) that were robustly associated with trabecular vBMD. There was no overlap between genes associated with cortical vBMD and trabecular vBMD. These findings identify novel genetic variants for cortical and trabecular vBMD and raise the possibility that some genetic loci may be unique for each bone compartment.

Cross-sectional geometry of the femoral midshaft in baboons is heritable

A great deal of research into the determinants of bone strength has unequivocally demonstrated that variation in bone strength is highly subject to genetic factors. Increasing attention in skeletal genetic studies is being paid to indicators of bone quality that complement studies of BMD, including studies of the genetic control of bone geometry. The aim of this study is to investigate the degree to which normal population-level variation in femoral midshaft geometry in a population of pedigreed baboons (Papio hamadryas spp.) can be attributed to the additive effect of genes. Using 110 baboons (80 females, 30 males), we 1) characterize normal variation in midshaft geometry of the femur with regard to age and sex, and 2) determine the degree to which the residual variation is attributable to additive genetic effects. Cross-sectional area (CSA), minimum (I(MIN)) and maximum (I(MAX)) principal moments of inertia, and polar moment of inertia (J) were calculated from digitized images of transverse midshaft sections. Maximum likelihood-based variance decomposition methods were used to estimate the mean effects of age, sex, and genes. Together age and sex effects account for approximately 56% of the variance in each property. In each case the effect of female sex is negative and that of age is positive, although of a lower magnitude than the effect of female sex. Increased age is associated with decreased mean cross-sectional geometry measures in the oldest females. Residual h(2) values range from 0.36 to 0.50, reflecting genetic effects accounting for 15% to 23% of the total phenotypic variance in individual properties. This study establishes the potential of the baboon model for the identification of genes that regulate bone geometric properties in primates. This model is particularly valuable because it allows for experimental designs, environmental consistency, availability of tissues, and comprehensive assessments of multiple integrated bone phenotypes that are not possible in human populations. The baboon is of particular importance in genetic studies, because it provides results that are likely highly relevant to the human condition due to the phylogenetic proximity of baboons to humans.

A comparison of principal component analysis and factor analysis strategies for uncovering pleiotropic factors

Principal component analysis (PCA) and factor analysis (FA) are often used to uncover genetic factors that contribute to complex disease phenotypes. The purpose of such an analysis is to distill a genetic signal from a large number of correlated phenotype measurements. That signal can then be used in genetic analyses (e.g. linkage analysis), presumably leading to greater success at finding genes than one would achieve with any one raw trait. Although both PCA and FA have been used this way, there has been no comparison of their performance in the literature. We compared the ability of these two procedures to extract unobserved underlying genetic components from complex simulated data on nuclear families. We first simulated seven underlying genetic and environmentally determined traits. Then we derived two sets of 50 complex (observed) traits using algebraic combinations of the underlying components. We next performed PCA and FA on the complex traits. We assessed two aspects of the performance of the methods: (1) ability to detect the underlying genetic components; (2) whether the methods worked better when applied to raw traits or to residuals (after regressing out significant environmental covariates). Our results indicate that both the methods behave similarly in most cases, although FA generally produced factors that had stronger correlations with the underlying traits. We also found that using residuals in PCA or FA analyses greatly increased the probability that the PCs or factors detected common genetic components instead of common environmental factors, except if there was statistical interaction between genetic and environmental factors.

Association analysis of WNT10B with bone mass and structure among individuals of African ancestry

Wnts comprise a family of secreted growth factors that regulate the development and maintenance of many organs. Recently, Wnt10b was shown to stimulate osteoblastogenesis and bone formation in mice. To evaluate further the role of Wnt10b in bone health in humans, we performed bidirectional sequencing of approximately 8 kb of the WNT10B gene region in 192 individuals (96 African, 96 white) to identify single nucleotide polymorphisms (SNPs). We identified 19 SNPs with minor allele frequency (MAF) > or =0.01. Ten of these SNPs were not present in the NCBI dbSNP database (build 127), whereas 10 of the 20 SNPs (50%) reported in dbSNP were not verified. We initially genotyped seven tagging SNPs that captured common (MAF > or = 0.05) variation in the region with r (2) > 0.80 and a potentially functional SNP in exon 5 in 1035 Afro-Caribbean men > or =40 yr of age. Association analysis showed three SNPs in a 3' region of linkage disequilibrium that were associated with DXA measures of hip BMD. Associations between two of these three SNPs (rs1051886, rs3741627) with hip BMD were replicated in an additional 980 Afro-Caribbean men (p < 0.05), in the combined sample of 2015 men (p < or = 0.006), and in 416 individuals > or =18 yr of age (mean, 44 yr) belonging to eight extended, multigenerational Afro-Caribbean families with mean family size >50 (3535 relative pairs; p < 0.05). Further analysis showed that rs1051886 and rs3741627 were associated with cortical cross-sectional area, periosteal circumference, and BMC in the radius, such that individuals with the minor alleles had lower biomechanical indices of long-bone bending strength. This analysis implicates the WNT10B locus as a genetic element in the regulation of bone mass and structural geometry.