The present GWAS study represents an effort to detect additional genes underlying human stature variation and replication evidence for previously identified stature loci. The most important result from this study is the finding that two genomic regions containing SBF2 and FLNB appear to be two novel loci that determine variation of stature. This study also provides additional replication evidence for some of the already published stature loci.
Previous GWAS studies of human stature have identified genetic variants that, collectively, explain <10% of the population variation in stature; thus most of the genetic basis for variations in stature remains unexplained. Results of the current GWAS study were able to confirm approximately a dozen previously identified genetic variants for their associations with stature (4
), but a large number of previously identified genetic variants failed to be replicated for their associations with stature. Most of the previously published loci explained <0.3% of stature variation. Using a threshold P
= 0.05, the statistical power in a sample size of 1000, estimated by the software Genetic Power Calculator (http://pngu.mgh.harvard.edu/~purcell/gpc/qtlassoc.html
), is <50% for detecting a gene that accounts for 0.3% of stature variation. Therefore, the most likely reason why so many loci did not replicate is a lack of robust statistical power. Another potential explanation for such failure to replicate is that some of the previously identified loci may be population specific.
We compared the associations for the four SNPs, which were selected for replication studies (listed in Table ), to the freely available height association results, which were deposited by Wellcome Trust Case Control Consortium (WTCCC) and published on-line from the British 1958 Birth Cohort DNA Collection (www.b58cgene.sgul.ac.uk/
), but the signals for these SNPs are negative [P
= 0.92 (β = 0.0248), 0.88 (β = −0.0466), 0.61 (β = −0.1219) and 0.59 (β = −0.1352), and one-tailed P
= 0.46, 0.56, 0.68 and 0.70, for rs10734652, rs1867138, rs11607174 and rs9834312, respectively]. There are many factors potentially resulting in lack of replication. First, the effect sizes of variants observed in our data may be very small and thus easily lead to failure of replication. Using the observed one-tailed P
-values in the public data as thresholds, the estimated power (by the software Genetic Power Calculator) is >91.7 to replicate a variant that accounts for 0.3% of stature variation. However, our estimated effect sizes for the identified markers in our initial GWAS study are from 0.43 to 1.04% (Table ). Therefore, the public data seem to suggest that our effect sizes are overestimated. Secondly, the difference in gene–gene or gene–environment interactions between the two data sets may result in inconsistency in replication. Thirdly, the association results for the four SNPs have a chance of 3.4–8% representing false positives, as the estimated FDR q
values are 0.034, 0.034, 0.071 and 0.08 for rs10734652, rs1867138, rs11607174 and rs9834312, respectively, at the genome-wide levels (Table ).
Since gender is an important factor influencing stature variation, we performed a gender-specific GWAS analyses (data not shown). The association results in the total sample can be generally replicated by the results in each gender group. However, the association signals are generally weaker, which may be largely due to the smaller sample sizes in gender-specific analyses, leading to lower statistical power. Additionally, in the association analyses we have used gender as an important covariate to correct for its potential confounding effects on human stature.
A cluster of eight contiguous SNPs in the FLNB
gene had P
-values between 5.94 × 10−4
and 1.04 × 10−5
, and three of these SNPs were significantly associated with human stature. FLNB
has previously been shown to regulate intracellular signaling pathways associated with skeletal development (14
). Interestingly, mutations in the FLNB
gene have been found to cause four human skeletal disorders (spondylocarpotarsal syndrome, autosomal dominant Larsen syndrome, type I atelosteogenesis and type III atelosteogenesis), characterized by a wide diversity of skeletal abnormalities, including short stature, block fusions, epiphyseal delay, disharmonious bone mineralization, etc. (14
). Further, functional studies observed strong FLNB
expression in condensing chondrocytes within vertebral bodies of sectioned embryos, and in the epiphyseal growth plate (14
). Another study confirmed that mutations of FLNB
may cause chondrocyte defects in skeletal development (15
). These findings indicate that FLNB
plays a pivotal role in vertebral patterning and skeletal morphogenesis. With further support from the current significant association results and from previous linkage results (17
), it appears highly likely that FLNB
is a novel gene involved in regulating human stature.
Another cluster of 18 contiguous SNPs in the region containing SBF2
had a raw point-wise testing P
< 0.001, and each of seven contiguous SNPs in this region were significantly associated with human stature. SBF2
is a member of the myotubularin-related protein family. To the best of our knowledge, no studies have demonstrated direct relevance of SBF2
to bone growth or developmental processes, both apparently associated with stature. However, mutation of the SBF2
gene has been shown to cause an autosomal recessive Charcot–Marie–Tooth disease type 4B, characterized by foot deformities and distal muscle weakness and atrophy (18
); this suggests possible involvement of the SBF2
gene in biological processes related to bone and muscle growth. This observation, together with the present significant association findings and linkage evidence from a previous study (17
), supports the concept that the SBF2
gene is a novel candidate gene underlying human stature.
In summary, we identified two novel genomic regions of about 230 and 160 kb, containing the SBF2 and FLNB genes, which were both significantly associated with human stature in Caucasians. These associations were supported by four independent replication studies in Caucasian and even in Chinese, an ethnic population different from Caucasian. These results, together with the known functions of FLNB and SBF2 genes related to growth processes, support that the two regions containing FLNB and SBF2 genes are two novel loci underlying human stature. Based on our findings, further identification of potential causative variants in the two novel loci will be pursued via genotyping denser SNPs or re-sequencing the novel genomic region containing the genes, plus potential in-depth functional studies.