Replication study of the association of SNPs in the LHX3-QSOX2 and IGF1 loci with adult height in the Japanese population; wide-ranging comparison of each SNP genotype distribution

Association of a single nucleotide polymorphism (rs27434) in the ERAP1 gene with plural tissue weight

Our study was designed to examine the correlation between single nucleotide polymorphism (SNP) in the endoplasmic reticulum aminopeptidase 1 (ERAP1) gene, specifically focusing on rs27434, and plural tissue weight. We conducted this investigation using autopsy samples from the Japanese population. Blood samples were collected from 178 Japanese subjects who had undergone autopsies in Shimane Prefecture. Genomic DNA was subsequently extracted from these samples. SNP (rs27434, G＞A substitution) was analyzed by polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) analysis. In the present study, rs27434 exhibited a statistically significant association with brain weight (g) in both female and male individuals. Among males, rs27434 displayed significant relationships with liver weight (g), and body surface area (m2). In females, rs27434 was significantly related to the length of the appendix. Across both genders, individuals with GA and AA genotypes tended to exhibit higher levels in these respective measurements compared to those with the GG genotype. These results suggest that genetic variant of ERAP1 gene may influence the weight of the organs. To the best of our knowledge, this is the first study investigating the interaction between the association of rs27434 in the ERAP1 gene and data routinely measured at autopsy, such as tissue weight. However, conducting further investigations with larger population samples could provide more comprehensive insights to clarify this issue.

Disorders of IGFs and IGF-1R signaling pathways

The insulin-like growth factor (IGF) system comprises two ligands, IGF-I and IGF-II, that regulate multiple physiological processes, including mammalian development, metabolism and growth, through the type 1 IGF receptor (IGF-1R). The growth hormone (GH)-IGF-I axis is the major regulator of longitudinal growth. IGF-II is expressed in many tissues, notably the placenta, to regulate human pre- and post-natal growth and development. This review provides a brief introduction to the IGF system and summarizes findings from reports arising from recent larger genomic sequencing studies of human genetic mutations in IGF1 and IGF2 and genes of proteins regulating IGF action, namely the IGF-1R, IGF-1R signaling pathway components and the IGF binding proteins (IGFBPs). A perspective on the effect of homozygous mutations on structure and function of the IGFs and IGF-1R is also given and this is related to the effects on growth.

Genetic Architecture Associated With Familial Short Stature

CONTEXT

Human height is an inheritable, polygenic trait under complex and multilocus genetic regulation. Familial short stature (FSS; also called genetic short stature) is the most common type of short stature and is insufficiently known.

OBJECTIVE

To investigate the FSS genetic profile and develop a polygenic risk predisposition score for FSS risk prediction.

DESIGN AND SETTING

The FSS participant group of Han Chinese ancestry was diagnosed by pediatric endocrinologists in Taiwan.

PATIENTS AND INTERVENTIONS

The genetic profiles of 1163 participants with FSS were identified by using a bootstrapping subsampling and genome-wide association studies (GWAS) method.

MAIN OUTCOME MEASURES

Genetic profile, polygenic risk predisposition score for risk prediction.

RESULTS

Ten novel genetic single nucleotide polymorphisms (SNPs) and 9 reported GWAS human height-related SNPs were identified for FSS risk. These 10 novel SNPs served as a polygenic risk predisposition score for FSS risk prediction (area under the curve: 0.940 in the testing group). This FSS polygenic risk predisposition score was also associated with the height reduction regression tendency in the general population.

CONCLUSION

A polygenic risk predisposition score composed of 10 genetic SNPs is useful for FSS risk prediction and the height reduction tendency. Thus, it might contribute to FSS risk in the Han Chinese population from Taiwan.

Association of SNPs in transferrin and transferrin receptor genes with blood iron levels in human

Iron is bound to mobile transferrin (TF) and ferritin in blood. TF receptors (TFRC and TFR2) regulate intracellular iron by delivering iron from TF into the cytoplasm. In this study, we examined the effects of 10 single nucleotide polymorphisms (SNPs) in each of the genes for TF and TF receptors on blood iron concentrations in Japanese subjects. Blood iron levels were determined by microwave plasma-atomic emission spectrometry and the SNPs were analyzed by polymerase chain reaction followed by restriction fragment length polymorphism analysis. Blood iron levels in males were significantly higher than those in females. Therefore, the analysis was performed only in males. Blood iron concentrations did not correlate with age and postmortem intervals in males. Among the 10 SNPs in TF, TFRC, and TFR2 genes, significant associations were observed between TF genotypes (rs12769) and male iron concentrations. Individuals with genotype GG in rs12769 had significantly higher blood iron concentrations than those with GA. Previous studies have shown the association between high tissue iron concentrations and disease, liver iron levels are higher in infants dying from sudden infant death syndrome and decreased blood iron concentrations were observed in critically ill children. Therefore, rs12769 in TF might be related to diseases and mortality risk.

Association of SNPs in genes encoding zinc transporters on blood zinc levels in humans

Zinc homeostasis in cells depends on zinc transporters, which are divided into 2 families: ZnT (SLC30A) and ZIP (SLC39A). In this study, we examined the effect of 20 single nucleotide polymorphisms (SNPs) in 10 genes encoding zinc transporters on blood zinc concentration in Japanese subjects (n = 102). Blood zinc levels were determined by microwave plasma-atomic emission spectrometry, and SNPs were analyzed by polymerase chain reaction followed by restriction fragment length polymorphism analysis. Among the 20 SNPs examined, 3 SNPs (SLC30A3 rs11126936, SLC39A8 rs233804, and SLC39A14 rs4872479) were significantly associated with blood zinc concentration. Individuals with genotype TT and TG in rs11126936 showed significantly higher blood zinc concentrations than those with GG. As for rs233804, individuals harboring the A allele had significantly higher blood zinc concentrations than those without this allele. Furthermore, the genotype TT and TG in rs4872479 had significantly higher blood zinc concentrations than those with GG. Among these three SNPs, combination of SLC30A3 rs11126936 and SLC39A8 rs233804 may strongly affect blood zinc levels. This study is the first comprehensive investigation of the effect of SNPs in genes encoding zinc transporters on blood zinc concentration. Adverse effects of zinc deficiency are reported and above 3 SNPs may be related to genetic susceptibility to zinc deficiency.

Increased detection of genetic loci associated with risk predictors of osteoporotic fracture using a pleiotropic cFDR method

Although GWAS have been successful in identifying some osteoporosis associated loci, the findings explain only a small fraction of the total genetic variance. In this study we use a recently developed novel pleiotropic conditional false discovery rate (cFDR) method to identify novel genetic loci associated with two risk traits for osteoporotic fracture (the clinical outcome and end result of osteoporosis), Height (HT) and Femoral Neck (FNK) BMD. The cFDR method allows us to improve the detection of associated variants by incorporating any potentially shared genetic mechanisms between the two associated traits. We analyzed the summary statistics from two GWAS meta-analyses for single nucleotide polymorphisms (SNPs) that are associated with HT and FNK BMD. Using the cFDR method, we show enrichment in the identification of SNPs associated with each trait conditioned on their strength of association with the second trait. The findings revealed 18 SNPs that are associated with both HT and FNK BMD, 4 of which had not previously been reported to play a role in bone health. The novel SNPs located at KIF1B and the intergenic region between FERD3L and TWISTNB are noteworthy as these genes may be associated with processes that are functionally important in bone metabolism. By leveraging GWAS results from related phenotypes we identified several novel loci that may contribute to the proportion of variability explained for each trait, although we cannot speculate about these potential contributions to heritability based on this analysis alone.