Polymorphisms of IRAK1 Gene on X Chromosome Is Associated with Hashimoto Thyroiditis in Korean Children

Endocrinology ◽  
2020 ◽  
Vol 161 (8) ◽  
Author(s):  
Hye-Ri Shin ◽  
Won Kyoung Cho ◽  
In-Cheol Baek ◽  
Na Yeong Lee ◽  
Yoon Ji Lee ◽  
...  
Keyword(s):  
X Chromosome ◽  
Hashimoto Thyroiditis ◽  
Categorical Variables ◽  
Graves Disease ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Korean Children ◽  
Autoimmune Thyroid ◽  
Thyroid Associated Ophthalmopathy

Abstract Autoimmune thyroid disease (AITD) is predominant in females and has been focused on the sexual diploid in immune response. The IL-1 receptor-associated kinase 1 (IRAK1) gene on the X chromosome was recently suggested as strong autoimmune disease-susceptible loci, second to the major histocompatibility complex region. We investigated the frequency of IRAK1 single-nucleotide polymorphisms (SNPs) in children with AITD. In this study, we observed that SNPs of IRAK1 including rs3027898, rs1059703, and rs1059702 in 115 Korean AITD pediatric patients (Graves’ disease = 74 [females = 52/males = 22]; Hashimoto disease [HD] = 41 [females = 38/males = 3]; thyroid-associated ophthalmopathy [TAO] = 40 (females = 27/males = 13); without TAO = 75 (females = 63/males = 12); total males = 25, total females = 90; mean age = 11.9 years) and 204 healthy Korean individuals (males = 104/females = 100). The data from cases and controls were analyzed from separate sex-stratified or all combined by χ 2 test for categorical variables and Student t test for numerical variables. Our study revealed that SNPs of IRAK1-associated HD and without TAO but Graves’ disease and TAO were not found significant. When cases and controls were analyzed by separate sex, we found that rs3027898 AA, rs1059703 AA, and rs1059702 GG showed disease susceptibility in female AITD, HD, and without TAO. Also, all rs3027898, rs1059703, and rs1059702 were found to be in strong linkage disequilibrium (D′ = 0.96-0.98, r2 = 0.83–0.97). The haplotype of 3 SNPs was higher in AITD than in controls (CGA, r2 = 5.42, P = 0.019). Our results suggest that IRAK1 polymorphisms may contribute to the pathogenesis of HD, AITD, and without thyroid-associated ophthalmopathy for females.

scholarly journals SUN-724 Associations of GPR174 and ITM2A Genes on X Chromosome with Early Onset Autoimmune Thyroid Disease in Korean

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Nayeong Lee ◽  
Wonkyoung Cho ◽  
Hyeri Shin ◽  
Yoonji Lee ◽  
Seulki Kim ◽  
...  
Keyword(s):  
X Chromosome ◽  
Thyroid Disease ◽  
Autoimmune Thyroid Disease ◽  
Nucleotide Polymorphisms ◽  
Autoimmune Thyroid Diseases ◽  
Single Nucleotide ◽  
Korean Children ◽  
Autoimmune Thyroid ◽  
Thyroid Associated Ophthalmopathy ◽  
Immune Related Genes

Abstract Background: Autoimmune thyroid diseases (AITDs) are female predominant and the biology of sexual dimorphism is not clearly understood. Recently, GPR174 and ITM2A on X chromosome have been newly suggested as autoimmune thyroid disease susceptible loci. Methods: Fourteen single nucleotide polymorphisms in immune related genes on X chromosome were analyzed in 108 Korean children (girls =90, boys =18) with AITD [Hashimoto disease (HD) = 40, Graves′ disease (GD) = 68, thyroid-associated ophthalmopathy (TAO) = 37, and non-TAO =60] with gender ratio matched normal control 106 controls (female = 43, male = 63). Results: In AITD, the frequencies of GPR174 rs3810711 T allele (OR=6.0, cP =0.000), GRP174 rs3827440 T allele (OR=6.0, cP =0.000), ITM2A-GPR174 rs5912838 A allele (OR=2.7, cP =0.001) were increased and of GPR174 rs3810711 CC genotype (OR=0.2, cP =0.000), GRP174 rs3827440 CC genotype (OR=0.2, cP =0.000), ITM2A-GPR174 rs5912838 CC genotype (OR=0.4, cP =0.000)were lower than controls. In GD, the frequencies of GPR174 rs3810711 T allele (OR=8.4, cP =0.000), GRP174 rs3827440 T allele (OR=8.4, cP =0.000), ITM2A-GPR174 rs5912838 A allele (OR=3.3, cP =0.000) were increased and GPR174 rs3810711 CC genotype (OR=0.1, cP =0.000), C allele (OR=0.5, cP =0.044), GRP174 rs3827440 CC genotype (OR=0.2, cP =0.000), C allele (OR=0.5, cP =0.044), ITM2A-GPR174 rs5912838 CC genotype (OR=0.4, cP =0.000) were lower than controls. In HD, the frequencies of GPR174 rs3810711 T allele (OR=3.9, cP =0.003), GRP174 rs3827440 T allele(OR=3.9, cP =0.003) were increased and GPR174 rs3810711 CC genotype (OR=0.3, cP =0.004), rs3827440 CC genotype (OR=3.9, cP =0.003) were lower than controls. In thyroid-associated ophthalmopathy, the frequencies of GPR174 rs3810711 T allele (OR=7.9, cP =0.000), GRP174 rs3827440 T allele (OR=7.9, cP =0.000), ITM2A-GPR174 rs5912838 A allele (OR=3.1, cP =0.001) were increased and of GPR174 rs3810711 CC genotype (OR=0.1, cP =0.000), GRP174 rs3827440 CC genotype (OR=0.1, cP =0.000), ITM2A-GPR174 rs5912838 CC genotype (OR=0.3, cP =0.014)were lower than controls. Conclusions. Our results suggest that polymorphisms of GPR174 and ITM2A genes on X chromosome might contribute to the pathogenesis of AITD.

scholarly journals GPR174 and ITM2A Gene Polymorphisms rs3827440 and rs5912838 on the X chromosome in Korean Children with Autoimmune Thyroid Disease

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 858
Author(s):  
Won Kyoung Cho ◽  
Hye-Ri Shin ◽  
Na Yeong Lee ◽  
Seul Ki Kim ◽  
Moon Bae Ahn ◽  
...  
Keyword(s):  
X Chromosome ◽  
Autoimmune Thyroid Disease ◽  
Integral Membrane Protein ◽  
Nucleotide Polymorphisms ◽  
Autoimmune Thyroid Diseases ◽  
Single Nucleotide ◽  
Korean Children ◽  
Autoimmune Thyroid ◽  
Thyroid Associated Ophthalmopathy ◽  
G Protein Coupled

(1) Background: Autoimmune thyroid diseases (AITDs) are female predominant and much attention has been focused on G protein-coupled receptor 174 (GPR174) and integral membrane protein 2A (ITM2A) on the X chromosome as Grave’s disease (GD) susceptible locus. (2) Methods: We genotyped four single nucleotide polymorphisms (SNPs), rs3810712, rs3810711, rs3827440, and rs5912838, of GPR174 and ITM2A in 115 Korean children with AITD (M = 25 and F = 90; GD = 74 (14.7 ± 3.6 years), HD = 41 (13.4 ± 3.2 years); GD-thyroid-associated ophthalmopathy (TAO) = 40, GD-non-TAO=34) and 204 healthy Korean individuals (M = 104 and F = 100). The data were analyzed by sex-stratified or combined. (3) Results: Three SNPs, rs3810712, rs3810711 and rs3827440, were found to be in perfect linkage disequilibrium (D’ = 1, r2 = 1). In AITD, HD, GD, GD-TAO, and GD-non-TAO patients, rs3827440 TT/T and rs5912838 AA/A were susceptible and rs3827440 CC/C and rs5912838 CC/C were protective genotypes. When analyzed by sex, rs3827440 TT and rs5912838 AA were susceptible and rs3827440 CC and rs5912838 CC were protective genotypes in female AITD, GD, GD-TAO, and GD-non-TAO subjects. In male AITD patients, rs3827440 T and rs5912838 A were susceptible and rs3827440 C and rs5912838 C were protective genotypes. (4) Conclusions: Polymorphisms in GPR174 and ITM2A genes on the X chromosome might be associated with AITD in Korean children.

scholarly journals Association of Polymorphisms in Toll-Like Receptors 4 and 9 with Autoimmune Thyroid Disease in Korean Pediatric Patients

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Won Kyoung Cho ◽  
Jung-Pil Jang ◽  
Eun-Jeong Choi ◽  
Moonbae Ahn ◽  
Shin Hee Kim ◽  
...  
Keyword(s):  
Autoimmune Thyroid Disease ◽  
Pediatric Patients ◽  
Nucleotide Polymorphisms ◽  
Toll Like Receptors ◽  
Single Nucleotide ◽  
Korean Children ◽  
Autoimmune Thyroid ◽  
Hashimoto Disease ◽  
Thyroid Associated Ophthalmopathy ◽  
Genotype C

Background. Toll-like receptors (TLRs) have been suggested to be associated with the development of AITD. Methods. Fifteen single-nucleotide polymorphisms in 7 TLR genes were analyzed in 104 Korean children (girls = 86, boys = 18) with AITD (Hashimoto disease (HD) = 44, Graves’ disease (GD) = 60, thyroid-associated ophthalmopathy (TAO) = 29, and non-TAO = 31) with 183 controls. Results. GD showed higher frequencies of the TLR4 rs1927911 C allele than control. TAO showed a lower frequency of the TLR4 rs1927911 CT genotype and non-TAO showed a higher frequency of the TLR4 rs1927911 CC genotype than control. The frequency of the TLR9 rs187084 CC genotype in TAO was higher than that in non-TAO. GD females showed a higher frequency of the TLR4 rs10759932 T allele, rs1927911 CC genotype, and the rs1927911 C allele than controls. GD males showed a higher frequency of the TLR4 rs10759932 CC genotype and rs1927911 TT genotype and lower frequency of the rs1927911 CT genotype than control. The frequency of the TLR4 rs10759932 CC genotype, C allele and rs1927911 TT genotype, and T allele in a GD female were lower than in a GD male. Conclusions. Our results suggest that TLR4 and 9 polymorphisms might contribute to the pathogenesis of GD and TAO.

scholarly journals Selection of X-chromosome Inactivation Model

2017 ◽  
Vol 16 ◽  
pp. 117693511774727 ◽  
Author(s):  
Jian Wang ◽  
Rajesh Talluri ◽  
Sanjay Shete
Keyword(s):  
X Chromosome ◽  
X Chromosome Inactivation ◽  
Association Test ◽  
Chromosome Inactivation ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Unified Approach ◽  
Cancer Genetic ◽  
Single Nucleotide ◽  
Selection Of

To address the complexity of the X-chromosome inactivation (XCI) process, we previously developed a unified approach for the association test for X-chromosomal single-nucleotide polymorphisms (SNPs) and the disease of interest, accounting for different biological possibilities of XCI: random, skewed, and escaping XCI. In the original study, we focused on the SNP-disease association test but did not provide knowledge regarding the underlying XCI models. One can use the highest likelihood ratio (LLR) to select XCI models (max-LLR approach). However, that approach does not formally compare the LLRs corresponding to different XCI models to assess whether the models are distinguishable. Therefore, we propose an LLR comparison procedure (comp-LLR approach), inspired by the Cox test, to formally compare the LLRs of different XCI models to select the most likely XCI model that describes the underlying XCI process. We conduct simulation studies to investigate the max-LLR and comp-LLR approaches. The simulation results show that compared with the max-LLR, the comp-LLR approach has higher probability of identifying the correct underlying XCI model for the scenarios when the underlying XCI process is random XCI, escaping XCI, or skewed XCI to the deleterious allele. We applied both approaches to a head and neck cancer genetic study to investigate the underlying XCI processes for the X-chromosomal genetic variants.

scholarly journals Association of non-synonymous SNPs of <i>OPN</i> gene with litter size traits in pigs

2015 ◽  
Vol 58 (2) ◽  
pp. 317-323 ◽  
Author(s):  
T. Kumchoo ◽  
S. Mekchay
Keyword(s):  
Litter Size ◽  
Reproductive Traits ◽  
Snp Markers ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Acid Exchange

Abstract. Osteopontin (OPN) gene is a secreted phosphoprotein which appears to play a key function in the conceptus implantation, placentation and maintenance of pregnancy in pigs. The objectives of this study were to verify the non-synonymous single nucleotide polymorphisms (SNPs) and their association with litter size traits in commercial Thai Large White pigs. A total of 320 Thai Large White sows were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Three SNPs at c.425G> A, c.573T> C and c.881C> T revealed amino acid exchange rates of p.110Ala> Thr, p.159Val> Ala and p.262Pro> Ser, respectively, and were then segregated. These three SNPs were significantly associated with total number born (TNB) and number born alive (NBA) traits. No polymorphisms of the two SNP markers (c.278A> G and c.452T> G) were observed in this study. Moreover, the SNPs at c.425G> A and c.573T> C were found to be in strong linkage disequilibrium. The association of OPN with litter size emphasizes the importance of porcine OPN as a candidate gene for reproductive traits in pig breeding.

Variation at the von Willebrand Factor (vWF) Gene Locus Is Associated With Plasma vWF:Ag Levels: Identification of Three Novel Single Nucleotide Polymorphisms in the vWF Gene Promoter

Blood ◽  
1999 ◽  
Vol 93 (12) ◽  
pp. 4277-4283 ◽  
Author(s):  
Angela M. Keightley ◽  
Y. Miu Lam ◽  
Jolene N. Brady ◽  
Cherie L. Cameron ◽  
David Lillicrap
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Von Willebrand Factor ◽  
Gene Locus ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Polymorphic Variation ◽  
Single Nucleotide ◽  
Haplotype 1 ◽  
Von Willebrand ◽  
Willebrand Factor

Abstract Both genetic and environmental factors contribute to the normal population variability of plasma von Willebrand Factor (vWF) levels, however, regulatory mechanisms at the vWF gene locus itself have not yet been identified. We have investigated the association between polymorphic variation in the 5′-regulatory region of the vWF gene and levels of plasma vWF:Ag in a study of 261 group O blood donors. Three novel single nucleotide polymorphisms (SNPs) were identified in the vWF promoter: C/T at -1234, A/G at -1185, and G/A at -1051. These SNPs had identical allele frequencies of 0.36 for the -1234C, -1185A, and -1051G alleles and 0.64 for the -1234T, -1185G, and -1051A alleles and were in strong linkage disequilibrium. In fact, these polymorphisms segregated as two distinct haplotypes: -1234C/-1185A/-1051G (haplotype 1) and -1234T/-1185G/-1051A (haplotype 2) with 12.6% of subjects homozygous for haplotype 1, 40.6% homozygous for haplotype 2, and 42.5% of subjects heterozygous for both haplotypes. Only 4.3% of individuals had other genotypes. A significant association between promoter genotype and level of plasma vWF:Ag was established (analysis of covariance [ANCOVA], P = .008; Kruskal-Wallis test,P = .006); individuals with the CC/AA/GG genotype had the highest mean vWF:Ag levels (0.962 U/mL), intermediate values of vWF:Ag (0.867 U/mL) were observed for heterozygotes (CT/AG/GA), and those with the TT/GG/AA genotype had the lowest mean plasma vWF:Ag levels (0.776 U/mL). Interestingly, when the sample was subgrouped according to age, the significant association between promoter genotype and plasma vWF:Ag level was accentuated in subjects &gt; 40 years of age (analysis of variance [ANOVA], P = .003; Kruskal-Wallis test, P= .001), but was not maintained for subjects ≤ 40 years of age (ANOVA, P &gt; .4; Kruskal-Wallis test, P &gt; .4). In the former subgroup, mean levels of plasma vWF:Ag for subjects with the CC/AA/GG, CT/AG/GA, and TT/GG/AA genotypes were 1.075, 0.954, and 0.794 U/mL, respectively. By searching a transcription factor binding site profile database, these polymorphic sequences were predicted to interact with several transcription factors expressed in endothelial cells, including Sp1, GATA-2, c-Ets, and NFκB. Furthermore, the binding sites at the -1234 and -1051 SNPs appeared to indicate allelic preferences for some of these proteins. Electrophoretic mobility shift assays (EMSAs) performed with recombinant human NFκB p50 showed preferential binding of the -1234T allele (confirmed by supershift EMSAs), and EMSAs using bovine aortic endothelial cell (BAEC) nuclear extracts produced specific binding of a nuclear protein to the -1051A allele, but not the -1051G allele. These findings suggest that circulating levels of vWF:Ag may be determined, at least in part, by polymorphic variation in the promoter region of the vWF gene, and that this association may be mediated by differential binding of nuclear proteins involved in the regulation of vWF gene expression.

scholarly journals Correlation of TSHR and CTLA-4 Single Nucleotide Polymorphisms with Graves Disease

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Weihua Sun ◽  
Xiaomei Zhang ◽  
Jing Wu ◽  
Wendi Zhao ◽  
Shuangxia Zhao ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
T Lymphocyte ◽  
Cytotoxic T Lymphocyte ◽  
Thyroid Stimulating Hormone ◽  
Taqman Probe ◽  
Graves Disease ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Han Population ◽  
Positive Correlations

This study was designed to explore the association between Graves disease (GD) and thyroid-stimulating hormone receptor (TSHR) and cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) single nucleotide polymorphisms (SNPs). We studied a total of 1217 subjects from a Han population in northern Anhui province in China. Six SNPs within TSHR (rs179247, rs12101261, rs2284722, rs4903964, rs2300525, and rs17111394) and four SNPs within CTLA-4 (rs10197319, rs231726, rs231804, and rs1024161) were genotyped via a Taqman probe technique using a Fluidigm EP1 platform. The TSHR alleles rs179247-G, rs12101261-C, and rs4903964-G were negatively correlated with GD, whereas the rs2284722-A and rs17111394-C alleles were positively correlated with GD. Analyzing TSHR SNPs at rs179247, rs2284722, rs12101261, and rs4903964 yielded 8 different haplotypes. There were positive correlations between GD risk and the haplotypes AGTA and AATA (OR=1.27, 95%CI=1.07‐1.50, P=0.005; OR=1.45, 95%CI=1.21‐1.75, P<0.001, respectively). There were negative correlations between GD risk and the haplotype GGCG (OR=0.56, 95%CI=0.46‐0.67, P<0.001). With respect to haplotypes based on SNPs at the TSHR rs2300525 and rs17111394 loci, the CC haplotype was positively correlated with GD risk (OR=1.32, 95%CI=1.08‐1.60, P=0.006). Analyzing CTLA-4 SNPs at rs231804, rs1024161, and rs231726 yielded four haplotypes, of which AAA was positively correlated with GD risk (OR=1.21, 95%CI=1.02‐1.43, P=0.029). Polymorphisms at rs179247, rs12101261, rs2284722, rs4903964, and rs17111394 were associated with GD susceptibility. Haplotypes of both TSHR and CTLA-4 were additionally related to GD risk.

Use of Tag single nucleotide polymorphisms (SNPs) to screen PTPN21: no association with Graves' disease

2006 ◽  
Vol 65 (3) ◽  
pp. 380-384 ◽  
Author(s):  
A. A. Zeitlin ◽  
J. M. Heward ◽  
O. J. Brand ◽  
P. R. Newby ◽  
J. A. Franklyn ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Graves Disease ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Contribution of Single Nucleotide Polymorphisms withinFCRL3andMAP3K7IP2to the Pathogenesis of Graves’ Disease

2006 ◽  
Vol 91 (3) ◽  
pp. 1056-1061 ◽  
Author(s):  
M. J. Simmonds ◽  
J. M. Heward ◽  
J. Carr-Smith ◽  
H. Foxall ◽  
J. A. Franklyn ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Graves Disease ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide
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