scholarly journals Genetic Variations and Frequencies of the Two Functional Single Nucleotide Polymorphisms of SLCO1B1 in the Thai Population

2020 ◽  
Vol 11 ◽  
Author(s):  
Chalitpon Na nakorn ◽  
Jariya Waisayarat ◽  
Charungthai Dejthevaporn ◽  
Pornpen Srisawasdi ◽  
Sansanee Wongwaisayawan ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
Thai Population ◽  
Single Nucleotide

Functional nonsynonymous single nucleotide polymorphisms from the TGF-β protein interaction network

2007 ◽  
Vol 29 (2) ◽  
pp. 109-117 ◽  
Author(s):  
Sevtap Savas ◽  
Ian W. Taylor ◽  
Jeff L. Wrana ◽  
Hilmi Ozcelik
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Protein Interactions ◽  
Transforming Growth Factor ◽  
Conservation Status ◽  
Genetic Variations ◽  
Phosphorylation Sites ◽  
Nucleotide Polymorphisms ◽  
Protein Protein Interactions ◽  
Single Nucleotide ◽  
Putative Protein

Protein complexes mediated by protein-protein interactions are essential for many cellular functions. Transforming growth factor (TGF)-β signaling involves a cascade of protein-protein interactions and malfunctioning of this pathway has been implicated in human diseases. Using an in silico approach, we analyzed the naturally occurring human genetic variations from the proteins involved in the TGF-β signaling (10 TGF-β proteins and 242 other proteins interacting with them) to identify the ones that have potential biological consequences. All proteins were searched in the dbSNP database for the presence of nonsynonymous single nucleotide polymorphisms (nsSNPs). A total of 118 validated nsSNPs from 63 proteins were retrieved and analyzed in terms of 1) evolutionary conservation status, 2) being located in a functional protein domain or motif, and 3) altering putative protein motif or phosphorylation sites. Our results indicated the presence of 31 nsSNPs that occurred at evolutionarily conserved residues, 37 nsSNPs were located in protein domains, motifs, or repeats, and 46 nsSNPs were predicted to either create or abolish putative protein motifs or phosphorylation sites. We undertook this study to analyze the human genetic variations that can affect the protein function and the TGF-β signaling. The nsSNPs reported in here can be characterized by experimental approaches to elucidate their exact biological roles and whether they are related to human disease.

scholarly journals Single Nucleotide Polymorphisms in PEMT and MTHFR Genes are Associated with Omega 3 and 6 Fatty Acid Levels in the Red Blood Cells of Children with Obesity

Nutrients ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 2600 ◽  
Author(s):  
Vlad Serafim ◽  
Adela Chirita-Emandi ◽  
Nicoleta Andreescu ◽  
Diana-Andreea Tiugan ◽  
Paul Tutac ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Red Blood Cells ◽  
Blood Cells ◽  
Methylenetetrahydrofolate Reductase ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
Dietary Intakes ◽  
Omega 3 ◽  
Single Nucleotide ◽  
Pufa Composition

Polyunsaturated fatty acids (PUFAs) play important roles in health and disease. PUFA levels are influenced by nutrition and genetic factors. The relationship between PUFA composition in red blood cells (RBCs) and genetic variations involved in PUFA metabolism has not been investigated in children with obesity. This study evaluated the association between several genetic variations and PUFA levels in RBCs in children with obesity. One hundred ninety-six children with obesity (101 females, 95 males) were evaluated using anthropometric measurements, dietary intakes, plasma and RBC PUFA quantification, blood biochemistry, and 55 single nucleotide polymorphisms within 14 genes. phosphatidylethanolamine N-methyltransferase (PEMT) rs1109859 and methylenetetrahydrofolate reductase gene (MTHFR) rs4846052 genotypes were associated with PUFA levels in RBCs. PUFA intake did not influence the RBC eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) levels. Higher RBC DHA and EPA levels were observed for PEMT rs1109859 GG and GA genotypes versus the AA genotype. Higher levels of RBC DHA, EPA, arachidonic acid (ARA), and linoleic acid (LA) and were observed for MTHFR rs4846052 TT genotype versus TC and CC genotypes. Genetic variations in PEMT rs1109859 and MTHFR rs4846052 were associated with different PUFA levels in RBC membranes and are estimators for PUFA species in RBCs. Further research is needed to establish whether these genotype-specific alterations are specific to overweight children.

scholarly journals Comparison between the HLA-B∗58 : 01 Allele and Single-Nucleotide Polymorphisms in Chromosome 6 for Prediction of Allopurinol-Induced Severe Cutaneous Adverse Reactions

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Niwat Saksit ◽  
Nontaya Nakkam ◽  
Parinya Konyoung ◽  
Usanee Khunarkornsiri ◽  
Wongwiwat Tassaneeyakul ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Strong Association ◽  
Chromosome 6 ◽  
Surrogate Markers ◽  
Nucleotide Polymorphisms ◽  
Thai Population ◽  
Single Nucleotide ◽  
Life Threatening ◽  
Sensitivity Specificity ◽  
Degree Of Association

Severe cutaneous adverse drug reactions (SCARs) are life-threatening reactions. The strong association between the HLA-B∗58 : 01 allele and allopurinol-induced SCARs is well recognized. Screening for HLA-B∗58 : 01 allele before prescribing allopurinol in some populations has been recommended. Several single-nucleotide polymorphisms (SNPs) in chromosome 6 have been found to be tightly linked with the HLA allele, and these SNPs have been proposed as surrogate markers of the HLA-B∗58 : 01 allele. This study aimed to evaluate the association between three SNPs in chromosome 6 and allopurinol-induced SCARs in a Thai population. The linkage disequilibrium between the HLA-B∗58 : 01 allele and these SNPs was also evaluated. Results showed that three SNPs including rs9263726, rs2734583, and rs3099844 were significantly associated with allopurinol-induced SCARs but with a lower degree of association when compared with the HLA-B∗58 : 01 allele. The sensitivity, specificity, PPV, and NPV of these SNPs were comparable to those of the HLA-B∗58 : 01 allele. Although detection of the SNP is simpler and less expensive compared with that of the HLA-B∗58 : 01 allele, these SNPs were not perfectly linked with the HLA-B∗58 : 01 allele. Screening using these SNPs as surrogate markers of the HLA-B∗58 : 01 allele to avoid SCARs prior to allopurinol administration needs caution because of their imperfect linkage with the HLA-B∗58 : 01 allele.

Genetic variations associated with long noncoding RNAs

2020 ◽  
Vol 64 (6) ◽  
pp. 867-873 ◽  
Author(s):  
Jianjun Luo ◽  
Runsheng Chen
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Development Process ◽  
Noncoding Rnas ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Immune Disease ◽  
Single Nucleotide

Abstract Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome, including the long noncoding RNA (lncRNA) regions. The changes at locus might produce numerous effects in a variety of aspects. Multiple bioinformatics resources and tools were also developed for systematically dealing with genetic variations associated with lncRNAs. Moreover, correlation of the genetic variations in lncRNAs with immune disease, cancers, and other disease as well as development process were all included for discussion. In this essay, we summarized how and in what aspects these changes would affect lncRNA functions.

Single nucleotide polymorphisms and haplotypes of protein C and protein S genes in the Thai population

2006 ◽  
Vol 17 (1) ◽  
pp. 13-18 ◽  
Author(s):  
Worawan Chumpia ◽  
Chayanon Peerapittayamongkol ◽  
Pantep Angchaisuksiri ◽  
Nantarat Komanasin ◽  
Koichiro Muta ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Protein C ◽  
Protein S ◽  
Nucleotide Polymorphisms ◽  
Thai Population ◽  
Single Nucleotide ◽  
S Genes

Three Novel Single Nucleotide Polymorphisms of UGT1A9 in a Thai Population

2009 ◽  
Vol 24 (5) ◽  
pp. 482-485 ◽  
Author(s):  
Porntipa Korprasertthaworn ◽  
Wandee Udomuksorn ◽  
Krongtong Yoovathaworn
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Thai Population ◽  
Single Nucleotide

scholarly journals Association of genetic variations in genes involved in glutathione metabolism with risk of development of uterine fibroids

2020 ◽  
pp. 52-54
Author(s):  
О.К. Кудрявцева ◽  
Е.М. Барышева ◽  
И.Н. Вдовина ◽  
А.А. Клиновская ◽  
Е.А. Новикова ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Multiplex Pcr ◽  
Uterine Fibroids ◽  
Genetic Variations ◽  
Glutathione Metabolism ◽  
Healthy Controls ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Increased Risk ◽  
Risk Of Disease

В исследование были включены 552 пациентки с миомой матки (ММ) и 337 женщин контрольной группы соответствующего возраста. Генотипирование однонуклеотидных полиморфизмов (rs713041 GPX4, rs4902346 GPX2, rs41303970 GCLM, rs17883901 GCLC, rs1050450 GPX1, rs1799811 и rs1695 GSTP1, rs2551715 GSR, rs1801310 GSS, rs4820599 GGT1, rs7674870 SLC7A11) было проведено методом ПЦР в режиме реального времени; генотипирование делеционных полиморфизмов (+/0 GSTM1 и +/0 GSTT1) было проведено методом мультиплексной ПЦР. С повышенным риском развития ММ ассоциировался rs7674870 SLC7A11 (OR=1,25, 95%CI=1,03-1,50; p=0,02). Полиморфизм rs2551715 GSR обладал протективным эффектом относительно развития заболевания (OR=0,83, 95%CI=0,70-0,99; p=0,04). A total of 552 females with uterine fibroids and 337 age-matched healthy controls were recruited for the study. Genotyping of single nucleotide polymorphisms (SNPs) of rs713041 GPX4, rs4902346 GPX2, rs41303970 GCLM, rs17883901 GCLC, rs1050450 GPX1, rs1799811 and rs1695 GSTP1, rs2551715 GSR, rs1801310 GSS, rs4820599 GGT1, rs7674870 SLC7A11 were done using Taq-Man-based assays. Genotyping of +/0 GSTM1 and +/0 GSTT1 polymorphisms were done using multiplex PCR. Polymorphism rs7674870 SLC7A11 was associated with increased risk of uterine fibroids (OR=1.25, 95%CI=1.03-1.50; p=0.02); rs2551715 GSR was associated with decreased risk of disease (OR=0.83, 95% CI=0.70-0.99; p=0.04)

scholarly journals Association between Vitamin D Receptor Single-Nucleotide Polymorphisms and Colorectal Cancer in the Thai Population: A Case-Control Study

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Sirinporn Suksawatamnuay ◽  
Supachaya Sriphoosanaphan ◽  
Prapimphan Aumpansub ◽  
Satimai Aniwan ◽  
Kessarin Thanapirom ◽  
...  
Keyword(s):  
Vitamin D ◽  
Single Nucleotide Polymorphisms ◽  
Vitamin D Receptor ◽  
Colorectal Carcinogenesis ◽  
Nucleotide Polymorphisms ◽  
Control Groups ◽  
Thai Population ◽  
Single Nucleotide ◽  
And Control ◽  
Control Study

Vitamin D and its cognate intracellular nuclear receptor, namely, vitamin D receptor (VDR), are involved in the regulation of a variety of body metabolic processes, immune function, and oncogenesis. A large number of studies demonstrated the association of low vitamin D levels and variations in five common single nucleotide polymorphisms (SNPs), FokI, BsmI, Tru9I, ApaI, and TaqI, with the risk of several cancers, including colorectal cancers. However, these associations vary among different populations. This case-control study was aimed at analysing whether common single-nucleotide polymorphisms (SNPs) and haplotypes of the vitamin D receptor (VDR) gene contribute to colorectal carcinogenesis in the Thai population. We enrolled 364 Thai participants from King Chulalongkorn Memorial Hospital between 2014 and 2015. Half of the participants underwent colonoscopy and showed a normal colon without polyps (control group) and another half were newly diagnosed patients with colorectal cancer (CRC) by colonoscopy during the index period, were under treatment, or were followed up at the outpatient clinic (case group). Differences in allele and genotype frequencies of five common VDR SNPs, between the case and control groups, were the primary outcome measures. Differences in haplotype frequencies of the five SNPs between the case and control groups were the secondary outcome measures. Among the 364 participants, baseline characteristics were not significantly different between the case and control groups, except for the higher proportion of males in the CRC group. The mean vitamin D level was also not significantly different between the case and control groups (24.6±9.1 vs. 25.3±10.6 ng/mL, p=0.52). None of the five VDR SNPs was associated with CRC development (p>0.05). However, haplotype analysis of these polymorphisms demonstrated that the AGGT haplotype was associated with a decreased risk of CRC (odds ratio 0.24, 95% confidence interval 0.07-0.81, p=0.01). The AGGT haplotype was associated with a lower risk of CRC in the Thai population. This genetic linkage might support the role of vitamin D in colorectal carcinogenesis. However, this finding requires further study within a larger population and a multivariate analysis of other established risk factors.

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