Influence of TLR-8 Gene Polymorphisms (rs3764880 and rs3788935) Associated to Pulmonary Tuberculosis in Kupang, Indonesia
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Toll-like receptor 8 (TLR-8) is known as part of intracellular signaling transduction for bacterial phagocytosis. Mycobacterium tuberculosis (Mtb) is intracellular pathogenic bacteria that is recognized by this receptor, and genetic variation of TLR-8 might alter susceptibility of the host towards pulmonary tuberculosis (PTB). This study aimed to determine whether TLR-8 gene polymorphisms were associated to PTB in Kupang, Indonesia. This case-control study compared demographic and clinical data between 115 PTB patients and 115 controls, then two TLR-8 single nucleotide polymorphisms (rs3764880 and rs3788935) were explored using the GoldenGate® Genotyping for VeraCode® / BeadXpress Illumina®. There is no significant difference between sex distribution of patient vs control groups. The polymorphisms (rs3764880 and rs3788935) are in Hardy-Weinberg Equilibrium in this population (p > 0.05). The distribution of major vs minor genotypes and alleles of TLR-8 polymorphisms in PTB patients were as followed: rs3764880 (GG vs GA vs AA, 50.0% vs 21.4% vs 28.6% ; G vs A, 60.9% vs 39.1% ) and rs3788935 (GG vs GA vs AA, 53.0% vs 21.7% vs 25.3%; G vs A, 62.9% vs 37.1%). Neither genotypes nor alleles were associated with PTB in this population (P > 0.05). Besides, when the analyses were stratified by gender, none of the alleles of polymorphism in both genders were associated with PTB cases. None of the TLR-8 polymorphisms have associated the risk of developing PTB in Kupang, East Nusa Tenggara population (as opposed to other studies in different ethnic groups). These might reflect the diversity of genetic polymorphisms in eastern Indonesia populations, suggesting different genetic backgrounds with western part of Indonesia.Keywords:
Minor allele frequency
1523 Background: The receptor activator of NfkappaB (RANK) and osteoprotegerin (OPG) cascade system have been reported to play a role in the pathogenesis of breast cancer (BC). Genetic variations in the genes coding for RANK, RANK ligand (RANKL), and OPG are supposed to play a role in the susceptibility of breast cancer. Methods: In the present case-control study genomic DNA was obtained from 307 BC patients (age: median 56) and 396 healthy female controls (healthy blood donors, HC; age median: 45). We studied six single nucleotide polymorphisms (SNPs) in the genes coding for RANK (2 SNPs, rs1805034, rs35211496), OPG (2 SNPs, rs3102735, rs2073618), and RANKL (2 SNPs, rs9533156, rs2277438) using TaqMan assay-guided PCR for the respective SNPs. The genotype and allelic frequencies comparing BC with HC were analyzed with χ2 test for 2x3 and 2x2 tables, respectively. Results: The genotype distributions as well as the allelic frequencies of the SNP rs3102735 in the OPG gene differed significantly (p=0.006 and p=0.019, respectively) between BC patients and HC; the genotypes containing the minor allele were more frequent in BC patients (table). In the OPG SNP rs2073618 the minor allele C was significantly less frequent in BC patients compared to HC (43.8 vs. 49.7%; OR: 0.788; p=0.031). In addition, BC patients carried less frequently the homozygous genotype of the minor allele compared to major allele (18.6 vs. 23.9%, p=0.083). No significant risk was detected for the other SNPs investigated in this study. Conclusions: This is the first study reporting a significant association of the SNP rs3102735 in the OPG gene with the susceptibility to develop BC in the Caucasian population. The minor allele C of OPG SNP rs2073618, however, seems to be protective against BC disease. The impact of the OPG SNP rs3102735 (location: 5`near region, chromosome 8q24) and of the OPG SNP rs2073618 (a missense SNP, leading to amino acid exchanges Leu3Asn) on the pathogenesis of BC are unclear. [Table: see text]
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Ιστορικό: Υπαρχουν συσσωρεύμενα στοιχεία για την ύπαρξη γενετικής ευαισθησίας στην ανάπτυξη διαβητικής αμφιβληστροειδοπάθειας (ΔΑ). Ο ρόλος του αναστολέα του ενεργοποιητή του πλασμινογόνου-1 (PAI-1) στον κινδυνο αναπτυξης ΔΑ παραμένει αμφιλεγόμενος.Σκοπός: Η παρούσα μελέτη σχεδιάστηκε για να διερευνήσει την πιθανή επίδραση των πολυμορφισμών της περιοχής του γονιδίου PAI-1 στον κίνδυνο ανάπτυξης της ΔΑ και στον κίνδυνο ανάπτυξης ΔΑ πρώιμα έναντι καθυστερημένα κατά τη διάρκεια του σακχαρώδους διαβήτη τύπου 2 (ΣΔ2). Μέθοδοι: Συνολικά 138 ασθενείς με ΔΑ, 107 ασθενείς με ΣΔ2 χωρίς ΔΑ και 315 υγιείς μάρτυρες προσλήφθηκαν. Για να καλυφθεί η πλειοψηφία της γενετικής μεταβλητότητας στην εκτεταμένη περιοχή του γονιδίου ΡΑΙ-1, πέντε πολυμορφισμοί μονού νουκλεοτιδίου (single-nucleotide polymorphisms SNPs) από το HapMap χρησιμοποιώντας μια προσέγγιση ανά ζεύγη και r2> 0,8 και μία μικρή συχνότητα αλληλόμορφων (minor allele frequency MAF)> 0,05 εντοπίστηκαν. Χρησιμοποιώντας αναλύσεις λογιστικής παλινδρόμησης, ετικέτες SNPs και απλότυποι δοκιμάστηκαν για ενώσεις με κίνδυνο ανάπτυξης ΔΑ και με κίνδυνο ανάπτυξης ΔΑ νωρίς ή αργά κατά τη διάρκεια του ΣΔ2. Ο γενικευμένος λόγος πιθανότητας (generalized odds ratio ORG) υπολογίστηκε για την εκτίμηση της επίδρασης μεταλλακτικού φορτίου στην ανάπτυξη ΔΑ μεταξύ όλων των συμμετεχόντων. Διενεργήθηκαν διορθώσεις για πολλαπλές συγκρίσεις (p-τιμή <0,01).Αποτελέσματα: Ένα σημαντικό αποτέλεσμα του rs2070682 στον κίνδυνο πρόωρης έναρξης ΔΑ βρέθηκε στο συνκυριαρχο μοντέλο κληρονομικότητας [αναλογία πιθανότητας, OR (95% διάστημα εμπιστοσύνης, CI): 5.04 (1.47-17.28), p = 0.018]. Ωστόσο, αυτή η σχέση οριακά δεν επιβίωσε πολλαπλών διορθώσεων και δοκιμών. Δεν αποκαλύφθηκε καμία άλλη σημαντική συσχέτιση μεταξύ των επισημάνσεων-SNPs και των απλοτύπων ΡΑΙ-1. Επιπλέον, δεν βρέθηκε σημαντική επίδραση του μεταλλακτικού φορτίου της ετικέττας SNPs στον PAI-1 στον κίνδυνο ανάπτυξης ΔΑ στη διαρκεια του ΣΔ2. Συμπεράσματα: Συμπερασματικά, η παρούσα μελέτη δεν παρέχει καμία ισχυρή απόδειξη ότι οι παραλλαγές του γονιδίου PAI-1 εμπλέκονται στον κίνδυνο ανάπτυξης της ΔΑ ή στην ανάπτυξη της ΔΑ κατά τη διάρκεια του ΣΔ2.
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To identify single nucleotide polymorphisms (SNPs) in the brain-derived neurotrophic factor (BDNF), vitamin D receptor (VDR), and DNASE1 genes that may be associated with dry eye disease (DED), and determine whether this association varies by the presence of depression.A case-control study was performed with 64 DED cases and 51 controls. We collected 2 mL of saliva following a routine eye exam. Genotyping was performed using both custom and predesigned TaqMan SNP genotyping assays for 12 hypothesized SNPs. Genotype and allele frequencies of cases and controls were evaluated. Odds ratios were calculated for allele frequencies. Stratified analysis was performed to determine if the association between SNPs and DED varied by depression status.A total of 18% of cases had the minor allele A of Val66Met (rs6265) SNP in the BDNF gene compared with 9% of the controls (P = 0.05). Odds ratio was 2.22. Two SNPs (Fokl-rs2228570 and Apal-rs7975232) in the VDR genes also varied between DED cases and controls. Cases were 1.72 and 1.66 times more likely to have the minor allele A in rs2228570 and rs7975232, respectively, than controls (P = 0.06 for both). While not statistically significant, among patients with depression, DED cases were 3.93 times more likely to have the minor allele A of the Val66Met SNP compared to controls.This pilot study showed that Val66Met in the BDNF gene and two SNPs, Fokl and Apal, in the VDR gene may potentially be associated with DED. Additionally, the association between DED and Val66Met may vary by depression status.
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Abstract Accurately resolving population structure in a sample is important for both linkage and association studies. In this study we investigated the power of single-nucleotide polymorphisms (SNPs) in detecting population structure in a sample of 286 unrelated individuals. We varied the number of SNPs to determine how many are required to approach the degree of resolution obtained with the Collaborative Study on the Genetics of Alcoholism (COGA) short tandem repeat polymorphisms (STRPs). In addition, we selected SNPs with varying minor allele frequencies (MAFs) to determine whether low or high frequency SNPs are more efficient in resolving population structure. We conclude that a set of at least 100 evenly spaced SNPs with MAFs of 40–50% is required to resolve population structure in this dataset. If SNPs with lower MAFs are used, then more than 250 SNPs may be required to obtain reliable results.
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The objective of this study was to develop and validate a customized cost-effective single nucleotide polymorphism (SNP) panel for genetic improvement of feed efficiency in beef cattle. The SNPs identified in previous association studies and through extensive analysis of candidate genomic regions and genes, were screened for their functional impact and allele frequency in Angus and Hereford breeds used as validation candidates for the panel. Association analyses were performed on genotypes of 159 SNPs from new samples of Angus (n = 160), Hereford (n = 329), and Angus-Hereford crossbred (n = 382) cattle using allele substitution and genotypic models in ASReml. Genomic heritabilities were estimated for feed efficiency traits using the full set of SNPs, SNPs associated with at least one of the traits (at P ≤ 0.05 and P < 0.10), as well as the Illumina bovine 50K representing a widely used commercial genotyping panel. A total of 63 SNPs within 43 genes showed association (P ≤ 0.05) with at least one trait. The minor alleles of SNPs located in the GHR and CAST genes were associated with decreasing effects on residual feed intake (RFI) and/or RFI adjusted for backfat (RFIf), whereas minor alleles of SNPs within MKI67 gene were associated with increasing effects on RFI and RFIf. Additionally, the minor allele of rs137400016 SNP within CNTFR was associated with increasing average daily gain (ADG). The SNPs genotypes within UMPS, SMARCAL, CCSER1, and LMCD1 genes showed significant over-dominance effects whereas other SNPs located in SMARCAL1, ANXA2, CACNA1G, and PHYHIPL genes showed additive effects on RFI and RFIf. Gene enrichment analysis indicated that gland development, as well as ion and cation transport are important physiological mechanisms contributing to variation in feed efficiency traits. The study revealed the effect of the Jak-STAT signaling pathway on feed efficiency through the CNTFR, OSMR, and GHR genes. Genomic heritability using the 63 significant (P ≤ 0.05) SNPs was 0.09, 0.09, 0.13, 0.05, 0.05, and 0.07 for ADG, dry matter intake, midpoint metabolic weight, RFI, RFIf, and backfat, respectively. These SNPs contributed to genetic variation in the studied traits and thus can potentially be used or tested to generate cost-effective molecular breeding values for feed efficiency in beef cattle.
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Aggressive periodontitis (AgP) is influenced by genetic factors. Recently, the single nucleotide polymorphisms (SNPs) rs1537415 (GLT6D1), rs6667202 (IL10), and rs1333048 (ANRIL) were associated with AgP in different European populations. However, these specific SNPs have not yet been determined in Brazilians. Therefore, this study investigated whether these SNPs previously associated with AgP could be replicated among Brazilians.The SNPs rs1537415, rs6667202, and rs1333048 were genotyped using 5'-nuclease allelic discrimination assay in AgP (n = 200), chronic periodontitis (CP, n = 190), and healthy patients (H, n = 196). Differences in allele and genotype frequencies were analyzed using chi-square tests and stepwise logistic regression.The minor C allele of rs6667202 was less frequently detected in AgP patients (23.5%) when compared to non-AgP groups (H = 34.2% and CP = 30.3%; p < 0.01), making the SNP protective against AgP occurrence. Moreover, the final logistic model for AgP diagnosis included gender (p = 0.001) and the SNP rs6667202 (p < 0.001) as significant variables. The SNPs rs1537415 and rs1333048 did not show associations with AgP.Only the SNP rs6667202 was associated with AgP in a Brazilian population, being the minor C allele protective against AgP. Moreover, SNPs rs1333048 and rs1537415, previously associated with AgP in other population, was not validated to Brazilian population.
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