scholarly journals Previously Unidentified Single Nucleotide Polymorphisms in HIV/AIDS Cases Associate with Clinical Parameters and Disease Progression

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Vladimir V. Anokhin ◽  
Liliia B. Bakhteeva ◽  
Gulshat R. Khasanova ◽  
Svetlana F. Khaiboullina ◽  
Ekaterina V. Martynova ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Hiv Infection ◽  
Multiplex Pcr ◽  
Disease Progression ◽  
Killer Cell ◽  
Clinical Parameters ◽  
Nucleotide Polymorphisms ◽  
Oligoadenylate Synthetase ◽  
Single Nucleotide ◽  
Hiv Aids

The genetic background of an individual plays an important role in the progression of HIV infection to AIDS. Identifying previously unknown or uncharacterized single nucleotide polymorphisms (SNPs) that associate with disease progression may reveal important therapeutic targets and provide a greater understanding of disease pathogenesis. In the present study, we employed ultra-high multiplex PCR on an Ion Torrent next-generation sequencing platform to sequence 23 innate immune genes from 94 individuals with HIV/AIDS. This data was used to identify potential associations of SNPs with clinical parameters and disease progression. SNPs that associated with an increased viral load were identified in the genes for the interleukin 15 receptor (IL15RA), toll-like receptor 7 (TLR7), tripartite motif-containing protein 5 (TRIM5), and two killer-cell immunoglobulin-like receptors (KIR2DL1andKIR2DL3). Additionally, SNPs that associated with progression from HIV infection to AIDS were identified in two 2′-5′-oligoadenylate synthetase genes (OAS2andOAS3). In contrast, other SNPs identified inOAS2andOAS3genes, as well as in theTRIM5andKIR2DS4genes, were associated with a slower progression of disease. Taken together, our data demonstrates the utility of ultra-high multiplex PCR in identifying polymorphisms of potential clinical significance and further,identifies SNPs that may play a role in HIV pathogenesis.

scholarly journals PXR and CAR single nucleotide polymorphisms influence plasma efavirenz levels in South African HIV/AIDS patients

2012 ◽  
Vol 13 (1) ◽  
Author(s):  
Marelize Swart ◽  
Heather Whitehorn ◽  
Yuan Ren ◽  
Peter Smith ◽  
Rajkumar S Ramesar ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
South African ◽  
Nucleotide Polymorphisms ◽  
Aids Patients ◽  
Single Nucleotide ◽  
Hiv Aids

Molecular identification of Allium ochotense and Allium microdictyon using multiplex-PCR based on single nucleotide polymorphisms

2018 ◽  
Vol 59 (6) ◽  
pp. 865-873 ◽  
Author(s):  
Yong-Bog Kim ◽  
Rahul Vasudeo Ramekar ◽  
Seong-Jin Choi ◽  
Byoung-Gon Choi ◽  
Se-Won Kim ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Multiplex Pcr ◽  
Molecular Identification ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals 2′-5′-Oligoadenylate synthetase single-nucleotide polymorphisms and haplotypes are associated with variations in immune responses to rubella vaccine

2010 ◽  
Vol 71 (4) ◽  
pp. 383-391 ◽  
Author(s):  
Iana H. Haralambieva ◽  
Neelam Dhiman ◽  
Inna G. Ovsyannikova ◽  
Robert A. Vierkant ◽  
V. Shane Pankratz ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Immune Responses ◽  
Nucleotide Polymorphisms ◽  
Oligoadenylate Synthetase ◽  
Rubella Vaccine ◽  
Single Nucleotide

scholarly journals The association between interferon lambda 3 and 4 gene single-nucleotide polymorphisms and the recovery of COVID-19 patients

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Pooneh Rahimi ◽  
Rahil Tarharoudi ◽  
Alireza Rahimpour ◽  
Jalal Mosayebi Amroabadi ◽  
Iraj Ahmadi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Factors ◽  
Clinical Parameters ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Interferon Lambda ◽  
Ct Value ◽  
Host Genetic ◽  
Interferon Lambda 3 ◽  
Host Genetic Factors

Abstract Background The recent pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has elevated several clinical and scientific questions. These include how host genetic factors influence the pathogenesis and disease susceptibility. Therefore, the aim of this study was to evaluate the impact of interferon lambda 3 and 4 (IFNL3/4) gene polymorphisms and clinical parameters on the resistance and susceptibility to coronavirus disease 2019 (COVID-19) infection. Methods A total of 750 SARS-CoV-2 positive patients (375 survivors and 375 nonsurvivors) were included in this study. All single-nucleotide polymorphisms (SNPs) on IFNL3 (rs12979860, rs8099917, and rs12980275) and IFNL4 rs368234815 were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) method. Results In this study, a higher viral load (low PCR Ct value) was shown in nonsurvivor patients. In survivor patients, the frequency of the favorable genotypes of IFNL3/4 SNPs (rs12979860 CC, rs12980275 AA, rs8099917 TT, and rs368234815 TT/TT) was significantly higher than in nonsurvivor patients. Multivariate logistic regression analysis has shown that a higher low-density lipoprotein (LDL), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and PCR Ct value, and lower 25-hydroxyvitamin D, and also IFNL3 rs12979860 TT, IFNL3 rs8099917 GG, IFNL3 rs12980275 GG, and IFNL4 rs368234815 ∆G/∆G genotypes were associated with the severity of COVID-19 infection. Conclusions The results of this study proved that the severity of COVID-19 infection was associated with clinical parameters and unfavorable genotypes of IFNL3/IFNL4 SNPs. Further studies in different parts of the world are needed to show the relationship between severity of COVID-19 infection and host genetic factors.

scholarly journals Smart approach for cost-effective genotyping of single nucleotide polymorphisms

2021 ◽  
Vol 48 (2) ◽  
Author(s):  
Muhammad U. Ghani ◽  
◽  
Muhammad F. Sabar ◽  
Muhammad Akram ◽  
◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Multiplex Pcr ◽  
Cost Effective ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Modified Method ◽  
Human Dna ◽  
Detection Assay ◽  
Genomic Studies ◽  
Snapshot Minisequencing

Single Nucleotide Polymorphisms (SNPs) are in the prime focus of genomic studies for their probable roles in diagnostics and prognosis of diseases and forensic science. SNaPshot/minisequencing reaction-based genotyping of targeted SNPs is a method of choice due to its fast and reliable detection assay. Here we described smart modifications in minisequencing reaction to make it cost-effective to detect 15 SNPs in a single assay. The target SNPs were amplified in a multiplex PCR from genomic DNA, and these multiplex PCR amplicons were utilized as a template in modified SNaPshot reaction for SNPs identification. The modified protocol was assessed for reproducibility on more than 50 human DNA samples, and it was observed that this modified method is at least five times more productive than the original protocol recommended by the manufacturer. The current smart modifications in SNaPshot reaction were successfully optimized for susceptible asthma SNPs. However, these can be applied for cost-effective genotyping of any type of genomic Single Nucleotide Polymorphisms.

Association of single-nucleotide polymorphisms in TLR7 (Gln11Leu) and TLR9 (1635A/G) with a higher CD4T cell count during HIV infection

2014 ◽  
Vol 160 (1) ◽  
pp. 58-64 ◽  
Author(s):  
E.A. Said ◽  
F. Al-Yafei ◽  
F. Zadjali ◽  
S.S. Hasson ◽  
M.S. Al-Balushi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Hiv Infection ◽  
Cell Count ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cd4t Cell
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