Association of Single Nucleotide Polymorphisms with Dyslipidemia in Antiretroviral Exposed HIV Patients in a Ghanaian population

AbstractDyslipidemia is a potential complication of long-term usage of antiretroviral therapy (ART) and also known to be associated with genetic factors. The host genetic variants associated with dyslipidemia in HIV patients on ART in Ghana have not been fully explored. The study constituted a total of 289 HIV-infected patients on stable ART for at least a year and 85 aged matched apparently healthy control subjects with no history of HIV and dyslipidemia. Fasting blood was collected into EDTA tube for lipids measurements. Lipid profiles were determined as a measure of dyslipidemia. HIV-infected patients were categorized into two groups; those with dyslipidemia(HIV-Dys+) (n=90; 31.1%) and without dyslipidemia (n=199; 68.9%) based on the NCEP-ATP III criteria. Four candidate single nucleotide polymorphisms (SNPs) genes (ABCA1-rs2066714, LDLR-rs6511720, APOA5-rs662799 and DSCAML1-rs10892151) were determined. Genotyping was performed on isolated genomic DNA of study participants using PCR followed by a multiplex Ligation Detection Reaction (LDR). The percentage of the population who had the rare homozygote alleles for rs6511720 (T/T), rs2066714 (G/G), and rs10892151 (T/T) and rs662799 (G/G) among HIV+Dys+ subjects were 5.5%, 14.4%, 6.6% and 10.0%; 2.0% 9.1%, 6.5% and 4.0% among HIV+Dys- subjects while 3.5%, 4.7%, 4.7% and 2.4% were observed in HIV-Dys- subjects. Statistically significant difference in genotypic prevalence of APOA5 polymorphisms was observed among different groups (p=0.0196). Compared to the AA genotype of the APOA5 polymorphisms, individuals with the rare homozygote genotype [aOR =4.01, 95%CI(1.57-22.39), p=0.004] were significantly more likely to develop dyslipidemia after controlling for age, gender, treatment duration and CD4 counts among the HIV+Dys+ subjects. There was also a significant associated between GG genotype of ABCA1 and dyslipidemia [aOR =3.29, 95% (1.08 −12.43); p=0.042]. Individuals with the rare homozygote variant (GG) of APOA5 (rs662799) were significantly associated with increased likelihood of developing dyslipidemia [OR =2.24, 95% CI (1.20 −6.83); p=0.0370] holding other variables constant in the HIV+Dys- subjects. Our data accentuate the presence of SNPs in four candidate genes and its association with dyslipidemia among HIV patients exposed to ART in the Ghanaian population especially variants in APOA5-rs662799 ABCA1-rs2066714 respectively. These findings provide baseline information that necessitates a pre-symptomatic strategy for monitoring dyslipidemia in ART-treated HIV patients. There is a need for longitudinal studies to validate a comprehensive number of SNPs and its association with dyslipidemia.

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Sex Differences in Circadian Clock Genes and Myocardial Infarction Susceptibility

Journal of Cardiovascular Development and Disease ◽

10.3390/jcdd8050053 ◽

2021 ◽

Vol 8 (5) ◽

pp. 53

Author(s):

Ivana Škrlec ◽

Jasminka Talapko ◽

Martina Juzbašić ◽

Robert Steiner

Keyword(s):

Myocardial Infarction ◽

Cardiovascular Disease ◽

Circadian Rhythm ◽

Single Nucleotide Polymorphisms ◽

Clock Genes ◽

P Value ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Biological Sex ◽

Significant Difference

The growing body of evidence shows a significant difference in the circadian rhythm of cardiovascular disease based on biological sex. The incidence of cardiovascular disease varies between women and men. Additionally, biological sex is vital for the timely application of therapy—chronotherapy, which benefits both sexes. This study aimed to examine the potential difference of single nucleotide polymorphisms (SNPs) of the circadian rhythm genes ARNTL, CLOCK, CRY2 and PER2 in women and men with myocardial infarction. A cross-sectional study was conducted, including 200 patients with myocardial infarction. Altogether, ten single nucleotide polymorphisms in the ARNTL, CLOCK, CRY2 and PER2 genes were analyzed. The Chi-square test yielded statistically significant differences in CLOCK gene rs11932595 polymorphism in a recessive genotype model between women and men with a p-value of 0.03 and an odds ratio 2.66, and a corresponding 95% confidence interval of 1.07 to 6.66. Other analyzed polymorphisms of the circadian rhythm genes ARNTL, CRY2, and PER2 did not significantly differ between the sexes. According to the study’s current results, the CLOCK gene’s genetic variability might affect myocardial infarction concerning biological sex.

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Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2

Biomedicines ◽

10.3390/biomedicines9070808 ◽

2021 ◽

Vol 9 (7) ◽

pp. 808

Author(s):

Laura Pérez-Lago ◽

Teresa Aldámiz-Echevarría ◽

Rita García-Martínez ◽

Leire Pérez-Latorre ◽

Marta Herranz ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Evolutionary Dynamics ◽

Viral Evolution ◽

Special Focus ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

New Variant ◽

History Of ◽

Evolution Dynamics ◽

The Uk

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13–15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1–2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.

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Single Nucleotide Polymorphisms in COL1A2 Gene and Dental Fluorosis Among 4 and 8-Year-Old Nigerian Children

Journal of Dentistry Open Access ◽

10.31487/j.jdoa.2020.02.04 ◽

2020 ◽

pp. 1-6

Author(s):

Ruth Valentine ◽

Olushola Ibiyemi ◽

Anne Maguire ◽

Fatemeh Vida Zohoori ◽

Simon Kometa ◽

...

Keyword(s):

Drinking Water ◽

Single Nucleotide Polymorphisms ◽

Dental Fluorosis ◽

Nucleotide Polymorphisms ◽

Cross Sectional ◽

Single Nucleotide ◽

Nigerian Children ◽

Col1a2 Gene ◽

Cooking Water ◽

Study Participants

Aim: To determine the association between single nucleotide polymorphisms (SNPs) within the COL1A2 gene and dental fluorosis among 4- and 8-year-old Nigerian children. Methods: A cross-sectional study was undertaken among 125 four and eight-year-old Nigerian children living in naturally fluoridated areas of Ibadan, Nigeria. Drinking and cooking water samples were collected for F analysis. Buccal mucosa swabs were collected from all children and genomic DNA extracted. Presence or absence of the SNP within the COL1A2 gene was identified by PCR and DNA sequencing for 70 of the participants. Results: The median (minimum, maximum) F concentration of drinking and cooking water were 0.05 (<0.1, 3.0) mg/L and 0.01 (<0.1, 4.0) mg/L respectively. The majority of the study participants (52.9%) were heterozygous for the SNP. There was a statistically significant association between F concentration in drinking water and the occurrence of dental fluorosis (p=0.04). F concentration in drinking water was the only statistically significant predictor of dental fluorosis (p=0.03, OR=3.64(CI=1.11-11.94)) after adjusting for F concentration in cooking water and SNPs. The risk of dental fluorosis tended to increase with the presence of SNPs AA and AC (RR > 1) but this association was not statistically significant. Conclusion: The majority of the study participants had the heterozygote SNP AC genotype of COL1A2 gene. F concentration in drinking water was the only statistically significant predictor of dental fluorosis. The risk of dental fluorosis tended to increase with the presence of SNPs AA and AC (RR > 1) but was not statistically significant.

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Genoset for CALCA and RAMP1 Single Nucleotide Polymorphisms Are Related to the Magnitude of Headache Symptoms After Concussion: A Preliminary Observation

Neurology ◽

10.1212/01.wnl.0000801948.78004.36 ◽

2021 ◽

Vol 98 (1 Supplement 1) ◽

pp. S22.3-S23

Author(s):

Michael F. La Fountaine ◽

Anthony Testa

Keyword(s):

Single Nucleotide Polymorphisms ◽

Saliva Sample ◽

Area Under The Curve ◽

Nucleotide Polymorphisms ◽

Blurred Vision ◽

Single Nucleotide ◽

Commercial Laboratory ◽

Pain Transmission ◽

Significant Difference ◽

A Prospective Study

ObjectiveDetermine whether single nucleotide polymorphisms (SNPs) of the calcitonin gene-related polypeptide (CGRP)-alpha (CALCA) and the receptor activity modifying protein-1 (RAMP1) are related to headache burden during the first week after concussion.BackgroundPost-traumatic headache is a commonly reported symptom after concussion. SNPs related to CGRP are involved in the pathogenesis of migraine headaches and contribute to pain transmission and neurogenic inflammation. It is unclear in concussed persons if the headache burden is associated with genetic variations related to CGRP.Design/MethodsA prospective study was performed in 34 concussed athletes (gender: 23 female, 11 male; age: 20 ± 1 years; height: 1.75 ± 0.12 meters; weight: 73 ± 14 kilograms). Participants completed the symptom evaluation checklist from the SCAT3 within 48 hours of injury (V1), and 4 (V2) and 7 (V3) days after injury. For each visit, the self-reported score (0–6) for headache, pressure in head, blurred vision, and sensitivity to light/noise were summed. The area under-the-curve (AUC) was computed for the early (EHB: V1 to V2) and late (LHB: V2 to V3) burden of headache-related symptoms. A saliva sample was obtained and a commercial laboratory identified the genotype for CALCA (rs3781719) and RAMP1 (rs10185142) using PMR-array. RAMP1 genotypes RAMP1 (TT, TC, CC) and CALCA (AA, AG, GG) genotypes were dichotomized (T+, T−, and A+, A− respectively) and concatenated (T + A+, T + A−, T−A+, T-A−) for analyses.ResultsA significant difference for EHB (p = 0.003, partial η2 = 0.417) was present across RAMP1+CALCA genotypes, but not for the LHB. The T + A+ subgroup had a significantly elevated EHB compared to the all-other subgroups (p < 0.05: T + A + [n = 16]: 31.6 ± 2.6; T + A − [n = 9]: 17.7 ± 3.6; T−A+ [n = 8]: 18.4 ± 3.7; T−A-[n = 1]: 0.0 ± 0.0). Gender served as a covariate and diagnosed concussion history had no impact.ConclusionsThe current analysis provides a proof-of-concept to suggest that the combined T + A+ genoset from RAMP1+CALCA are associated with a greater headache burden in the first 4 days after concussion injury.

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ADIPOQ single nucleotide polymorphisms and breast cancer in northeastern Mexican women

BMC Medical Genetics ◽

10.1186/s12881-020-01125-8 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Ricardo M. Cerda-Flores ◽

Karen Paola Camarillo-Cárdenas ◽

Gabriela Gutiérrez-Orozco ◽

Mónica Patricia Villarreal-Vela ◽

Raquel Garza-Guajardo ◽

...

Keyword(s):

Breast Cancer ◽

Single Nucleotide Polymorphisms ◽

Mexican Women ◽

Genotype Distribution ◽

Nucleotide Polymorphisms ◽

Allelic Discrimination Assay ◽

Allelic Discrimination ◽

Single Nucleotide ◽

Significant Difference ◽

Hardy Weinberg Equilibrium

Abstract Background Adiponectin gene (ADIPOQ) polymorphisms have been shown to affect adiponectin serum concentration and some have been associated with breast cancer (BC) risk. The aims of this study were to describe the frequency of single nucleotide polymorphisms (SNPs) of ADIPOQ in Mexican women with BC and to determine if they show an association with it. Methods DNA samples from 397 patients and 355 controls were tested for the ADIPOQ gene SNPs: rs2241766 (GT) and rs1501299 (GT) by TaqMan allelic discrimination assay. Hardy–Weinberg equilibrium (HWE) was tested. Multiple SNP inheritance models adjusted by age and body mass index (BMI) were examined for the SNP rs1501299. Results We found that in the frequency analysis of rs1501299 without adjusting the BMI and age, the genotype distribution had a statistically significant difference (P = 0.003). The T allele was associated with a BC risk (OR, 1.99; 95% CI 1.13–3.51, TT vs. GG; OR, 1.53; 95% CI 1.12–2.09, GT vs. GG). The SNP rs2241766 was in HW disequilibrium in controls. In conclusion, the rs1501299 polymorphism is associated with a BC risk. Conclusions Identification of the genotype of these polymorphisms in patients with BC can contribute to integrate the risk profile in both patients and their relatives as part of a comprehensive approach and increasingly more personalized medicine.

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Single Nucleotide Polymorphisms of FCRL3 in Iranian Patients with Behcet’s Disease

Iranian Journal of Public Health ◽

10.18502/ijph.v48i6.2926 ◽

2020 ◽

Author(s):

Farhad SHAHRAM ◽

Javad KAZEMI ◽

Mahmoud MAHMOUDI ◽

Zohreh JADALI

Keyword(s):

Single Nucleotide Polymorphisms ◽

Behçet’S Disease ◽

Behcet’S Disease ◽

Behçet's Disease ◽

Polymorphism Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Behcet's Disease ◽

Significant Difference ◽

Iranian Patients

Background: Both genetic and environmental factors influence, susceptibility to autoimmune disorders including Behcet’s disease (BD). FCRL3 (Fc receptor like 3 genes), a novel immunoregulatory gene, has recently been reported as a new promising candidate gene for general autoimmunity. This study was conducted to explore the potential association of FCRL3 polymorphisms with BD. Methods: This study was conducted from 2010 to 2015 in Tehran University of Medical Sciences, Tehran, Iran. Four single-nucleotide polymorphisms of FCRL3 (rs7528684, rs11264799, rs945635, and rs3761959) were genotyped in 220 patients and 220 healthy controls. Typing of the polymorphisms in this case-control study was carried out using polymerase chain reaction-restriction fragment length polymorphism analysis. Results: Analysis of the alleles revealed a significantly lower frequency of the A allele at the -169 site (rs7528684) in BD patients compared with that in controls (P=0.000, 66.4% versus 82%, χ2= 30.23). Moreover, a significant lower frequency of AA genotype and higher frequency of GG genotype was recorded for rs7528684. There was also relationship between posterior uveitis as a clinical sign of disease and polymorphism of allele A at the -169 site (P=0.015). Conclusion: This study revealed a significant difference in both allele and genotype frequency at position -169 of FCRL3 gene between Iranian patients with BD and normal subjects. These data suggest FCRL3 gene polymorphisms might be the autoimmunity risk factor for BD.

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Short Communication: Does Interleukin-28B Single Nucleotide Polymorphisms Influence the Natural History of Hepatitis B?

AIDS Research and Human Retroviruses ◽

10.1089/aid.2011.0365 ◽

2012 ◽

Vol 28 (10) ◽

pp. 1262-1264 ◽

Cited By ~ 9

Author(s):

Luz Martín-Carbonero ◽

Norma I. Rallón ◽

José M. Benito ◽

Eva Poveda ◽

Juan González-Lahoz ◽

...

Keyword(s):

Natural History ◽

Hepatitis B ◽

Single Nucleotide Polymorphisms ◽

Short Communication ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Interleukin 28B ◽

History Of

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Polymorphism of MUC1 gene in Vietnamese gastric cancer patients: a case-control study

10.21203/rs.2.14183/v1 ◽

2019 ◽

Author(s):

Lan Thi Ngoc Nguyen ◽

Dzung Thi Ngoc Dang ◽

Van Thanh Ta ◽

Huy Quang Dang ◽

Chuc Van Tran ◽

...

Keyword(s):

Gastric Cancer ◽

Family History ◽

Single Nucleotide Polymorphisms ◽

Cancer Patients ◽

Nucleotide Polymorphisms ◽

Mucin 1 ◽

Single Nucleotide ◽

History Of ◽

Gastric Cancer Patients ◽

Multifactor Regression

Abstract Background Gastric cancer is a malignant type of cancer associated with many factors such as environment, behavior, infection, and genetics, which include Single Nucleotide Polymorphism. A few studies revealed polymorphisms of the Mucin 1 gene have a role and significance as a susceptible factor contributing to gastric cancer. The aim of this research is to evaluate the association between Single Nucleotide Polymorphisms of the Mucin 1 gene and Vietnamese gastric cancer patients.Methods 302 gastric cancer patients and 304 controls were interviewed for social-economic characteristics, smoking and drinking status, personal and family history of gastric diseases. Genotyping was done using polymerase chain reaction-restriction fragment length polymorphism analysis. The association of Single Nucleotide Polymorphisms with gastric cancer was evaluated using multifactor regression models.Results AA genotype for rs4072037 was found to be highly associated with gastric cancer (OR: 2.07 (95% CI: 1.46-2.90). GG genotype for rs2070803 increased the risk of gastric cancer (OR:1.96 (95% CI: 1.37-2.78). These genotypes in combination with other factors such as old age, male gender, alcoholism and personal history of gastric disease also showed an increased risk of having gastric cancer.Conclusions rs4072037 and rs2070803 of Mucin 1 genes are two genotypic risk factors of gastric cancer. Those in combination with other factors such as gender, family history, smoking and drinking habits significantly increase the risk of gastric cancer.

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Association of Polymorphism in Survivin gene and the risk of Liver Cancer resulting from Hepatitis C Virus among Egyptian patients

Current Cancer Drug Targets ◽

10.2174/1568009621666210302090917 ◽

2021 ◽

Vol 21 ◽

Author(s):

Amal A. Mohamed ◽

Aymen S. Yassin ◽

Basma S. Gomaa ◽

Hossam Darwish ◽

Rasha S. Mohamed ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Hepatitis C ◽

Single Nucleotide Polymorphisms ◽

Nucleotide Polymorphisms ◽

Hepatitis C Infection ◽

Allelic Discrimination ◽

Single Nucleotide ◽

Survivin Gene ◽

Increased Risk ◽

Significant Difference

Background: This study aims to investigate the relation between Survivin gene polymorphisms, and the risk of Hepatocellular carcinoma (HCC) resulting from hepatitis C infection among Egyptian population. Methods: This prospective study was conducted on 164 patients, 57 patients were diagnosed with hepatitis C, where other 57 were diagnosed with HCC in addition to 50 healthy volunteers as controls. Genotyping for Survivin rs1042489 and rs8073069 single nucleotide polymorphisms was carried out by the allelic discrimination Real-Time Polymerase Chain Reaction Single Nucleotide Polymorphisms genotyping technology. Results: The results of Survivin rs1042489 polymorphism, revealed that the TC and CC genotypes were significantly different between hepatocellular carcinoma patients (OR=15.5, 95%CI: 3.299-72.825,P<0.001), and controls (OR=44, 95%CI: 8.025-241.254, P<0.001). Furthermore, CC genotype was significantly different between cirrhotic and hepatocellular carcinoma patients (OR=19.2, 95%CI: 3.097-119.049, P=0.002). Moreover the TC genotype shows a significant different between controls and cirrhotic patients (OR=5.5, 95%CI: 2.111-14.328, P<0.001). However when comparing TT genotypes, CC+TC genotypes results showed a significant association with increasing the risk of cirrhosis and hepatocellular carcinoma (OR=4.812, 95%CI: 1.893-12.233, P=0.001), (OR=21.607, 95%CI: 4.738-98.532, P<0.01), respectively. On the other hand, there was no significant difference among all studied groups for all genotypes, regarding Survivin rs8073069. Also CC+GC genotype showed no significant association with increased the risk of hepatocellular carcinoma (P=0.999) compared with the GG genotypes. Conclusion: The study indicates that functional Survivin rs1042489 polymorphism may contribute to the risk of hepatocellular carcinoma while Survivin rs8073069 polymorphism has no significant association with increased risk of hepatocellular carcinoma among the studied groups.

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Association of three single nucleotide polymorphisms of the E-cadherin gene with endometriosis in a Chinese population

Reproduction ◽

10.1530/rep-07-0104 ◽

2007 ◽

Vol 134 (2) ◽

pp. 373-378 ◽

Cited By ~ 12

Author(s):

Kang Shan ◽

Ma Xiao-Wei ◽

Wang Na ◽

Zhang Xiu-Feng ◽

Wen Deng-Gui ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Chinese Women ◽

Gene Promoter ◽

Nucleotide Polymorphisms ◽

Promoter Polymorphisms ◽

Single Nucleotide ◽

Altered Expression ◽

Significant Difference ◽

And Control ◽

E Cadherin

Endometriosis, one of the most frequent diseases in gynecology, is a benign but invasive and metastatic disease. The altered expression of E-cadherin may play an important role in developing endometriosis. In this paper, we discuss the association of three single nucleotide polymorphisms (SNPs) on the E-cadherin gene and risk of endometriosis. We examined the genotype frequency of three polymorphisms in 152 endometriosis patients and 189 control women. There was a significant difference in the frequency of the E-cadherin 3′-UTR C → T genotypes between endometriosis and controls (P = 0.01). The frequency of the C allele in patients (71.1%) was significantly higher than in the controls (63.8%; P = 0.04). When compared with the T/T + T/C genotypes, the C/C genotype had a significantly increased susceptibility to endometriosis, with an adjusted odds ratio of 1.79 (95% confidence interval = 1.17–2.76). No significant difference was found between endometriosis and control women on two polymorphisms (−160 C → A, −347 G → GA) at the gene promoter region of E-cadherin. The −160 C → A and −347 G → GA polymorphisms displayed linkage disequilibrium (D′ = 0.999). The −160 A/−347 GA haplotype was only detected in endometriosis patients (2%). These data show a relation between the E-cadherin 3′-UTR C → T polymorphism, the −160 A/−347 GA haplotype of two promoter polymorphisms and risk of endometriosis, suggesting a potential role in endometriosis development, at least in North Chinese women.

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