Gene Polymorphisms and Their Association to Coronavirus Family Infections: Susceptibility in Different Populations

2020 ◽  
Vol 5 ◽  
Keyword(s):  
Genetic Variants ◽  
Viral Infections ◽  
Human Leukocyte ◽  
Asian Population ◽  
African Region ◽  
Mediterranean Populations ◽  
Susceptibility To Infection ◽  
Asian Populations ◽  
Spread Pattern ◽  
Different Populations

Human leukocyte antigen (HLA) loci are highly polymorphic and determine differential features of the immune response in subjects from different regions. HLA genes have been proposed to determine genetic susceptibility to several diseases, particularly to viral infections. Moreover, it has been suggested that each ethnic group could have a different specificity of T-lymphocyte reactivity to the same viral infections. In this review, we analyzed the distribution of HLA types in countries of the Asian, European and North African region. Also, we studied the relation between these HLA polymorphisms and susceptibility to infection by the coronavirus. Our findings indicated that homozygosity would increase susceptibility to viral infections and, in some cases, to coronavirus infection. HLA types showing higher susceptibility were reported in Asian population, including China, Singapore, and Taiwan. In contrast, lower susceptibility HLA variants were detected among African populations, some Asian populations, and Mediterranean populations. The presented evidence along with the spread pattern of COVID-19 infection suggests that HLA genetic variants might be related to its infection susceptibility and severity. The investigation of HLA genetic variants distribution would be a useful tool to predict different populations’ susceptibility to viral infections.

scholarly journals Human Leukocyte Antigen Genetic Variations in Obstructive Sleep Apnea Patients that were positive for HLA-DQB1*0602.

2019 ◽  
Vol 18 (3) ◽  
pp. 473-478
Author(s):  
ThamerA Fattah Al Qatarneh ◽  
Suleiman Mohammad Momany ◽  
Nizar Mohammad Abuharfil ◽  
Amjad Abduallah Mahasneh ◽  
Yousef Saleh Khader ◽  
...  
Keyword(s):  
Obstructive Sleep Apnea ◽  
Sleep Apnea ◽  
Dna Sequencing ◽  
Genetic Variants ◽  
Medical Science ◽  
Human Leukocyte ◽  
Genetic Variations ◽  
P Value ◽  
Obstructive Sleep ◽  
Different Populations

Background: Genetic variations in the HLA system may cause susceptibility to a large number of autoimmune and infectious diseases, and the complexity of HLA makes it hard to investigate HLA types associated with diseases. The association between HLA and Obstructive Sleep Apnea (OSA) is not well investigated due to the complexity of OSA pathogenesis; including genetic and non-genetic in different populations. Our previous study using PCR-SSPs technique showed that HLA-DQB1*0602 allele is associated with almost 6 times increase in risk in North Jordan OSA patients. Aim: The aim of this study was to see if there are any HLA genetic variations using DNA sequencing technique in the region in which HLA-DQB1*0602 is located that might interact with HLA-DQB1*0602 and affect OSA development in OSA patients who were positive for HLA-DQB1*0602 allele. Result: The DNA sequencing results showed 8 nucleotide substitution variations, which are p.G77E (c.230G>A), p.R80R (c.240C>G), p.Q85L (c.254A>T), p.R87P (c.260G>C), p.Y69D (c.205T>G), p.A70V (c.209C>T), p.A70A (c.210G>A), p.Y79Y (c.237C>T). Although only 5 variants resulted in amino acid change, all 8 variants were included in the statistical analysis, and none of these genetic variants was significant (p-value> 0.05). Additionally, eight haplotypes were detected. Some of these haplotypes might have a role in disease development through the interaction with HLA-DQB1*0602 and other genetic variants or could be as markers for OSA by the mechanism of linkage disequilibrium. Conclusion: Further studies are needed to explain the pathogenesis of OSA in terms of possible self or non-self-antigens involved. Bangladesh Journal of Medical Science Vol.18(3) 2019 p.473-478

scholarly journals Human leukocyte antigen B*0702 is protective against ocular Stevens–Johnson syndrome/toxic epidermal necrolysis in the UK population

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gibran F. Butt ◽  
Ali Hassan ◽  
Graham R. Wallace ◽  
Shigeru Kinoshita ◽  
Sajjad Ahmad ◽  
...  
Keyword(s):  
Human Leukocyte Antigen ◽  
Toxic Epidermal Necrolysis ◽  
Human Leukocyte ◽  
Stevens Johnson Syndrome ◽  
Ocular Complications ◽  
Leukocyte Antigen ◽  
Asian Populations ◽  
Risk Alleles ◽  
Johnson Syndrome ◽  
The Uk

AbstractStevens–Johnson Syndrome and Toxic Epidermal Necrolysis (SJS/TEN) are part of a disease continuum of vesiculobullous mucocutaneous reactions affecting the skin and mucous membranes including the ocular surface. Manifestations of disease range from mild dry eye to progressive conjunctival cicatrisation, limbal epithelial stem cell failure and corneal blindness. In Far Eastern and South East Asian populations where SJS/TEN is prevalent, numerous human leukocyte antigen (HLA) gene variants at the A, B and C loci have been identified as risk factors for developing SJS/TEN with severe ocular complications (SOC). By contrast, the incidence of SJS/TEN with SOC in European countries is relatively low. To date, ocular SJS/TEN risk altering alleles have not been widely investigated in European populations. In this study, we analysed the association of HLA -A, -B and -C alleles with SJS/TEN in 33 patients residing in the UK with age matched controls. The data showed statistically significant novel negative allele association with HLA-B*0702 and a trend with HLA-C*0702 in the patient group, indicating these alleles are protective. Further characterisation of protective and risk alleles in other ethnic groups is required to fully elucidate the putative role of these alleles in the susceptibility of SJS/TEN with or without severe ocular complications in patients in the UK.

scholarly journals PARP1 rs1136410 Val762Ala contributes to an increased risk of overall cancer in the East Asian population: a meta-analysis

2021 ◽  
Vol 49 (3) ◽  
pp. 030006052199295
Author(s):  
Yijuan Xin ◽  
Liu Yang ◽  
Mingquan Su ◽  
Xiaoli Cheng ◽  
Lin Zhu ◽  
...  
Keyword(s):  
Cancer Risk ◽  
Odds Ratio ◽  
Chinese Population ◽  
Meta Analysis ◽  
Asian Population ◽  
Cancer Type ◽  
East Asians ◽  
Asian Populations ◽  
Increased Risk ◽  
Meta Analyses

Objectives To investigate the association between poly(ADP-ribose) polymerase 1 ( PARP1) rs1136410 Val762Ala and cancer risk in Asian populations, as published findings remain controversial. Methods The PubMed and EMBASE databases were searched, and references of identified studies and reviews were screened, to find relevant studies. Meta-analyses were performed to evaluate the association between PARP1 rs1136410 Val762Ala and cancer risk, reported as odds ratio (OR) and 95% confidence interval (CI). Results A total of 24 studies with 8 926 cases and 15 295 controls were included. Overall, a significant association was found between PARP1 rs1136410 Val762Ala and cancer risk in East Asians (homozygous: OR 1.19, 95% CI 1.06, 1.35; heterozygous: OR 1.10, 95% CI 1.04, 1.17; recessive: OR 1.13, 95% CI 1.02, 1.25; dominant: OR 1.13, 95% CI 1.06, 1.19; and allele comparison: OR 1.09, 95% CI 1.03, 1.15). Stratification analyses by race and cancer type revealed similar results for gastric cancer among the Chinese population. Conclusion The findings suggest that PARP1 rs1136410 Val762Ala may be significantly associated with an increased cancer risk in Asians, particularly the Chinese population.

scholarly journals A large-scale investigation into the role of classical HLA loci in multiple types of severe infections, with a focus on overlaps with autoimmune and mental disorders

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ron Nudel ◽  
Rosa Lundbye Allesøe ◽  
Wesley K. Thompson ◽  
Thomas Werge ◽  
Simon Rasmussen ◽  
...  
Keyword(s):  
Autoimmune Disease ◽  
Psychiatric Disorders ◽  
Large Scale ◽  
Viral Infections ◽  
Human Leukocyte ◽  
Severe Infection ◽  
Small Sample ◽  
Disease Etiology ◽  
Hla Alleles ◽  
Severe Infections

Abstract Background Infections are a major disease burden worldwide. While they are caused by external pathogens, host genetics also plays a part in susceptibility to infections. Past studies have reported diverse associations between human leukocyte antigen (HLA) alleles and infections, but many were limited by small sample sizes and/or focused on only one infection. Methods We performed an immunogenetic association study examining 13 categories of severe infection (bacterial, viral, central nervous system, gastrointestinal, genital, hepatitis, otitis, pregnancy-related, respiratory, sepsis, skin infection, urological and other infections), as well as a phenotype for having any infection, and seven classical HLA loci (HLA-A, B, C, DPB1, DQA1, DQB1 and DRB1). Additionally, we examined associations between infections and specific alleles highlighted in our previous studies of psychiatric disorders and autoimmune disease, as these conditions are known to be linked to infections. Results Associations between HLA loci and infections were generally not strong. Highlighted associations included associations between DQB1*0302 and DQB1*0604 and viral infections (P = 0.002835 and P = 0.014332, respectively), DQB1*0503 and sepsis (P = 0.006053), and DQA1*0301 with “other” infections (a category which includes infections not included in our main categories e.g. protozoan infections) (P = 0.000369). Some HLA alleles implicated in autoimmune diseases showed association with susceptibility to infections, but the latter associations were generally weaker, or with opposite trends (in the case of HLA-C alleles, but not with alleles of HLA class II genes). HLA alleles associated with psychiatric disorders did not show association with susceptibility to infections. Conclusions Our results suggest that classical HLA alleles do not play a large role in the etiology of severe infections. The discordant association trends with autoimmune disease for some alleles could contribute to mechanistic theories of disease etiology.

scholarly journals Genetic Polymorphisms of Pharmacogenes among the Genetically Isolated Circassian Subpopulation from Jordan

2020 ◽  
Vol 10 (1) ◽  
pp. 2 ◽  
Author(s):  
Laith N. AL-Eitan ◽  
Doaa M. Rababa’h ◽  
Nancy M. Hakooz ◽  
Mansour A. Alghamdi ◽  
Rana B. Dajani
Keyword(s):  
Genetic Variants ◽  
Rare Variants ◽  
Optimal Dose ◽  
Nucleotide Polymorphisms ◽  
Treatment Efficiency ◽  
Isolated Populations ◽  
Single Nucleotide ◽  
Interindividual Variations ◽  
Different Populations ◽  
Pharmacogenomic Studies

Several genetic variants have been identified that cause variation among different populations and even within individuals of a similar descent. This leads to interindividual variations in the optimal dose of the drug that is required to sustain the treatment efficiency. In this study, 56 single nucleotide polymorphisms (SNPs) within several pharmacogenes were analyzed in 128 unrelated subjects from a genetically isolated group of Circassian people living in Jordan. We also compared these variant distributions to other ethnic groups that are available at two databases (Genome 1000 and eXAC). Our results revealed that the distribution of allele frequencies within genes among Circassians in Jordan showed similarities and disparities when compared to other populations. This study provides a powerful base for clinically relevant SNPs to enhance medical research and future pharmacogenomic studies. Rare variants detected in isolated populations can significantly guide to novel loci involved in the development of clinically relevant traits.

Effects of CYP4F2 and GGCX genetic variants on maintenance warfarin dose in a multiethnic Asian population

2011 ◽  
Vol 105 (06) ◽  
pp. 1100-1102 ◽  
Author(s):  
Sze Ling Chan ◽  
Boon Cher Goh ◽  
Kee Seng Chia ◽  
Benjamin Chuah ◽  
Andrea Wong ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Warfarin Dose ◽  
Asian Population

scholarly journals Neolithic genomes reveal a distinct ancient HLA allele pool and population transformation in Europe

2019 ◽  
Author(s):  
Alexander Immel ◽  
Christoph Rinne ◽  
John Meadows ◽  
Rodrigo Barquera ◽  
András Szolek ◽  
...  
Keyword(s):  
Western Europe ◽  
Viral Infections ◽  
Human Leukocyte ◽  
Neolithic Period ◽  
Late Neolithic ◽  
Leukocyte Antigen ◽  
Cultural Transformations ◽  
Farming Community ◽  
Genome Wide ◽  
A Genome

AbstractThe Wartberg culture (WBC, 3,500-2,800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We perform a genome-wide analysis of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3,300-3,200 cal. BCE). Our results highlight that the Niedertiefenbach population indeed emerged at the beginning of the WBC. This farming community was genetically heterogeneous and carried a surprisingly large hunter-gatherer ancestry component (40%). We detect considerable differences in the human leukocyte antigen gene pool between contemporary Europeans and the Niedertiefenbach individuals whose immune response was primarily geared towards defending viral infections.

scholarly journals Rare Genetic Variants in Immune Genes and Neonatal Herpes Simplex Viral Infections

PEDIATRICS ◽  
2020 ◽  
Vol 147 (1) ◽  
pp. e20200687
Author(s):  
Lauren Cummings ◽  
Megan Tucker ◽  
Margaret Gibson ◽  
Angela Myers ◽  
Tomi Pastinen ◽  
...  
Keyword(s):  
Herpes Simplex ◽  
Genetic Variants ◽  
Viral Infections ◽  
Neonatal Herpes ◽  
Immune Genes ◽  
Rare Genetic Variants ◽  
Neonatal Herpes Simplex

Comparison of the Genetic Structure of Rheumatoid Arthritis Between European and Asian Population

2021 ◽  
Author(s):  
Chun'e Li ◽  
Xiaomeng Chu ◽  
Shiqiang Cheng ◽  
Yan Wen ◽  
Chuyu Pan ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Genetic Structure ◽  
Genome Wide Association Study ◽  
Inflammatory Diseases ◽  
Enrichment Analysis ◽  
Asian Population ◽  
Arginine Deiminase ◽  
Gene Set Enrichment Analysis ◽  
Asian Populations ◽  
Shared Risk

Abstract Background: Rheumatoid arthritis (RA) is one of the chronic inflammatory diseases that primarily influences the joints, and its prevalence is 0.5-1.0%. Previous studies have shown that there are differences in the genetic structure of RA between European and Asian populations, and most of the studies have been conducted using meta-analysis. This study analyzed the genetic structure of rheumatoid arthritis in European and Asian populations using a new method. Methods: The Genome-Wide Association Study (GWAS) summary statistics of RA from Europe (N=8383) and Asia (N=19190) were derived from an article published in Nature. First, the GWAS data was divided into 1368 blocks, in which SNPs were approximately independent of linkage disequilibrium (LD). Second, we calculated the LD matrix of SNP in each block by using PLINK 1.9. Then, PESCA analysis was performed to detect population-specific/shared risk genes of RA. Finally, Metascape platform was used to perform gene set enrichment analysis. Results: In European population, we found multiple genes which were associated with RA, including HLA-DPA1, HLA-DPB1 (rs2856822, PTP=1.000), MICA (rs2844518, PTP=1.000). In Asian population, C6orf10 (rs3129915, PTP=1.000), PTPN2 (rs2847288, PTP=0.995), were significant related to RA. The population-shared genes included PADI2 (rs2235920, PTP=1.000), STAT4 (rs12612769, PTP=1.000). Furthermore, gene sets enrichment analysis reported population-specific/shared pathway terms, such as interferon-gamma-mediated signaling pathway (P=2.884×10-9), negative regulation of innate immune response (P=1.841×10-7), protein-arginine deiminase activity (P=7.047×10-8). Conclusions: The results of our study indicate differences in risk loci between Asian and European populations, which provided clues for exploring the population-specific/shared genetics and pathogenesis of RA.

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