Allelic Association Research Articles

The association of rs25487 of theXRCC1geneandrs13181 of theERCC2genepolymorphisms with the ovarian cancer risk.

Ovarian cancer (OC) is the most lethal gynecological cancer worldwide. DNA damage plays an important role in cancer development, and the proteins encoded by XRCC1 and ERCC2 are important components of the DNA repair system. This study aimed to examine the relationship between the rs25487 XRCC1 and rs13181 ERCC2 polymorphisms and the risk of OC development in women from the Moscow region. DNA was isolated from the blood of 129 healthy donors and tissues and blood samples from 125 patients with OC and studied using real-time PCR. An increase in odds ratios (OR) was obtained for OC tissue and blood for both T (OR = 1.46, 95% confidence interval [CI] = 1.22-1.76, P = 0.00005), and for T/T of rs25487 XRCC1. The most significant OR values were found for the T/T genotype using the codominant model (OR = 2.11, 95% CI = 1.44-3.07, P = 0.00006) and dominant model (OR = 3.13, 95% CI = 1.44-6.79, P = 0.0025) for the pooled blood and tissue groups. For rs13181 ERCC2, differences were observed for the T/G genotype in OC tissues (OR = 0.69, 95% CI = 0.51-0.92, P = 0.011) in the codominant model. In this study, the association of allele T and genotypes of rs25487 XRCC1 and T/G of rs13181 ERCC2 with OC was shown. Our results indicate that these polymorphisms may be involved in the pathogenesis of OC and are promising for further studies on therapeutic applications in OC.

Enabling efficient analysis of biobank-scale data with genotype representation graphs.

Computational analysis of a large number of genomes requires a data structure that can represent the dataset compactly while also enabling efficient operations on variants and samples. However, encoding genetic data in existing tabular data structures and file formats has become costly and unsustainable. Here we introduce the genotype representation graph (GRG), a fully connected hierarchical data structure that losslessly encodes phased whole-genome polymorphisms. Exploiting variant-sharing across samples enables GRG to compress 200,000 UK Biobank phased human genomes to 5-26 gigabytes per chromosome, also enabling graph-traversal algorithms to reuse computed values in random access memory. Constructing and processing GRG files scales to a million whole genomes. Using allele frequencies and association effects as examples, we show that computation on GRG via graph traversal runs the fastest among all tested alternatives. GRG-based algorithms have the potential to increase the scalability and reduce the cost of analyzing large genomic datasets.

Association of BoLA-DRB3 Alleles with the Progression of Bovine Leukosis in the Lucerna Breed

Association of BoLA-DRB3 Alleles with the Progression of Bovine Leukosis in the Lucerna Breed

Multi-locus high-risk alleles association from interleukin’s genes with female infertility and certain comorbidities

Objective There is evidence that cytokine genes’ single nucleotide polymorphisms could be the reasons behind female infertility. This study aimed to identify the role for Interleukin33 rs1048274 (G > A) and rs16924243 (T > C), Interleukin22 rs1397852121 (C > T), rs1295978671 (C > T) and rs2227483 (A > T), Interleukin17A rs2275913 (G > A,C) and Interleukin17F rs763780 (T > C), Interleukin13 1512 (A > C) and IL13 2044 (G > A), and Interleukin4 rs2243250 (C > T) and rs2070874 (C > T) gene polymorphisms in female infertility to gain a richly more detailed understanding of its genetic predisposition. Five distinct groups, each comprising 200 infertile women and 200 age-matched fertile controls, were recruited to each Interleukins (33, 22, 17, 13 and 4) in this case–control study and were genotyped by using an amplification refractory mutation system. Statistical analysis is conducted by SPSS software V. 22 and using Chi-square (χ2) and logistic regression tests. Strength of association was estimated by multiple-comparison correction, population structure test and Haplotype analysis. The study was approved by the Academic Ethics Committee and each enrolled patient signed an informed consent.Results Our statistical results revealed risk alleles in all of the substitution lines for women infertility. Current findings provided evidence that in the presence of Interleukin33 Ap-value rs1048274 = 0.002 and Cp-value rs16924243 < 0.0001, Interleukin 22Tp-value rs1397852121 < 0.0001 and Tp-value rs2227483 = 0.000, Interleukin17A Ap-value rs2275913 = 0.003 and Interleukin17F Cp-value rs763780 = 0.000 and Interleukin13 Cp-value 1512 = 0.000 and Ap-value 2044 = 0.003, Interleukin4 Tp-value rs2243250 = 0.001 and Tp-value rs2070874 = 0.009 risk alleles, risk genotype also were significantly associated with increased chances of developing infertility. The relationship between risk genotypes and several well-established infertility risk factors including, polycystic ovary syndrome, premature ovarian failure, oophorectomy, diminished ovarian reserve, endometriosis, uterine fibroids, ovarian cysts, uterine polyps, fallopian tube blockage and thyroid dysfunction, also exhibited. This study suggests the significant role of interleukin gene polymorphisms in human reproductive success.

Revisiting the Link Between HLA-DRB1 Alleles and Autoantibodies in Rheumatoid Arthritis: Association of non-Shared Epitope Alleles *09 and *15 With High Levels of Anti-Citrullinated Peptide/Protein Antibodies.

Autoantibodies serve as essential clinical biomarkers and may indicate etiological mechanisms in rheumatic diseases. In light of the increasing knowledge concerning the diversity and biologic implications of anti-citrullinated peptide/protein antibodies (ACPAs), we have re-evaluated the association between the ACPA response and the HLA-DRB1 allelic groups, known to represent a major genetic risk factor for rheumatoid arthritis (RA). We explored a collection of 4,392 well-characterized incident patients with RA of White European descent from the Epidemiological Investigation of Rheumatoid Arthritis (EIRA) new-onset RA study, as well as 1,199 cases of patients with RA of Southeast Asian origin from the Malaysian EIRA study. We focused on a quantitative analysis of the levels of anti-cyclic citrullinated peptide IgG antibodies, including those falling below the diagnostic threshold. Our data show that non-shared epitope alleles HLA-DRB1*09 and *15 exhibit significant associations with ACPA levels. Notably, these novel associations were independent of ethnicity. To validate our findings, we conducted an additional replication study in an independent pool of 4,109 patients with RA of White European origin. These results indicate a new, previously overlooked, role for the HLA locus in the regulation of the levels of ACPA RA-specific autoantibodies that goes beyond the shared epitope-defined gene variants.

Genomic variants associated with type 2 diabetes mellitus among Filipinos.

Type 2 diabetes mellitus leads to debilitating complications that affect the quality of life of many Filipinos. Genetic variability contributes to 30% to 70% of T2DM risk. Determining genomic variants related to type 2 diabetes mellitus susceptibility can lead to early detection to prevent complications. However, interethnic variability in risk and genetic susceptibility exists. This study aimed to identify variants associated with type 2 diabetes mellitus among Filipinos using a case-control design frequency matched for age and sex. A comparison was made between 66 unrelated Filipino adults with type 2 diabetes mellitus and 121 without. Genotyping was done using a candidate gene approach on genetic variants of type 2 diabetes mellitus and its complications involving allelic association and genotypic association studies with correction for multiple testing. Nine (9) significant variants, mostly involved in glucose and energy metabolism, associated with type 2 diabetes mellitus in Filipinos were found. Notably, a CDKAL1 variant (rs7766070) confers the highest level of risk while rs7119 (HMG20A) and rs708272 (CETP) have high risk allele frequencies in this population at 0.77 and 0.66, respectively, making them potentially good markers for type 2 diabetes mellitus screening. The data generated can be valuable in developing genetic risk prediction models for type 2 diabetes mellitus to diagnose and prevent the condition among Filipinos.

Effect of FTO Gene polymorphism on anthropometric, hemodynamic, and autonomic variables in adolescents

Objective: The study aimed to analyze the influence of physical activity levels and the rs9939609 polymorphism (FTO gene) on anthropometric, hemodynamic, and cardiac autonomic variables in public school students. Methods: A total of 288 students (aged 11 to 18, both sexes) from public schools in São Luís, Maranhão, were divided into four groups: sedentary AA+AT (AA+AT sed), active AA+AT (AA+AT activ), sedentary TT (TT sed), and active TT (TT activ). Evaluations included the International Physical Activity Questionnaire, weight, height, body mass index (BMI), buccal cells collection for DNA extraction, systolic (SBP) and diastolic (DBP) blood pressure measurements, and heart rate variability (HRV) analysis. A chi-square test for allelic associations was applied a 5% significance level. Results: No significant differences were observed in DBP or heart rate (HR). The active groups (AA+AT activ and TT activ) exhibited reductions in weight and METs/min/week compared to their respective sedentary groups (P&lt;0.05). The TT activ group also demonstrated reductions in SBP and BMI compared to the TT sed group (P&lt;0.05). The TT activ group had higher HRV in the RR time domain (ms) compared to the TT sed group (P&lt;0.05), though no significant differences were found in other HRV variables. Conclusions: The FTO gene polymorphism influences cardiac autonomic modulation, while physical activity levels affect anthropometric variables.

Mutation Screening of ATXN1, ATXN2, and ATXN3 in Amyotrophic Lateral Sclerosis.

Emerging evidence suggests potential disease modifying roles of ATXN1, ATXN2, and ATXN3 in amyotrophic lateral sclerosis (ALS). We aimed to provide a comprehensive variants profile of the ATXN1, ATXN2, and ATXN3 genes and examine the association of these variants with the risk and clinical characteristics of ALS. We screened and analyzed the rare variants in a cohort of 2220 ALS patients from Southwest China, using controls from the Genome Aggregation Database (gnomAD) and the China Metabolic Analytics Project (ChinaMAP). The over-representation of rare variants and their association with disease risk in ALS patients were assessed using Fisher's exact test with Bonferroni correction at both allele and gene levels. Kaplan-Meier analysis was employed to explore the relationship between the distribution of variants and survival. A total of 62 eligible rare missense variants were identified, comprising 32 from ATXN1, 21 from ATXN2, and 9 from ATXN3. Allelic association testing revealed a significant enrichment of the ATXN1 (c.2122C > G, p.Leu708Val) variant and the ATXN2 (c.3778C > G, p.Pro1260Ala) variant in ALS. Gene burden analysis indicated that variants in the ATXN1 and ATXN3 genes had a higher burden in ALS. Substantial heterogeneity in survival time was observed among patients carrying different variants within the same gene. However, there were no significant differences in survival between ALS patients grouped by N-terminal or C-terminal distribution. Our results provided a genetic variation profile of ATXN1, ATXN2, and ATXN3 in ALS patients, along with the clinical characteristics of individuals carrying these variations. This information might offer valuable insights for the ongoing ALS disease-modifying treatments.

New Associations with the HIV Predisposing and Protective Alleles of the Human Leukocyte Antigen System in a Peruvian Population.

The accurate determination of an individual's unique human leukocyte antigen (HLA) allele holds important significance in evaluating the risk associated with autoimmune and infectious diseases, such as human immunodeficiency virus (HIV) infection. Several allelic variants within the HLA system have been linked to either increased protection or susceptibility in the context of infectious and autoimmune diseases. This study aimed to determine the frequency and association of HLA alleles between people living with HIV (PLHIV) as the case group and Peruvian individuals without HIV with high-risk behaviors of sexually transmitted diseases as the control group. Whole exome sequencing (WES) was used to determine high-resolution HLA allelotypes using the OptiType and arcas HLA tools. The HLA alleles present in HLA classes I (A, B, and C loci) and II (DPB1, DQA1, DQB1, and DRB1 loci) were determined in a cohort of 59 PLHIV (cases) and 44 individuals without HIV (controls). The most frequent HLA alleles were A*02:01, DPB1*04:02, and DQB1*03:419 at 36%, 30%, and 28% prevalence in general population. We found that C*07:01 (p = 0.0101; OR = 10.222, 95% IC: 1.40-74.55), DQA1*03:02 (p = 0.0051; OR = 5.297, 95% IC: 1.48-19.02), and DRB1*09:01 (p = 0.0119; OR = 4.788, 95% IC: 1.39-16.44) showed an association with susceptibility to HIV infection, while DQB1*03:419 (p = 0.0478; OR = 0.327, 95% IC: 0.11-0.96) was associated with protection from HIV infection. Our findings contribute to the knowledge of HLA allele diversity in the Peruvian population (around 70% South American indigenous ancestry) lays the groundwork for further valuable large-scale use of HLA typing and offers a novel association with HIV infection that is relevant to vaccine studies.

A genome-wide association study of adults with community-acquired pneumonia

BackgroundCommunity-acquired pneumonia (CAP) is associated with high morbidity and hospitalization rate. In infectious diseases, host genetics plays a critical role in susceptibility and immune response, and the immune pathways involved are highly dependent on the microorganism and its route of infection. Here we aimed to identify genetic risk loci for CAP using a case-control genome-wide association study (GWAS).MethodsWe performed a GWAS on 3,765 Spanish individuals, including 257 adult patients hospitalized with CAP and 3,508 population controls. Pneumococcal CAP was documented in 30% of patients; the remaining 70% were selected among patients with unidentified microbiological etiology. We tested 7,6 million imputed genotypes using logistic regressions. UK Biobank GWAS of bacterial pneumonia were used for results validation. Subsequently, we prioritized genes and likely causal variants based on Bayesian fine mapping and functional evidence. Imputation and association of classical HLA alleles and amino acids were also conducted.ResultsSix independent sentinel variants reached the genome-wide significance (p < 5 × 10-8), three on chromosome 6p21.32, and one for each of the chromosomes 4q28.2, 11p12, and 20q11.22. Only one variant at 6p21.32 was validated in independent GWAS of bacterial and pneumococcal pneumonia. Our analyses prioritized C4orf33 on 4q28.2, TAPBP on 6p21.32, and ZNF341 on 20q11.22. Interestingly, genetic defects of TAPBP and ZNF341 are previously known inborn errors of immunity predisposing to bacterial pneumonia, including pneumococcus and Haemophilus influenzae. Associations were all non-significant for the classical HLA alleles.ConclusionsWe completed a GWAS of CAP and identified four novel risk loci involved in CAP susceptibility.

Genomic and Serological Rheumatoid Arthritis Biomarkers, MUC5B Promoter Variant, and Interstitial Lung Abnormalities.

Rheumatoid arthritis (RA) has been implicated in interstitial lung disease (ILD) as majority of studies have been comprised of patients with known RA. However, it remains unclear whether an underlying risk for RA in combination with genetic risk for pulmonary fibrosis is associated with radiological markers of early lung injury and fibrosis in broader population samples. Determine whether genetic and serological biomarkers of RA risk in combination with the MUC5B (rs35705950) risk allele (T) are associated with interstitial lung abnormalities (ILA) on computed tomography (CT) scans. Associations of RA-risk HLA-DRB1 alleles (*04:01, *04:08, *04:05, *04:04, *10:01) and serum RA autoantibodies with ILA in the Multi-Ethnic Study of Atherosclerosis (MESA, n=4,018) and COPDGene (n=5,963) cohorts were modeled using logistic regression and adjusted for age, sex, self-reported race and ethnicity, smoking history, body mass index, and principal components of genetic ancestry. The prevalence of an RA risk HLA-DRB1 allele was 16.5% and 21.9% in MESA and COPDGene, respectively. ILA was present in 3.9% and 11% in MESA and COPDGene, respectively. An RA risk HLA-DRB1 allele was not significantly associated with ILA in MESA and COPDGene. In MESA, higher serum levels of IgA rheumatoid factor (RF) and anti-cyclic citrullinated peptide were associated with an odds ratio (OR) for ILA of 1.20 (95% CI 1.07-1.35) and 1.19 (95% CI 1.04-1.37), respectively. Among smokers without baseline ILA, per doubling of IgM RF was associated with an OR for ILA 10 years later of 1.25 (95% CI 1.08-1.43). Associations were not significantly different by MUC5B risk allele status. RA-related HLA-DRB1 alleles were not associated with ILA, whereas higher serum levels of IgM RF among smokers without baseline ILA were associated with subsequent ILA.

Common SYNE2 Genetic Variant Associated With Atrial Fibrillation Lowers Expression of Nesprin-2α1 With Downstream Effects on Nuclear and Electrophysiological Traits.

Atrial fibrillation GWAS (genome-wide association studies) identified significant associations for rs1152591 and linked variants in the SYNE2 gene encoding Nesprin-2, which connects the nuclear membrane with the cytoskeleton. Reporter gene vector transfection and CRISPR-Cas9 editing were used to identify the causal variant regulating the expression of SYNE2α1. After SYNE2 knockdown or SYNE2α1 overexpression in human stem cell-derived cardiomyocytes, nuclear phenotypes were assessed by imaging and atomic force microscopy. Gene expression was assessed by RNAseq and gene set enrichment analysis. Fura-2 AM staining assessed calcium transients. Optical mapping assessed action potential duration and conduction velocity. The risk allele of rs1152591 had lower promoter and enhancer activity and was significantly associated with lower expression of the short SYNE2α1 isoform in human stem cell-derived cardiomyocytes, without an effect on the expression of the full-length SYNE2 mRNA. SYNE2α1 overexpression had dominant negative effects on the nucleus with its overexpression or SYNE2 knockdown leading to increased nuclear area and decreased nuclear stiffness. Gene expression results from SYNE2α1 overexpression demonstrated both concordant and nonconcordant effects with SYNE2 knockdown. SYNE2α1 overexpression had a gain of function on electrophysiology, leading to significantly faster calcium reuptake and decreased assessed action potential duration, while SYNE2 knockdown showed both shortened assessed action potential duration and decreased conduction velocity. rs1152591 was identified as a causal atrial fibrillation variant, with the risk allele decreasing SYNE2α1 expression. Downstream effects of SYNE2α1 overexpression include changes in nuclear stiffness and electrophysiology, which may contribute to the mechanism for the risk allele's association with AF.

Associations of classical HLA alleles with sleep behaviours.

Immune dysregulation has been observed in individuals with sleep disturbance, with HLA molecules play a crucial role in the immune response. This study aimed to investigate the associations between HLA alleles and sleep behaviours, considering several environmental factors. Data were sourced from the UK Biobank. Logistic regression analyses were performed to explore the associations between 359 HLA alleles and 4 sleep behaviours, including chronotype (n = 204,636), insomnia (n = 227,553), snoring (n = 214,350) and daytime dozing (n = 227,197). Furthermore, gene-environmental interaction studies (GEIS) were conducted to evaluate the interactions of HLA alleles with environmental factors on sleep behaviours. This study analysed a total sample and subgroups stratified by sex to elucidate the impact of HLA alleles on sleep behaviours. Our findings revealed several associations between specific HLA alleles and sleep behaviours. Notably, HLA-A*23:01 was associated with evening chronotype in the total sample (OR = 0.918, 95%CI: 0.872-0.965), while HLA-A*32:01 was associated with evening chronotype in males (OR = 1.089, 95%CI: 1.037-1.144). Furthermore, GEIS identified multiple sets of interactions associated with sleep behaviours. For example, the interaction of HLA-DPA1*01:04 with alcohol consumption was associated with daytime dozing in the total sample (OR = 1.993, 95%CI: 1.351-2.941), while the interaction of HLA-DQB1*05:04 with ever suffered mental distress preventing usual activities was associated with insomnia in males (OR = 0.409, 95%CI: 0.254-0.658). Our findings highlight the involvement of HLA in sleep regulation and underscore the potential interactions between HLA alleles and environmental factors in modulating susceptibility to sleep behaviours.

Prospective associations of interleukin-6 and APOE allele with cognitive decline in biracial community-dwelling older adults: The Chicago Health and Aging Project (CHAP).

It is unclear whether inflammation, that is, high interleukin-6 (IL-6) levels, and genetic risk, that is, apolipoprotein E (APOE) ε4 allele, have a compounding effect on cognitive decline (CD). We analyzed a subset of participants from the longitudinal cohort study, Chicago Health and Aging Project, comprising 1120 biracial community-dwelling older adults (60% Black and 62% women), and mean follow-up=6.4 years. We ran adjusted mixed-effects models on2 longitudinal CD. In APOE ε4 carriers, higher serum IL-6 was not associated with the rate of CD (β=-0.0091 [standard deviation (SD)=0.0165, p=0.5800]). Conversely, in non-ε4 carriers, compared to the lower tertile, those with the upper tertile of serum IL-6 levels experienced significantly accelerated CD (β=-0.0257 [SD=0.0084, p=0.0023]). Even without the largest genetic risk factor for late-onset Alzheimer's disease/Alzheimer's disease and related dementias (AD/ADRD), elevated serum IL-6 still accelerate the rate of CD in non-APOE ε4 carriers. Hence, interventions ameliorating inflammation may prevent AD/ADRD. Interleukin-6 (IL-6) and the apolipoprotein E (APOE) ε4 allele have been separately associated with an increased risk for cognitive decline, but their interaction remains unclear.In ε4 carriers, IL-6 was not associated with cognitive decline. However, even without the biggest genetic risk factor for Alzheimer's disease (AD), that is, APOE ε4, elevated serum IL-6 still could confer accelerated rate of cognitive decline, with a detrimental effect half of that imposed by APOE ε4 alone.We found no racial differences in these associations.These findings contribute complementary evidence on non-APOE ε4-dependent and non-AD biological pathways through which cognitive decline can still be accelerated in non-APOE ε4 carriers and highlight a specific subgroup of older adults who are at a higher risk of AD and thus may benefit from anti-inflammatory interventions.

Efficiency of Vascular Endothelial Growth Factor-2549 Insertion/Deletion variation and VEGF level to predict Retinopathy in Diabetes Mellitus Type 2 Cases

The current work was suggested to study Vascular Endothelial Growth Factor (VEGF) level and VEGF -2549 Insertion/Deletion (I/D) to predict retinopathy in Diabetes Mellitus type 2 cases. Three groups were used to implement the study aim: Diabetes Mellitus type 2 (DM) with and without retinopathy and healthy individuals. Glycemic parameters, VEGF level and VEGF -2549 (I/D) were involved in the present study. The findings demonstrated that there were significant differences between DM cases and control in all glycemic biomarkers. The VEGF level (p&lt;0.001) in DM with retinopathy significant elevation was shown VEGF level (p=0.047) and non-sig changes were observed in other parameters. The VEGF -2549 (I/D) showed non-significant association (p=0.245) of allele (I, D) in study groups while significant association (p=4.44e-04) was observed in DM with and without retinopathy. The genotypes of VEGF -2549 (I/D) showed low frequents of heterozygote (I/D) in case-control groups and slight changes in (D/D) and (I/I) (P=0.603). significant association of (I/I) with DM with retinopathy was observed while D/D was associated with DM without retinopathy group (P= 0.034). The effect of VEGF -2549 (I/D) in study biomarkers showed non-sig changes in case and control groups in all parameters (beta =-1.421, p= 0.999), while in DM with and without retinopathy, biomarkers showed non-sig differences association by regression test (beta =0.865, p=0.999). From the present results, it can be proposed that VEGF level was elevated in DM with retinopathy, VEGF -2549 (I/D) was significantly associated with DM with retinopathy and may be used to predict retinopathy in DM.

Common Hyperglycemia Susceptibility Loci in Metabolic Syndrome Patients from Karachi, Pakistan: A Cross Sectional Study

Background: More than 75 genetic susceptibility loci have been implicated with hyperglycemia. SNPs in genes linked with satiety, insulin sensitivity, BMR (Adiponectin, FTO, and MC4R), and inflammation and autoimmunity (TNF-a) have been shown to have a relationship with metabolic syndrome. Objectives: To measure the frequency of ADIPOQ, FTO, MCR4, and TNF SNPs in metabolic syndrome patients and controls, and to assess the association of these with hyperglycemia and adiposity status. Methods: A cross-sectional study was conducted. Baseline investigations including lipid profiles, blood glucose levels, and BMI calculation were conducted for n=113 Metabolic Syndrome and n=47 healthy controls. Tetra ARMS PCR and gel electrophoresis were conducted for Adiponectin rs266729, Adiponectin rs1501299, FTO rs9939609, MCR4 rs1297013, and TNF rs1800629. Statistical analysis was performed using SPSS version 26. Results: Difference was observed in lipid profiles (including LDL, triglycerides, and cholesterol but not HDL), body fat percentage (p= 0.034), and both fasting (p=0.000) and random (p=0.000) blood glucose levels among metabolic syndrome patients versus controls. Adiponectin rs1501299, FTO rs9939609, and MCR4 rs1297013 showed genotype frequency differences between groups. Spearman’s correlation was applied to test any association of risk allele with study variables and MCR4 rs1297013 showed an independent association with Fasting Blood Glucose Level (r=0.238; p=0.024) irrespective of age, weight, or gender. Conclusion: MCR4 rs1297013 polymorphism is an independent risk factor leading to hyperglycemia in the study population, however, no other SNPs were identified to carry a significant risk. Large-scale genome-wide studies are required to identify the unique set of risk genes for the Pakistani population

The PARK2_e01(-697) Polymorphism does not Associate with Susceptibil-ity to Typhoid in Punjabi Population, Pakistan: A Case Control Study.

SNP based association studies have revolutionized the field of biomed-icines. Enteric fever is a systemic disease with etiologic agents Salmonella enterica serovar typhi and paratyphi. It is a serious health issue worldwide and presents wide variations in incidence, rates, and severity. Previous investigations have revealed that genetic variations may lead to sus-ceptibility to typhoid fever. A current study was performed to investigate the potential association of PARK2_e01(-697) polymorphism with the susceptibility to typhoid in the Punjabi population. For this case-control study, blood samples obtained from typhoid patients with positive Typhidot or blood culture test (n=72) and healthy controls (n=73) were processed for DNA ex-traction. The polymorphism PARK2_e01(-697) analysis was carried out by using PCR and RFLP. No allelic association was found between PARK2_e01(-697) and susceptibility to ty-phoid fever in the understudy population. This case control study is the demonstration of the non-association of PARK2_e01(-697) with typhoid in the Pakistani population. Future research, using a larger population size, will help to elucidate the role of PARK2_e01(-697) polymorphism in typhoid pathogenesis.

Characterization of Bila Tserkva winter common wheat cultivars with respect to marker loci

Aim. We studied special features of the sample of Bila Tserkva winter common wheat cultivars with respect to storage protein loci and some disease resistance genes. Methods. To identify alleles at gliadin and high-molecular-weight glutenin loci, acid polyacrylamide gel electrophoresis and SDS-electrophoresis of grain proteins were carried out. Alleles of markers for the disease resistance genes Lr34, Tsn1, and TDF_076_2D were identified using PCR. Results. The composition and frequencies of alleles at the Gli-1, Glu-1, and Gli-A3 loci were studied in samples of Bila Tserkva cultivars released before 2011 and after 2010. For the latter group of cultivars, alleles of the disease resistance gene markers were identified. We observed a significant increase in the frequency of the allele Gli-A1x(9) and a decrease in the frequency of Gli-A1c, as well as a tendency for an increase in the frequency of Gli-A3c. In the total sample of Bila Tserkva cultivars, nonrandom associations of pairs of certain storage protein alleles were revealed. Conclusions. The group of Bila Tserkva cultivars is similar to the previously studied groups of the Central Forest Steppe of Ukraine with respect to allele set and frequencies of the main prolamin loci, but differs in the frequencies of the disease resistance genes. A special feature of the group of Bila Tserkva cultivars is a high frequency of the allele c at the minor locus Gli-A3, as well as the allele association Gli-A1x Gli-B1l Gli-A3c.

Identification of novel bovine leukocyte antigen alleles and association of BoLA-DRB3.2*020:02:01 with resistance to Theileria orientalis infection in crossbred Kedah-Kelantan cattle: a pilot study.

The bovine leukocyte antigen (BoLA) gene is a significant genetic part of the immune system and has been used as a disease marker in cattle. In this study, we detected Theileria orientalis, T. sinensis, Anaplasma marginale, Anaplasma platys, Candidatus Mycoplasma haemobos and Trypanosoma evansi by PCR amplification and sequencing of the amplicons. The allelic association of the BoLA-DRB3.2 gene with blood pathogen disease resistance and susceptibility in 87 Kedah-Kelantan x Brahman (KKB) and 38 Bali cattle was determined by Fisher's exact test and Cochran Mantel Haenszel (CMH) correction test. Sequence-based typing of the BoLA-DRB3.2 gene identified 43 alleles (27 previously reported alleles and 16 novel alleles) across the two cattle breeds. Alignment analysis of the 16 novel alleles revealed 90.7-95.8% and 85-92% nucleotide and amino acid identities, with the reference allele, BoLA-DRB3*016:01 cDNA clone NR-1. BoLA-DRB3*009:02 (25.6%) and BoLA-DRB3*036:01 (36%) were the most frequent alleles in KKB and Bali cattle, respectively. In KKB cattle, BoLA-DRB3*020:02:01 was significantly associated with resistance to T. orientalis whereas *007:01 and *009:02 were significantly associated with resistance to C. Mycoplasma haemobos. Also, DRB3*017:01 was associated with susceptibility to T. orientalis in KKB cattle. In the Bali cattle, BoLA-DRB3*015:01 was found to be a genetic marker of susceptibility to C. Mycoplasma haemobos infection. Therefore, this study identified BoLA-DRB3.2 alleles associated with resistance and susceptibility to T. orientalis infection in KKB cattle and susceptibility to C. Mycoplasma haemobos infection in Bali cattle for the first time. Therefore, this study suggests that these BoLA-DRB3 resistance alleles could be used as candidate markers for selection, whereas susceptibility alleles could be used as candidate markers for culling in the beef industry.

Association of Human Leukocyte Antigen Alleles with COVID-19 Severity and Mortality in a Spanish Population.

Background and Objectives: The aim of the following cross-sectional study is to determine the association between human leukocyte antigen (HLA) alleles and outcomes in patients presenting to the emergency department (ED) with SARS-CoV-2 infection. Methods and Materials: Genotyping was made using the Axiom Human Genotyping SARS-CoV-2 Research Array. Statistical analysis was made with Fisher's exact test and multivariable logistic regression, adjusted for sex, age and clinical variables. Results: Of 190 patients, 11.1% were discharged from the ED; 57.9% were admitted to the COVID-19 ward, without intensive care unit (ICU) admission; 15.3% survived an ICU admission; and 15.8% died. After multivariable analysis, two HLA alleles protected against hospital admission (HLA-C*05:01, adjusted odds ratio [aOR] 0.2, 95% confidence interval [CI] 0.055-0.731; and HLA-DQB1*02:02, aOR 0.046, CI 0.002-0.871) and one was associated with higher risk for ICU admission or death (HLA-DQA1*05:01, aOR 2.517, CI 1.086-5.833). Conclusions: In this population, HLA-C*05:01 and HLA-DQB1*02:02 are associated with a protective effect against hospital admission and HLA-DQA1*05:01 is associated with higher risk of ICU admission or death in the multivariable analysis. This may help stratify risk in COVID-19 patients.