Genotype Frequencies Of Single Nucleotide Polymorphisms Research Articles

Comprehensive breast cancer risk analysis with whole exome sequencing and the prevalence of BRCA1 and ABCG2 mutations and oncogenic HPV.

Breast cancer is the most prevalent cancer and also the leading cause of cancer death in women worldwide. A comprehensive understanding of breast cancer risk factors and their incidences is useful information for breast cancer prevention and control planning. The present study aimed to provide information on single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) in breast cancer, the allele frequency of two SNPs in breast cancer-related genes BRCA1 DNA repair associated (BRCA1; rs799917) and ATP binding cassette subfamily G member 2 (ABCG2; rs2231142), and the prevalence of human papillomavirus (HPV) infections in a normal population living in Phayao Province, Northern Thailand. One breast cancer and 10 healthy samples were investigated by whole exome sequencing (WES) and compared for genetic variation. The WES data contained SNPs in genes previously implicated in breast cancer and provided data on CNVs. The allele frequencies for SNPs rs799917 and rs2231142 were also examined. The SNP genotype frequencies were 35.88% CC, 46.54% CT, and 17.58% TT for rs799917 and 33.20% CC, 46.88% CA, and 19.92% AA for rs2231142. A total of 825 human whole blood samples were examined for HPV infection by PCR, and the pooled DNA was tested for HPV infection using metagenomic sequencing. No HPV infections were detected among all 825 samples or the pooled blood samples. The incidence of breast cancer among the tested samples was estimated based on acceptable breast cancer risk factors and demographic data and was 1.47%. The present study provided data on SNPs and CNVs in breast cancer-related genes. The associations between SNPs rs2231142 and rs799917 and breast cancer should be further investigated in a case-control study since heterozygous and homozygous variants are more common. Based on the detection of HPV infection in the blood samples, HPV may not be associated with breast cancer, at least in the Northern Thai population.

Deciphering the genetic impact of signal peptide missense CTLA-4 polymorphism with rheumatoid arthritis in the Indian population: A case-control and in silico studies

Cytoplasmic T Lymphocyte Antigen-4 (CTLA-4) gene encodes for a glycoprotein, expressed on activated T-cells to transfer an inhibitory signal to control T-cell activation and proliferation. Techniques coupled with Real-time Polymerase Chain Reaction (PCR) and High-Resolution Melting Analysis (HRMA) were used to screen a missense signal peptide polymorphism (CTLA-4 + 49 A/G rs231775) in the Indian population to detect its association with Rheumatoid Arthritis (RA). Further, the resulting outcome was confirmed by Sanger’s sequencing technique, and genotype frequencies were calculated. In eukaryotic cells, the M domain of the Signal Recognition Particle (SRP-54) recognizes the N-terminal region of the Signal Peptide (SP) sequence. SP directs the polypeptide chain into the Sec-61 translocon of the Endoplasmic Reticulum (ER) for further protein modification. As the Single Nucleotide Polymorphism (SNP) rs231775 lies in the signal peptide region of CTLA-4, an in-silico study was also performed to predict the mRNA stability and SP-SRP protein interaction. From the study, it was observed that the genotype frequency of rs231775 SNP G/G homozygous dominant was significantly higher in RA patients than G/A heterozygous dominant and A/A homozygous recessive conditions (Odd Ratio (OR) = 2.0862; 95 % Confidence Interval (C.I) = 1.2584 to 3.4584; Relative Risk (RR) = 1.8507; p = 0.0044). Moreover, the rs231775 SNP G allele frequency was higher in RA than the control group G = 0.407 (40.7 %) vs 0.32 (32 %). In silico approaches of Protein-Protein docking and Molecular Dynamics (MD) simulation reveal CTLA-4 rs231775 SNP (G allele) has destabilized the SP-SRP protein complex, which may affect the translocation of CTLA-4 nascent polypeptide chains into the ER via activating Regulation of Aberrant Protein Production (RAPP) pathway.

The association between endoplasmic reticulum aminopeptidase 2 gene single nucleotide polymorphisms and the risk of psoriasis and psoriatic arthritis in Egyptians.

Psoriasis (Ps) is a disorder attributed to the immune system that involves inflammation of the skin and joints. Psoriasis is a multifactorial disorder in which genetic factors represent about 70% of the disease risk. This study aims to establish the correlation between the ERAP2 gene's single nucleotide polymorphisms (SNPs) rs2910686 and rs2248374 with the susceptibility to Ps and/or psoriatic arthritis (PsA) among the Egyptian population. Genotyping of ERAP2 gene SNPs (rs2910686 and rs2248374) in 120 psoriatic patients with and without arthritis and 100 controls was done using real-time PCR. The genotype frequency and distribution of the ERAP2 SNP (rs2910686 and rs2248374) were in Hardy-Weinberg equilibrium (HWE). For rs2910686, the TC and CC genotypes and C allele frequency were significant risk factors for PsA compared to the controls (OR = 5.708, OR = 10.165, and OR = 4.282, respectively). They also were significant risk factors for Ps compared to the controls (OR = 5.165, OR = 5.040, and OR = 3.258, respectively). For rs2248374, the AG genotype significantly increased the risk of PsA (OR = 2.605) and Ps (OR = 3.768) compared to controls. The AG genotype was significantly related to the risk of Ps (OR = 3.369) G allele with PsA (OR = 1.608) and Ps (OR = 1.965) compared to controls. In Egyptian individuals, the ERAP2 gene polymorphisms (rs2248374 and rs2910686) may contribute genetically to the pathophysiology of psoriasis and PsA.

Human TMPRSS2 and ACE2 genetic variability on COVID-19 outcomes in patients from Brazil

Angiotensin-converting enzyme 2 (ACE2) and the transmembrane serine protease 2 (TMPRSS2) are recognized as entry proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and recently their Single Nucleotide Polymorphisms (SNP) have been studied in different populations to elucidate the impact on disease. This study aimed to evaluate the genetic SNP of ACE2 (rs35803318) and TMPRSS2 (rs2070788) genes in COVID-19 patients from Northeast Brazil compared with global populations, as well as the expression quantitative trait locus (eQTL). For ACE2 (rs35803318), we found 92.6% CC, 3.4% CT, and 4.0% TT genotype carriers in SARS-CoV-2-positive patients. Surprisingly, only the genotype frequencies of ACE2 SNP were not in Hardy-Weinberg equilibrium. For TMPRSS2 rs2070788, we found 22.3% GG, 50.7% AG, and 27% AA genotype carriers in SARS-CoV-2-positive patients. The expression quantitative trait loci (eQTLs) revealed that rs35803318 was associated with an altered PIR gene expression, and rs2070788 was found to eQTLs association only with lung tissue. No significant association was identified between the genotype distribution of SNPs and the ‘patient's outcome. In conclusion, our results suggest that ACE2 and TMPRSS2 may not be protective factors for global populations, including the Brazilian population, since the presence of SNPs does not affect the ‘patient's outcome as described by other studies.

Serum osteoprotegerin and its gene polymorphisms in patients with Takayasu’s arteritis: a bicentric cross-sectional study

IntroductionTakayasu’s arteritis (TAK) patients are at an elevated risk of metabolic syndrome and cardiovascular diseases (CVD). Currently, there are no well-validated biomarkers to assess this risk in this population. Previous research in different cohorts has linked serum levels of osteoprotegerin (OPG) and its polymorphisms to accelerated atherosclerosis and a marker of poor prognosis in CVD. Thus, we assessed this protein as a potential biomarker of CVD in TAK patients.ObjectivesTo evaluate the serum levels of OPG and its SNPs (single nucleotide polymorphisms) in TAK patients and healthy controls, and to associate these parameters with clinical data.MethodsThis bicentric cross-sectional study included TAK patients who were compared with healthy individuals (control group). The serum levels of OPG and the frequency of OPG SNPs [1181G > C (rs2073618), 245 A > C (rs3134069), 163T > C (rs3102735), and 209 C > T (rs3134070)] were compared between the both groups and associated with clinical data.ResultsIn total, 101 TAK patients and 93 controls were included in the study. The serum levels of OPG (3.8 ± 1.9 vs. 4.3 ± 1.8pmol/L, respectively; P = 0.059), and its four polymorphisms were comparable between both groups. In an additional analysis of only TAK patients, serum OPG levels and its four genes were not associated with any CVD parameters, except for higher OPG levels among patients without dyslipidemia.ConclusionNo significant differences were observed in serum OPG levels or in the genotype frequencies of OPG SNPs between the patient and control groups. Similarly, no correlation was found between laboratory parameters and clinical data on CVD risk in TAK patients.

Investigation of Liver X Receptor Gene Variants and Oxysterol Dysregulation in Autism Spectrum Disorder.

The NR1H2 gene produces the Liver X Receptor Beta (LXRB) protein, which is crucial for brain cholesterol metabolism and neuronal development. However, its involvement in autism spectrum disorder (ASD) remains largely unexplored, aside from animal studies. This study is the first to explore the potential link between autism and rs2695121/rs17373080 single nucleotide polymorphisms (SNPs) in the regulatory regions of NR1H2, known for their association with neuropsychiatric functions. Additionally, we assessed levels of oxysterols (24-Hydroxycholesterol, 25-Hydroxycholesterol, 27-Hydroxycholesterol), crucial ligands of LXR, and lipid profiles. Our cohort comprised 107 children with ASD and 103 healthy children aged 2-18 years. Clinical assessment tools included the Childhood Autism Rating Scale, Autistic Behavior Checklist, and Repetitive Behavior Scale-Revised. Genotyping for SNPs was conducted using PCR-RFLP. Lipid profiles were analyzed with Beckman Coulter kits, while oxysterol levels were determined through liquid chromatography-tandem mass spectrometry. Significantly higher total cholesterol (p = 0.003), LDL (p = 0.008), and triglyceride (p < 0.001) levels were observed in the ASD group. 27-Hydroxycholesterol levels were markedly lower in the ASD group (p ≤ 0.001). ROC analysis indicated the potential of 27-Hydroxycholesterol to discriminate ASD diagnosis. The SNP genotype and allele frequencies were similar in both groups (p > 0.05). Our findings suggest that disturbances in oxysterol metabolism, previously linked to neurodegeneration, may constitute a risk factor for ASD and contribute to its heterogeneous phenotype.

The effects of IL-27 and IL-35 gene variation and expression levels on the susceptibility and clinical manifestations of pulmonary tuberculosis.

Inflammatory cytokines have crucial roles in the pathogenesis of tuberculosis (TB), and interleukin (IL)-27 and IL-35 have a pro-inflammatory and anti-inflammatory effect on many diseases, including infectious diseases. Therefore, we evaluated the relationship between IL-27 and IL-35 gene polymorphism, expression levels, and pulmonary TB (PTB) susceptibility. Nine single-nucleotide polymorphisms (SNPs) in the IL-27 gene (rs181206, rs153109, and rs17855750) and the IL-35 gene (rs4740, rs428253, rs9807813, rs2243123, rs2243135, and rs568408) were genotyped by the SNPscan technique in 497 patients with PTB and 501 controls. There was no significant difference regarding the genotype and allele frequencies of the above SNPs in the IL-27 and IL-35 genes between patients with PTB and controls. Haplotype analysis showed that the frequency of the GAC haplotype in the IL-35 gene was significantly decreased in patients with PTB when compared to controls (p = 0.036). Stratified analysis suggested that the frequency of the IL-27 rs17855750 GG genotype was significantly increased in patients with PTB with fever. Moreover, the lower frequency of the IL-35 rs568408 GA genotype was associated with drug-induced liver injury in patients with PTB. The IL-35 rs428253 GC genotype, as well as the rs4740 AA genotype and A allele, showed significant relationships with hypoproteinemia in patients with PTB. When compared with controls, the IL-27 level was significantly increased in patients with PTB. Taken together, IL-35 gene variation might contribute to a protective role on the susceptibility to PTB, and IL-27 and IL-35 gene polymorphisms were associated with several clinical manifestations of patients with PTB.

Association of HLA rs3135388 and rs9271366 Single-Nucleotide Polymorphisms With Multiple Sclerosis in the Chaharmahal and Bakhtiari Province, Iran

Background and aims: Genetics and environment are synergistic in multiple sclerosis (MS). Human leukocyte antigen (HLA) class II has a strong genetic association with MS. The aim of this study was to determine the association of HLA rs3135388 and rs9271366 single-nucleotide polymorphisms (SNPs) with MS. Methods: The rs3135388, rs9271366, and rs422951 SNPs were genotyped in 173 Iranian relapsing-remitting MS (RRMS) patients and 200 matched healthy controls, using the polymerase chain reaction-restriction fragment length polymorphism method. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using statistical software to estimate the risk factor for disease. The allele and genotype frequencies of SNPs were determined based on data analysis using SPSS, version 20. Results: Our results identified a strong association in the allele distribution for both rs3135388 and rs9271366 SNP, such that the A allele of rs3135388 (OR=1.765; 95% CI: 1.071–2.909) and the G allele of rs9271366 were found to be more frequent in MS patients than in healthy controls (OR=1.861; 95% CI: 1.025–3.3378). The mutated G allele for rs422951 SNP was relatively frequent (OR=1.128; 95% CI: 0.745–1.707). Conclusion: Our findings revealed the critical role of the rs3135388 and rs9271366 SNPs in MS disease progression. Genotyping MS patients could facilitate personalized medical management.

Association between GABRG2 Gene Single Nucleotide Polymorphisms and Susceptibility to Ischemic Stroke in a Chinese Population.

Current evidence suggests that Gamma-aminobutyric acid (GABA) receptors are associated with the occurrence and progression of cerebrovascular diseases. The present study investigated the association between single nucleotide polymorphisms (SNPs) in the Gamma-aminobutyric acid type A receptor gamma2 subunit (GABRG2) gene and ischemic stroke (IS). A total of 120 healthy volunteers and 187 patients with IS were recruited. Patients underwent complete neurological assessment and classification with the National Institute of Health Stroke Scale (NIHSS) and the Trial of ORG 10172 in Acute Stroke Treatment (TOAST). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to analyze SNP sites in 4 different regions (rs211037, rs418210, rs211035, and rs424740) of the GABRG2 gene. SHEsis online platform was used to assess SNP allele and genotype frequencies. Multivariate logistic regression analysis was performed to identify the risk factors for IS. Univariate analysis showed that the T allele and TT genotype distribution for rs211037 were significantly more frequent in the IS group compared to controls (pallele = 0.01, odds ratio (OR) = 1.673, 95% confidence intervals (CI), 1.119-2.500, pgenotype = 0.03). Furthermore, multivariate logistic regression analysis revealed the TT genotype for rs211037 was an independent risk factor for IS (p = 0.017, OR = 1.925, 95% CI, 1.122-3.303). Age was also found to be an independent risk factor, and the older the age, the higher the risk of IS (p = 0.001, OR = 1.047, 95% CI, 1.020-1.073). Finally, subgroup analysis revealed that patients with the rs211037 TT genotype were associated with a higher NIHSS score (p = 0.03), and that large-artery atherosclerosis (LAA) subtype was predominant in patients with the rs211037 TT genotype (p = 0.042). These findings suggest the rs211037 polymorphism in the GABRG2 gene is an independent risk factor for IS in the Chinese population. GABRG2 could thus be a potential biomarker to assess the risk of IS.

MiRNA-423 rs6505162and miRNA-6811 rs2292879SNP AssociatedwithLung Cancer in Hainan, China.

MicroRNAs (miRNAs) are known to exert significant influence on various physiological processes and diseases, including cancers. The primary objective of this present study was to examine the impact of eightsingle nucleotide polymorphisms(SNPs)in miRNA on the susceptibility to lung cancer (LC) within the Chinese Southernpopulation. Thegenotypes of these eight polymorphisms weredeterminedin132 LC patients and 214cancer-free controls. In overall analyses, GG genotype of miRNA-6811 rs2292879 polymorphismwas significantly correlated with increased risk ofLC (GG vs. AA,adjusted OR = 5.10, 95% CI = 1.02 ~ 25.43, P= 0.047), yet the genotype frequenciesof rs2292879SNP in controlsdid notmet the Hardy-Weinberg equilibrium (HWE)(P= 0.001) in present study. Stratified analysesby smoking revealed that miRNA-423 rs6505162 variants significantly decreased the LC risk in heterozygous (CA vs. CC, adjusted OR = 0.14, 95% CI = 0.03 ~ 0.81, P= 0.028), recessive(AA vs. CA + CC, adjusted OR = 0.17, 95% CI = 0.03 ~ 0.90, P= 0.038)genetic models in smoking population. However, miRNA-196A2rs11614913, miRNA-196A2rs12304647, miRNA-146Ars2910164, miRNA-16-1rs1022960, miRNA-608rs4919510, andmiRNA-27a rs895819polymorphisms were not significantly associated withLC. The findings of our study indicate a potential decrease inLC risk among smokers with the miRNA-423 rs6505162variants, while an increase in risk is associated with miRNA-6811 rs2292879 polymorphismsin the population of SouthernChinese. However, further well-designed researchis necessary to fully understand the precise impact of these twoSNPs on the development of LC.

Evaluation of Immunity-related GTPase Family M Protein (IRGM) SNPs among Egyptian Lupus Patients: A Case-control Study.

One of the potential factors that cause systemic lupus erythematosus (SLE) development is autophagy. Immunity-related GTPase family M protein (IRGM) has been shown to be linked to immune-mediated diseases. The aim of the current study was to assess the role of the IRGM-autophagy gene in SLE susceptibility in an Egyptian population and its relation to lupus nephritis. A case-control study was conducted in which a total of 200 subjects (100SLE and 100 healthy controls) were enrolled. Two single-nucleotide polymorphisms (SNPs) (rs10065172 and rs4958847) were genotyped. Genotypes and alleles analysis was conducted to compare between cases and controls, as well as a stratification analysis was conducted on the presence or absence of lupus nephritis. Among selected SNPs of IRGM, no association was found between both SNPs and SLE susceptibility. For rs10065172, the major expressed genotype was CC (61% and 71%) (Adj OR= 2.9, 95%= 0.545-15.5), followed by TC (34% and 27%) (Adj OR= 1.985, 95% = 0.357-11.041) in cases and controls, respectively. For rs4958847, AA and AG were comparably expressed in case [(43% and 39%) (Adj OR= 1.073, 95% = 0.483-2.382)] and control [(41% and 43%) (Adj OR= 1.24, 95% = 0.557- 2.763)], respectively. Additionally, no relationship among both SNPs and gender, lupus nephritis, disease activity, or disease duration, was observed. IRGM SNPs (rs10065172 and rs4958847) expression was comparable among SLE patients and controls of the Egyptian cohort. Genotype and allele frequency of IRGM SNPs did not differ in lupus nephritis and non-lupus nephritis patients.

Association of NPPB rs198389 and NPPA rs5068 single-nucleotide polymorphisms with natriuretic peptide levels and heart failure progression risks in patients with atrial fibrillation

Natriuretic peptides (NUPs) are the strongest predictors of poor prognosis in patients with heart failure (HF). Single-nucleotide polymorphisms (SNPs) rs198389 of the NPPB gene and rs5068 of the NPPA gene are associated with altered levels of NUP. The role of candidate gene polymorphisms in the activity of the NUP system and the association of NPPA/ NPPB SNPs with the risk of cardiovascular disease (CVD) in individuals with HF and atrial fibrillation (AF) is not well understood.The study aims to evaluate the allele and genotype frequencies of NPPA rs5068 and NPPB rs198389 SNPs in a selective sample of the Belarusian population, to determine the relationship of these SNPs with NUP concentrations, and to assess the prognostic significance of these SNPs on the risk of HF hospitalization in patients with HF and permanent AF.The study involved 187 patients. The main group included 152 patients with HF with left ventricular ejection fraction (LVEF) &lt; 50 %. Group 1 included 48 patients with HF and AF; group 2 – 51 patients with HF and sinus rhythm (SR) and 35 patients in the control group. The levels of atrial and brain natriuretic peptides (ANP and BNP) and the N-terminal fragment of the brain natriuretic peptide (NT-proBNP) were determined. A genetic testing of polymorphic loci of the rs5068 NPPA gene and the rs198389 NPPB gene was performed. The primary endpoint of the study was hospitalization due to HF progression.The average observation period was 12.1 [from 9 to 14] months. The distribution of the genotype and allele frequencies of rs198389 NPPB and rs5068 NPPA in HF patients with LVEF &lt; 50 % is comparable to that in individuals without CVD. In patients with HF and persistent AF, the minor allele C rs198389 NPPB is associated with higher BNP levels compared to patients with HF and SR (542 [333.7; 909.4] pg/ml versus 247.3 [244; 365.2] pg/ml; p &lt; 0.05), but it has no relationship with the NT-proBNP level. In patients with HF and permanent AF, the ANP levels are not associated with rs5068 NPPA.The frequency of the T allele rs198389 NPPB in hospitalized patients was significantly lower compared to patients who were not hospitalized (22 patients (44 %) versus 83 patients (62 %); p = 0.04). The presence of the C allele rs198389 NPPB was associated with a higher risk of HF progression in patients with HF and AF, the odds ratio (OR) = 2.071 [95 % CI from 1.072 to 4.001], p &lt; 0.05.

FTO genotypes (rs9939609 T>A) are Associated with Increased Added Sugar Intake in Healthy Young Adults

Introduction: Single-nucleotide polymorphism (SNP) rs9939609 in the FTO gene has been associated with dietary intake and appetite traits, mainly in participants with obesity; however, it remains widely unexplored in normal weight participants. Thus, the aims of this study were (1) to compare the changes in subjective appetite sensations, ghrelin, and insulin concentrations according to the SNP rs9939609 T>A in FTO and (2) to compare dietary intake between rs9939609 genotype groups in normal weight young participants. Methods: We conducted a quasi-experimental study involving 88 normal weight participants to analyze subjective perception of appetite, hormonal response for hunger and satiety, and dietary intake according to the rs9939609 SNP. Participants received a standardized single breakfast. Visual analogue scales (VAS) were utilized for assessing the subjective perception of appetite at fasting and immediately after breakfast and at 30, 60, 90, and 120 min postprandially. Glucose, lipid profile, ghrelin, and insulin were measured at fasting and at 120 min after breakfast. Dietary intake was assessed with a 3-day food record. The SNP was determined by allelic discrimination with TaqMan probes. To compare dietetic, biochemical, and the subjective appetite sensations, Student t test, ANCOVA test, and the repeated measures ANOVA were used. The linear regression model and the linear mixed model were used for the association analysis. Pearson correlation was used to test the correlation between two quantitative variables. Results: A total of 88 people participated, 81.8% were female, with a mean body mass index of 21.8 ± 2.0 kg/m² and a mean age of 20.6 ± 2.0. Genotype frequencies of the rs9939609 SNP were 52% for the TT allele and 48% for the TA/AA. The subjective perception of appetite named hunger, fullness, satiety, desire to eat, and prospective food consumption were similar between genotypes of the rs9939609. Participants with the TA/AA genotype showed a higher intake of added sugar (p = 0.039) than TT participants. No differences were found in ghrelin, insulin, glucose, or lipid parameters between genotypes. Conclusion: Carriers of the A allele from FTO gene SNP rs9939609 may have an increased preference for foods, specifically for added sugars.

P1526: AUTOIMMUNE HEMOLYTIC ANEMIAS: RELATIONSHIP BETWEEN SINGLE NUCLEOTIDE POLYMORPHISMS OF CYTOKINE GENES AND CLINICAL/HEMATOLOGICAL PARAMETERS

Background: Autoimmune hemolytic anemia (AIHA) is highly heterogeneous and involves several pathogenic mechanisms including autoantibody production, complement activation, and cytokine dysregulation. Hb levels at baseline and the degree of bone marrow compensation are the main predictors of outcome. The contribution of high, intermediate, and low producer genetic profile cytokine genes may give further insights into the pathogenesis of the disease. Aims: To evaluate the frequency of cytokine single nucleotide polymorphisms (SNPs) in warm (wAIHA) and cold agglutinin disease (CAD) and their relationship with clinical and hematological parameters, including the degree of anemia, treatment refractoriness and number of therapies lines. Methods: We investigated SNPs of five cytokine genes [tumour necrosis factor (TNF)-alpha, interferon (IFN)-gamma, transforming growth factor (TGF)-beta, interleukin (IL)-6 and IL-10] in 72 Italian warm AIHA patients, using the Cytokine Tray (One Lambda, Canoga Park, CA) according to the manufacturer’s recommendations. Allele and genotype frequency results were compared to those described in the Italian population by Uboldi de Capei et al. (2003) and Poli et al. (2002). Results: One hundred and twenty AIHA patients have been evaluated: median age 63 years (range 17-90), classified as wAIHA (n=75) and CAD (n=45). Demographic and hematological characteristics of patients are described in Figure 1A. Regarding cytokine SNP frequencies (Figure 1B), we observed that the TNF-alpha-308 high producers genotypes (G/G and G/A) were significantly more frequent in AIHA patients (37% vs 16%, p=0.0003 or 37% vs 23%, p=0.01) and in wAIHA (43% vs 16%, p<0.0001 or 43% vs 23%, p=0.0014) compared to controls. No differences were observed in CAD patients versus controls. Likewise, no significant differences between AIHA (including wAIHA and CAD subtypes) and controls were noted regarding other cytokine SNPs. Concerning the clinical severity at presentation, the frequency of TGF-beta (82% vs 58%, p=0.01) and IL-10 (17% vs 5%, p=0.03) high producers was higher in patients with Hb ≤7.5 g/dL (median of all AIHA) versus those with less severe presentation. Similarly, the frequency of high/intermediate IFN-gamma producers was higher within the group with Hb levels ≤7.5 g/dL at onset (75% vs 58%, p=0.03). No characteristic patterns were observed regarding IL-6 and TNF-alpha. Finally, the patterns of TNF-alpha and TGF-beta production were differently distributed considering the number of therapy lines: the first both in all AIHA and in CAD patients (p=0.004 and p=0.01, respectively), the second only in CAD patients (p=0.03). No differences in genotype frequencies of cytokine SNPs were observed regarding the number of relapses. Image:Summary/Conclusion: These preliminary data show that AIHA patients display a more pro-inflammatory cytokine signature at molecular level (TNF-alpha high producer genotype) as compared to the Italian control population. Moreover, cytokine SNPs were also associated with clinical severity at onset, and requirement of multiple treatments.

Functional Single-Nucleotide Polymorphisms in the MBL2 and TLR3 Genes Influence Disease Severity in Influenza A (H1N1)pdm09 Virus-Infected Patients from Maharashtra, India.

The clinical outcome in influenza A (H1N1)pdm09 virus-infected subjects is determined by several factors, including host genetics. In the present study, single-nucleotide polymorphisms (SNPs) in the IFITM, MBL2, TLR3, TLR8, DDX58, IFIH1, CD55, and FCGR2, genes were investigated in influenza A (H1N1)pdm09 virus-infected subjects to find out their association with disease severity. Influenza A (H1N1)pdm09 virus-infected subjects with severe disease (n = 86) and mild disease (n = 293) from western India were included in the study. The SNPs were investigated by PCR-based methods. The results revealed a higher frequency of TLR3 rs5743313 T/T genotype [odds ratio (OR) with 95% confidence interval (CI) 2.55 (1.08-6.04) p = 0.039] and TLR3 two-locus haplotype rs3775291-rs3775290 T-A [OR with 95% CI 7.94 (2.05-30.68)] in severe cases. Lower frequency of the mutant allele of MBL2 rs1800450 [OR with 95% CI 0.51 (0.27-0.87), p = 0.01] and TLR3 two-locus haplotype rs3775291-rs3775290 T-G [OR with 95% CI 0.48 (0.27-0.85)] was observed in severe cases compared with cases with mild disease. Higher frequency of TLR3 two-locus haplotype rs3775291-rs3775290 T-A was observed in severe cases [OR with 95% CI 7.9 (2.0-30.7)]. The allele and genotype frequencies of other SNPs were not different between the study categories. The results suggest that the functional SNPs in MBL2 and TLR3 are associated with severe disease in influenza A (H1N1)pdm09 virus-infected subjects.

Genotype Frequency of the Common TLR4 SNPs in a Kurdish Population: Global Reviews and Out-of-African Migrations.

Toll-like receptors (TLRs) are cellular innate immune receptors that explore microbial molecules. For instance, TLR4 can sense bacterial lipopolysaccharides, inducing cytokines and antimicrobial peptides against the bacteria. Single-nucleotide polymorphisms (SNPs) in TLR4 are associated with diseases such as septic shock. Therefore, investigations of common SNPs may help explain the pathogenesis of diseases and various innate immune responses to infections. This study investigated genotypic frequencies of the two common TLR4 SNPs, Asp299Gly and Thr399Ile, in a Kurdish population using restriction length fragment polymorphisms (RFLPs). Global frequencies of both TLR4 SNPs in different populations of sub-Saharan Africa, North Africa, western Asia, Eurasia, and East Asia were also used to infer human migrations and past settlements. The RFLP data demonstrate that, in the Kurdish population, the genotypic frequencies of both SNPs are similar to Iranian or other West Asian populations, which in turn are comparable to Eurasian populations, suggesting past admixture due to migrations, population intermixing, and common ancestry. Globally, the frequencies of the homozygous wild-types of TLR4 variants are prevalent, but homozygous mutants are rare or lacking in almost all global populations. Frequencies of the heterozygotes varied among populations. For instance, in sub-Saharan Africa the frequency of the Asp299Gly SNP is higher than that of Thr399Ile, whereas in the Arabian Peninsula both SNPs are present at high frequencies. In contrast, East Asian populations lack or have very low frequencies of both TLR4 SNPs of interest. Moreover, co-segregation of the TLR4 SNPs is common in some populations, which may indicate important associations with certain diseases. Future studies are required to link the TLR4 SNPs with either resistance or susceptibility to diseases.

Association Study of the M132L Single Nucleotide Polymorphism With Susceptibility to Chronic Wasting Disease in Korean Elk: A Meta-Analysis.

Chronic wasting disease (CWD) is a deleterious brain proteinopathy caused by a pathogenic form of prion protein (PrPSc), which is converted from a benign form of prion protein (PrPC) encoded by the prion protein gene (PRNP). In elk, the M132L single nucleotide polymorphism (SNP) of the PRNP gene likely plays a pivotal role in susceptibility to CWD. However, the association of the M132L SNP with susceptibility to CWD has not been evaluated in Korean elk to date. To estimate the association of the M132L SNP with susceptibility to CWD in Korean elk, we investigated the genotype and allele frequencies of the M132L SNP by amplicon sequencing and performed association analysis between CWD-positive and CWD-negative elk. In addition, we performed a meta-analysis to evaluate the association between the M132L SNP and susceptibility to CWD in quantitatively synthesized elk populations. Furthermore, we estimated the effect of the M132L SNP on elk PrP using in silico programs, including PolyPhen-2, PROVEAN, AMYCO and Swiss-PdbViewer. We did not identify a significant association between the M132L SNP of PRNP and susceptibility to CWD in Korean elk. The meta-analysis also did not identify a strong association between the M132L SNP of PRNP and susceptibility to CWD in quantitatively synthesized elk populations. Furthermore, we did not observe significant changes in structure, amyloid propensity or electrostatic potential based on the M132L SNP in elk PrP. To the best of our knowledge, this was the first report of an association analysis and meta-analysis in Korean elk and quantitatively synthesized elk populations, respectively.

Single Nucleotide Polymorphisms of Cytokine Genes in Warm Autoimmune Hemolytic Anemias: Relationship with Clinical and Hematological Parameters

Background: Autoimmune hemolytic anemia (AIHA) is due to an increased immune peripheral destruction of red blood cells. The disease is characterized by high heterogeneity regarding anemia severity, treatment requirement and occurrence of complications. It has been shown that Hb levels at baseline, presence of complement activation, and the degree of bone marrow compensation are the main predictors of outcome. Moreover, multi-relapsing cases show bone marrow dysmyelopoiesis, and fibrosis suggesting an immune attack against bone marrow precursors. An interesting area to investigate is the genetic landscape of AIHA, including cytokine gene signature and other molecular mechanisms of refractoriness.Aim: To evaluate the frequency of cytokine single nucleotide polymorphisms (SNPs) in warm AIHA and their correlation with clinical and hematological parameters, including the degree of anemia, treatment refractoriness and number of therapies lines.Methods: We investigated SNPs of five cytokine genes [tumour necrosis factor (TNF)-alpha, interferon (IFN)-gamma, transforming growth factor (TGF)-beta, interleukin (IL)-6 and IL-10] in 72 Italian warm AIHA patients, using the Cytokine Tray (One Lambda, Canoga Park, CA) according to the manufacturer's recommendations. Allele and genotype frequency results were compared to those described in the Italian population by Uboldi de Capei et al. (2003) and Poli et al. (2002).Results: Seventy-two warm AIHA patients have been evaluated: median age 63 years (range 17-90), classified as per DAT positivity in IgG+ (N=48), IgG+C (N=17), IgA+ (N=1), and DAT negative AIHA (N=6). Demographic and hematological characteristics of patients are described in Figure 1A. Regarding cytokine SNP frequencies, we observed that AIHA patients had a significantly higher prevalence of the TNF-alpha-308 high producers genotypes (G/G and G/A) compared to controls (40.3% vs 16% or 23%, p=0.0003 and p=0.006, respectively). No differences were detected regarding genotype frequencies of the other cytokine SNPs (Figure 1B). By dividing patients according to anemia severity at onset, a more frequent low producer genotype of IFN-gamma (A/A) was observed in patients with Hb levels >7.4 g/dL (median value of patients cohort) compared to the other group (p=0.05). Finally, considering the number of relapses or therapy lines, an increased frequency of TNF-alpha -308 high producers genotypes were found among multi-relapsing (> 3 relapses, 70.5% vs 56%) and multi-treated patients (> 3therapy lines, 52% vs 35%), although not significantly.Conclusions: These preliminary data show that wAIHA patients display a more pro-inflammatory cytokine signature at molecular level as compared to the Italian control population. This is highlighted by an increased prevalence of TNF-alpha high producer genotype that is also associated with multiple relapses and greater treatment requirement. Additionally, cytokine SNPs may be also associated with anemia severity at onset, as observed for IFN-gamma low producer genotype that was more frequent in less severe cases. [Display omitted] DisclosuresFattizzo: Alexion, Amgen, Annexon, Apellis, Grifols, Novartis, Momenta: Consultancy, Speakers Bureau. Bianchi: Agios pharmaceutics: Consultancy, Membership on an entity's Board of Directors or advisory committees. Barcellini: Agios: Honoraria, Research Funding; Bioverativ: Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria; Alexion Pharmaceuticals: Honoraria; Incyte: Membership on an entity's Board of Directors or advisory committees.

Association of ATG5 gene polymorphism with Parkinson’s disease in a Han Chinese population

PurposeThere is growing evidence that autophagy-related gene 5 (ATG5) is involved in neural development, neuronal differentiation, and neurodegenerative diseases. The purpose of this study was to investigate the association between ATG5 gene single-nucleotide polymorphisms (SNPs) and Parkinson’s disease (PD) in the Han population.MethodsA case–control study was conducted in 120 PD patients and 100 healthy volunteers. MassArray platform was used to analyze polymorphisms in three different regions of ATG5 gene (rs510432, rs573775 and rs17587319). In the included subjects, 50 PD patients and 50 healthy volunteers were selected, and the plasma ATG5 concentration was detected by enzyme-linked immunosorbent assay (ELISA). The allele and genotype frequencies of SNPs were assessed using the SHEsis program.ResultsWe found a significant correlation between rs17587319 and PD, and the subcomponent showed a high correlation between rs17587319 with cognitive impairment and age at onset in PD patients. At the same time, the total plasma ATG5 level of PD patients and the plasma ATG5 expression level of early-onset Parkinson’s disease (EOPD) patients were significantly higher than the control group, while there was no significant difference of ATG5 expression between late-onset Parkinson’s disease (LOPD) patients and the control group.ConclusionThese findings suggest that genetic variations in the ATG5 gene and low levels of the ATG5 protein are associated with susceptibility to PD and with cognitive impairment in PD patients. ATG5 could be a potential biomarker to assess the severity and prognosis of PD.

Inherited GATA3 genetic Variants Are Associated With Childhood BCR-ABL1-Like Acute Lymphoblastic Leukemia and Increased Risk Of Relapse

Recent genomic profiling of acute lymphoblastic leukemia (ALL) has identified a novel high-risk subtype with a gene expression signature similar to that of BCR-ABL1-positive (Ph+) ALL and a poor prognosis. This novel BCR-ABL1-like ALL subtype is characterized by genomic aberrations targeting lymphoid development, cytokine receptor, and tyrosine kinase signaling pathways, e.g., IKZF1 deletion, CRLF2 rearrangements, and JAK mutations. However, the role of the inherited genetic variation in the pathogenesis of BCR-ABL1-like ALL remains unknown.Taking a genome-wide association study (GWAS) approach, we sought to examine germline single-nucleotide polymorphisms (SNPs) for their association with the predisposition to BCR-ABL1-like ALL. In the discovery GWAS, we compared germline SNP genotype frequencies between ALL cases with (N=75) vs. without (N=436) the BCR-ABL1-like expression signature enrolled on the high risk Children's Oncology Group (COG) AALL0232 protocol, and between BCR-ABL1-like ALL (N=75) vs. non-ALL controls (N=6,661). BCR-ABL1-like ALL was identified by prediction analysis of microarrays. After adjusting for genetic ancestry, we observed a single susceptibility locus on 10p14 signified by two SNPs within the GATA3 gene with genome-wide significant association (P=1.05×10-8 and P=2.62×10-7 [BCR-ABL1-like ALL vs. non-BCR-ABL1-like ALL]; P=2.17×10-14 and P=4.94×10-12 [BCR-ABL1-like ALL vs. non-ALL controls]). In a replication cohort of high-risk ALL, namely COG P9906, the disease risk alleles at both GATA3 polymorphisms were consistently over-represented in BCR-ABL1-like ALL (N=32) compared with 139 non-BCR-ABL1-like ALL (P=0.01 and P=0.004, respectively) and compared with an independent set of 5,755 non-ALL controls (P=3.69×10-5 and P=0.0001, respectively). This GATA3 SNP was also associated with GATA3 expression in lymphoblastoid cell lines (N=56, P=0.034) and in primary ALL blasts (COG AALL0232, N=511, P=9.2×10-8; COG P9906, N=173, P=3.6×10-6), indicating that this variant may function as a cis-acting element regulating GATA3 transcription. Ectopic overexpression of GATA3 in ALL cell lines led to global changes in gene expression, with a particular enrichment of genes within the BCR-ABL1-like ALL expression signature.In the discovery cohort (COG AALL0232), the GATA3 SNP was also significantly associated with CRLF2 rearrangements (P=9.64×10-7), JAK mutations (P=2.06×10-5), and IKZF1 deletion (P=0.0002), which was validated in COG P9906 (P=0.08, 0.008, and 0.002, respectively) and in a third independent cohort, COG P9905 (P=0.009, 0.05, and 0.0002, respectively). The GATA3 risk allele was further enriched among patients with multiple “BCR-ABL1-like ALL-related” lesions concurrently, with the highest frequency observed in cases with three genomic lesions, followed by those with one or two lesions, and lowest among patients without any of the three lesions (COG AALL0232, P=6.09×10-5; COG P9906, P=0.0005; and COG P9905, P=7.6×10-5). Interestingly, the association of the GATA3 SNP with BCR-ABL1-likeness remained significant after adjusting for all three genomic lesions (P=0.001).We further examined the relationships between GATA3 SNP genotype and ALL relapse. In the COG P9906 cohort, the GATA3 allele linked to BCR-ABL1-like ALL was associated with a higher risk of relapse (N=222, P=0.002) and poor early treatment response as measured by minimal residual disease (N=193, P=9.8×10-5), which was validated in COG P9905 (N=777, P=0.007 and N=710, P=0.039, respectively). Of interest, the GATA3 allele associated with relapse and BCR-ABL1-like ALL was more frequent in Hispanics (40%) than in populations of European descent (12%), consistent with the inferior treatment outcome for Hispanic children with ALL.In conclusion, we have identified common GATA3 germline variants associated with BCR-ABL1-like ALL, somatic molecular lesions characteristic of this subtype, and importantly the risk of ALL relapse. These results suggest plausible interactions between host and tumor genomic variations in ALL pathogenesis and drug response. Disclosures:Evans:St. Jude: In accordance with institutional policy, St. Jude allocates a portion of the income it receives from licensing inventions and tangible research materials to those researchers responsible for creating this intellectual property. Patents & Royalties, Under this policy, I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics., Under this policy, I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics. Other. Relling:St. Jude: In accordance with institutional policy, St. Jude allocates a portion of the income it receives from licensing inventions and tangible research materials to those researchers responsible for creating this intellectual property. Patents & Royalties, Under this policy, I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics., Under this policy, I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics. Other.