Single Nucleotide Polymorphism SNP Research Articles

Polymorphism of IL13 (rs1295685) Gene and Its Serum Level in a Sample of Iraqi Patients with Allergic Asthma

Interleukin 13 (IL-13) is an immune-regulatory cytokine, primarily secreted by activated T Helper-Type (Th) 2 cells, which inhibits inflammatory cytokine production in allergic asthma. Single nucleotide polymorphism SNP (1295685A˃G) of the IL-13 gene and its serum level was included in a case-control study on 60 Iraqi asthmatics and 60 controls. ELISSA-linked immune-sorbent assay was used to estimate blood serum levels. The real-time high-resolution melting polymerase-chain-reaction (Real-time PCR-HRM) method was used to determine this variant. The results showed that the mean level of IL-13 was high in asthmatic patients compared to the control group (22.90 pg/ml vs.13.99 pg/ml), respectively, and significant differences were (p=0.0001). ROC curve analysis of IL-13 described an AUC of 0.882. Regarding the allele and genotype of (A˃G 1295685) SNP, there were clear differences between patients and the control group, as the frequency of the GG +AG genotype was significantly higher (p=0.001) in patients compared to the control group (81.7%vs.23.3%) respectively, and the G allele frequency was higher in patients compared to the control group (48.8% vs. 16.6%) respectively, with significant difference (p=0.001). In conclusion, increased levels of IL-13 in serum and the presence of the G allele, GG + AG genotype in the IL13 gene may be associated with the pathogenesis of allergic asthma in Iraqi adult patients. Keywords: Allergic Asthma, IL-13, SNP, RT-HRM-PCR

Association between vitamin D receptor gene TaqI (731236) polymorphisms and breast cancer risk in Iraqi women

Breast cancer BC is the most frequent cancer among women worldwide. Vitamin D inhibits cell proliferation through the vitamin D receptor (VDR), which may have an impact on the risk of BC. This studywas designed to association between VDR (Taq1 T/C)(rs 731236) single nucleotide polymorphism SNP with risk of BC in Iraqi women together with serum levels 25-hydroxyvitamin D [25-(OH) D] and CA 15-3. A case -control study women was carried out at Department of Biochemistry, College of Medicine, University of Baghdad, during the period from in the period from to October 2019 to January 2021. It included 95 women with period BC that had not received any chemotherapy. The phenotyping included the measurements of serum CA 15-3 and 25-(OH) D by using ELISA Kits. The genotyping analysis comprised of VDR- Taq1 (T/C) [rs731236] by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) analysis. The mean (±SD) value of serum CA15-3 and 25-(OH)D levels were significantly increase (p < 0.05), in BC women than in control. The risk of BC was significantly increased with VDR Taq 1 SNP (T/C) (rs 731236) in heterozygous and dominant genotypes in women with BC. The TC carriers (OR=1.904, 95% C.I= 1.055, 3.43, X2=4.612, p= 0.03) and dominant TC+CC (OR=1.895, 95%C.I=1.664, 3.37, X2 = 4.75, P= 0.02). Homozygous CC carriers (OR=1.798, 95%C.I = 0.382, 8.457, X2= 0.565, p= 0.45) did not observe significant difference, and border line allele frequency C allele carriers (OR=1.888, 95%C.I=0.941..3.789, X2=3.239, p= 0.07) when compared with wild TT genotype. The significant association between VDR Taq 1 SNP (T/C) (rs 731236) and plasma V D levels among BC women (p= 0.04). In Conclusion the VDR Taq 1 SNP (T/C) (rs 731236) variant could be regarded genetic risk factor for BC development. Vitamin D receptor gene-Taq1 polymorphism was associated with plasma VD.

Reliable DNA Markers for a Previously Unidentified, Yet Broadly Deployed Hessian Fly Resistance Gene on Chromosome 6B in Pacific Northwest Spring Wheat Varieties.

Hessian fly [Mayetiola destructor (Say)] is a major pest of wheat (Triticum aestivum L.) throughout the United States and in several other countries. A highly effective and economically feasible way to control Hessian fly is with resistant cultivars. To date, over 37 Hessian fly resistance genes have been discovered and their approximate locations mapped. Resistance breeding is still limited, though, by the genes’ effectiveness against predominant Hessian fly biotypes in a given production area, genetic markers that are developed for low-throughput marker systems, poorly adapted donor germplasm, and/or the inadequacy of closely linked DNA markers to track effective resistance genes in diverse genetic backgrounds. The purposes of this study were to determine the location of the Hessian fly resistance gene in the cultivar “Kelse” (PI 653842) and to develop and validate Kompetitive Allele Specific PCR (KASP) markers for the resistance locus. A mapping population was genotyped and screened for Hessian fly resistance. The resulting linkage map created from 2,089 Single Nucleotide Polymorphism SNP markers placed the resistance locus on the chromosome 6B short arm, near where H34 has been reported. Three flanking SNPs near the resistance locus were converted to KASP assays which were then validated by fine-mapping and testing a large panel of breeding lines from hard and soft wheat germplasm adapted to the Pacific Northwest. The KASP markers presented here are tightly linked to the resistance locus and can be used for marker-assisted selection by breeders working on Hessian fly resistance and allow confirmation of this Hessian fly resistance gene in diverse germplasm.

NEW SELECTION TECHNIQUES TO DETECT SOURCES OF RESISTANCE AGAINST STRIPE RUST IN WHEAT

Stripe rust is the most important biotic constraint in wheat production. Deployment of resistant wheat cultivars is the most practical way to decrease yield losses attributed to stripe rust. Usage of wild germplasm of wheat is the best technique to detect new resistant genes for the evolution of new varieties and mainstream of these hold capacity for disease resistance. Traditional procedures of gene identification by using conventional screening through diversified races do not generate accurate data. In conventional breeding, transferring desired traits, for instance, stripe rust resistance, from a donor parent is offered into a genotype of interest, typically high yielding. Identification of the sources of resistance by conventional screening through diversified races and backcross breeding is time-consuming which could be avoided through the usage of DNA markers. Marker-assisted selection (MAS) is practiced for the improvement of a variety of traits in wheat around the world through introgression of disease resistance against diseases including stripe rust, which may in any case partially support in providing the anticipated result. MAS has been valuable for the development of quite a lot of significant traits such as resistance against diseases. Marker-assisted backcrossing, forward breeding, and MAS involving doubled haploid technology have been effectively used for this objective. Novel skills based on high throughput genotyping related with new marker systems (e.g., Diversity arrays technology DArT and as Single Nucleotide Polymorphism SNP), and new selection strategies such as (Advanced backcross QTL AB-QTL), mapping-as-you-go, marker-assisted recurrent selection, and genome-wide selection will have to be tried in future for upgrading of compound multigenic traits. The improvement made in all these features of marker-assisted wheat breeding, and the restrictions and future scenarios of this incipient technology have been reviewed in this article.

Novel single nucleotide polymorphism in the prolactin gene of Awassi ewes and its role in the reproductive traits

This study was conducted to determine the genetic variation of the prolactin (PRL) gene in 5' flanking region and its role with several reproductive traits in Awassi sheep. One-hundred six Iraqi sexually mature and healthy Awassi ewes that aged between 2 and 2.5 years were included in this study. Ewes were classified into two the main divisions: ewes producing twins and ewes producing single offspring. Two genotypes (AA and AT) were observed in Awassi sheep. While genotype AA was detected in Awassi ewes that produced twins, genotype AT was detected in ewes that produced a single offspring. The sequencing reactions identified nine SNPs in the prolactin gene at the 5′ flanking region in Awassi sheep, differing from the prolactin reference sequence (GenBank accession number X16641.1). Genotype AT possessed one single nucleotide polymorphism SNP substitute comparison with the AA genotype in Awassi ewes. The association analysis revealed that the AA genotype is characterized by significantly higher levels of the progesterone concentration, twinning ratio, fecundity, and prolificacy than the AT genotype. In conclusion, a new SNP (g.1209 A>T) was discovered within the ovine flanking region which potentially influences prolactin gene expression. These results showed that the genotype AA associated with high prolificacy of Awassi sheep may be used as a selection criterion for improving the reproductive performance of Iraqi Awassi sheep.

Sera Level and Polymorphism of Interleukin-33 Gene in Iraqi Females Patients with Breast Cancer

Interleukin-33 [IL-33] is a specific ligand for the ST2 receptor, and a member of theIL-1 family. It is a dual-function protein that acts both as an extracellular alarmin cytokine,and an as an intracellular nuclear factor participates in maintaining barrier function byregulating gene expression of IL-33 modulating tumor growth and anti-tumor immunity incancer patients. The present study aimed to investigate the role of IL-33 serum level and genepolymorphism in Iraqi women with breast cancer. Materials and methods: Blood sampleswere collected from 66 Iraqi patient women diagnosed with breast cancer, which were dividedinto two groups: pre-treatment [PT] and under treatment with chemotherapy [UTC] patients inaddition to 34 apparently healthy women who were matched with patients as a control.ELISA technique was used to determine the IL-33 serum level. The PCR-RFLP techniquewas performed to determine IL-33 gene polymorphisms at single nucleotide polymorphismSNP [rs1929992]. Results: IL-33 serum level recorded lower significant in PT [182.22 ±29.86pg/ml] and UTC [129.87 ± 45.11pg/ml] patients compared with control [258.08 ± 39.54 pg/ml] under [p<0.05]. In a polymorphism study on IL-33 SNP [rs1929992] showed AG genotype recorded the high frequency in control than in patients [76.47, 58.46] compared to other genotypes AA, GG with no significant difference according to fisher’s exact probability. In conclusion: IL-33 serum level decreased after performing surgery on breast cancer patients. There was no association between breast cancer development and IL-33 SNP [rs1929992]. The heterozygous genotype AG was a common genotype in the Iraqi population. Allele G had an environmental fraction, while allele A had preventive fraction, which related to increasing the level of IL-33 with both genotypes AA, AG in the healthy control group, in contrast with GG genotype which showed the highest level in the patients’ group.

Evaluation of the Correlation between the rs4918 Polymorphism of AHSG Gene and Coronary Artery Calcification in Patients with Coronary Artery Disease

Objectives: Fetuin-A is a circulating calcification inhibitor that prevents coronary artery calcification (CAC) by increasing calcium phosphate solubility and inhibiting VSMC differentiation and apoptosis. In this study, we investigated the correlation between rs4918 and CAC in patients with coronary artery disease (CAD). Methods: Forty-two healthy individuals and eighty-one CAD patients were recruited in the present study. The CAC score (CACS) was measured by CT angiography and the genotype analysis of rs4918 single-nucleotide polymorphism SNP was performed by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Results: The CACS was significantly higher in CAD patients compared to healthy individuals (p < 0.001); however, there was no significant difference between the mean CACS in the presence and absence of rs4918 (p = 0.792). The mean calcium score of the left main coronary artery (LMCA) was significantly lower in carriers of the rs4918 allele (p = 0.036). The frequency of rs4918 SNP was almost similar in the control group and CAD patients (p = 0.846). Conclusions: in patients with CAD, we found no significant association between rs4918 SNP and CACS, indicating that carriers of this allele are not at increased risk of developing cardiovascular diseases compared with those without.

Quantification of permethrin resistance and kdr alleles in Florida strains of Aedes aegypti (L.) and Aedes albopictus (Skuse).

Recent outbreaks of locally transmitted dengue and Zika viruses in Florida have placed more emphasis on integrated vector management plans for Aedes aegypti (L.) and Aedes albopictus Skuse. Adulticiding, primarily with pyrethroids, is often employed for the immediate control of potentially arbovirus-infected mosquitoes during outbreak situations. While pyrethroid resistance is common in Ae. aegypti worldwide and testing is recommended by CDC and WHO, resistance to this class of products has not been widely examined or quantified in Florida. To address this information gap, we performed the first study to quantify both pyrethroid resistance and genetic markers of pyrethroid resistance in Ae. aegypti and Ae. albopictus strains in Florida. Using direct topical application to measure intrinsic toxicity, we examined 21 Ae. aegypti strains from 9 counties and found permethrin resistance (resistance ratio (RR) = 6-61-fold) in all strains when compared to the susceptible ORL1952 control strain. Permethrin resistance in five strains of Ae. albopictus was very low (RR<1.6) even when collected from the same containers producing resistant Ae. aegypti. Characterization of two sodium channel kdr alleles associated with pyrethroid-resistance showed widespread distribution in 62 strains of Ae. aegypti. The 1534 phenylalanine to cysteine (F1534C) single nucleotide polymorphism SNP was fixed or nearly fixed in all strains regardless of RR. We observed much more variation in the 1016 valine to isoleucine (V1016I) allele and observed that an increasing frequency of the homozygous V1016I allele correlates strongly with increased RR (Pearson corr = 0.905). In agreement with previous studies, we observed a very low frequency of three kdr genotypes, IIFF, VIFF, and IIFC. In this study, we provide a statewide examination of pyrethroid resistance, and demonstrate that permethrin resistance and the genetic markers for resistance are widely present in FL Ae. aegypti. Resistance testing should be included in an effective management program.

Higher incidence of emergence agitation in children with genetic intronic variant GABRγ2 rs2279020 after sevoflurane anesthesia

Emergence agitation (EA) is very common in Preschool children who receive Sevoflurane anesthesia. The GABA receptors are the target effect site of Sevoflurane. The aim of this study Is to investigate if GABRγ2 Genetic variant (or Single nucleotide polymorphism SNP) rs211037 and an intronic nucleotide number rs2279020 polymorphism from A to G, is associated with EA after Sevoflurane anesthesia in Preschool children. Patients and Methods This study included 60 pre-school children, ASA I, of both sexes who underwent lower abdominal surgery, anesthetized by Sevoflurane and caudal blockade. At emergence, children were assessed for EA every 5 min, in PACU by Watcha scale1: (0: Asleep, 1: calm, 2: crying, can be consoled, 3: crying, cannot be consoled, or 4: agitated and thrashing). Children were divided into 2 groups. Gr.I: Non-agitated children; scored (0, 1 or 2) Gr.2: Agitated children; scored (3 or 4). GABA receptor gene polymorphisms rs211037 and intronic rs2279020 were genotyped by PCR-RFLP. Results GABRγ2 rs211037 stratified the cases into wild homozygous CC in (65%) and Heterozygous CT in (35%) of children, none of the cases was homozygous mutant (TT). The two groups showed insignificant EA between them. The intronic polymorphism rs2279020, however, was heterozygous AG in 73.3% of the cases; it was associated with EA in 54.50% of children versus 9 % in AA and 0.0% in GG Introns, (P < 0.001). Conclusion There was high incidence of EA in children with genetic intronic variant GABRγ2 (SNP) rs2279020 (A/G) after Sevoflurane anesthesia.

How Well Do Molecular and Pedigree Relatedness Correspond, in Populations with Diverse Mating Systems, and Various Types and Quantities of Molecular and Demographic Data?

Kinship analyses are important pillars of ecological and conservation genetic studies with potentially far-reaching implications. There is a need for power analyses that address a range of possible relationships. Nevertheless, such analyses are rarely applied, and studies that use genetic-data-based-kinship inference often ignore the influence of intrinsic population characteristics. We investigated 11 questions regarding the correct classification rate of dyads to relatedness categories (relatedness category assignments; RCA) using an individual-based model with realistic life history parameters. We investigated the effects of the number of genetic markers; marker type (microsatellite, single nucleotide polymorphism SNP, or both); minor allele frequency; typing error; mating system; and the number of overlapping generations under different demographic conditions. We found that (i) an increasing number of genetic markers increased the correct classification rate of the RCA so that up to >80% first cousins can be correctly assigned; (ii) the minimum number of genetic markers required for assignments with 80 and 95% correct classifications differed between relatedness categories, mating systems, and the number of overlapping generations; (iii) the correct classification rate was improved by adding additional relatedness categories and age and mitochondrial DNA data; and (iv) a combination of microsatellite and single-nucleotide polymorphism data increased the correct classification rate if <800 SNP loci were available. This study shows how intrinsic population characteristics, such as mating system and the number of overlapping generations, life history traits, and genetic marker characteristics, can influence the correct classification rate of an RCA study. Therefore, species-specific power analyses are essential for empirical studies.

Role of FDFT1 polymorphism for fibrosis progression in patients with chronic hepatitis C

In chronic hepatitis C (CHC), steatosis is associated with fibrosis and impaired response to antiviral therapy. Recently, a polymorphism of single nucleotide polymorphism SNP rs2645424 of farnesyl diphosphate farnesyl transferase 1 (FDFT1) was identified in NAFLD/NASH as a possible causal link to steatosis and fibrosis progression. SNP rs738409 in the adiponutrin gene (PNPLA3) is a well described factor for steatosis. This study evaluated the relation of these SNPs on steatosis, fibrosis and treatment response in CHC. The SNPs rs738409478 and rs2645424 were determined by real-time PCR in 478 patients with CHC (m/f: 314/164; mean age: 44.9 ± 10.7; GT1: 387, GT4: 91) who completed treatment with peg-IFN-α-2a/ribavirin. All had a pretreatment liver biopsy. Steatosis and fibrosis were graded by board-certified pathologists according to Brunt and METAVIR respectively. The distribution of FDFT1 rs2645424 was GG: 186 (38.9%), AG: 222 (46.4%) and AA: 70 (14.6%) and of the rs738409 PNPLA3 allele: CC: 269 (56.3%), CG: 177 (37.0%) and GG: 32 (6.7%). Overall, FDTF1 polymorphism was not linked to the extent of steatosis or fibrosis. However, in patients without steatosis the AA genotype was associated with advanced fibrosis [AA: 8/20 (40.0%), AG: 6/70 (8.5%), GG: 9/57 (16.1%), P = 0.003]. In contrast, the minor PNPLA3 allele was associated with both steatosis and advanced fibrosis (P < 0.001). Both SNPs did not influence treatment response. The minor allele in FDFT1 was associated with advanced fibrosis in the non-steatotic but not in the steatotic subgroup. This may reflect different metabolic pathways in fibrosis progression for steatotic and non-steatotic patients with CHC.

Genotyped adipocytes to monitor adiponectin expression in response to environmental stressors

In 2008, the world health organization reported more than 1.4 billion adults are overweight in the world. Obesity is associated with diabetes, heart disease and certain cancers. Adiponectin is an adipocyte synthesized and secreted by adipose tissue. Several studies indicated that obese patients are presented with hypoadiponectinemia. A set of single nucleotide polymorphism SNP's associated with hypoadiponectinemia are of used to characterize the cells in this study. The goal is to develop normal human genotyped cell lines and load them in the well defined “body‐on‐a‐chip” BOAC systems. The BOAC is a microfabricated device based on a physiologically based‐pharmacokinetic (PBPK) model. The aim is to identify ways to modulate the expression of adiponectin using drugs, dietary supplements or functional components in the food matrix. Bone marrow or omental fat are collected from patients corresponding to IRB approved clinical trial GHS # 1207–27. Each patients is genotyped for a series of SNP's including ARL15 (rs4311394‐G), ADIPOQ (rs6444175‐G), ADIPOQ (rs266717‐T), ADIPOQ (rs1426810‐G), ADIPOQ (rs1648707‐C). Mesenchymal stem cells are isolated, expanded and differentiated into organ like cell lines. Preadipocytes are loaded onto the BOAC device and adiponectin released on media is monitored in response to environmental stressors applied to the system. Funding Cornell University Center on the Microenvironment and Metastasis (CMM) outreach pilot grant and Guthrie Foundation Investigator‐Initiated Research Grant.

An Association Study of SNP + 45 T &gt; G of the AdipoQ Gene with Type 2 Diabetes in Yi and Han People in China

The Yi people are considered the most primitive society in China, and live in the remote mountainous areas of Southwestern China. There have been no previous publications on genetic research concerning type 2 diabetes (T2D) in the Yi people. This is the first report that presents the association between SNP + 45 T > G (rs2241766) of the AdipoQ gene and T2D in Yi people. Our previous study showed that the prevalence of T2D in Yi people was lower than the national level in 2008. Genetic differences between Yi and Han people might be one possible explanation for this observation. Studies on the single nucleotide polymorphism SNP + 45 T > G (rs2241766) of the AdipoQ gene in Chinese Han people showed inconsistent results. This study was designed to identify genetic variants of the AdipoQ gene that contribute to the development of T2D in Yi and Han people. A case-control study on the association between SNP + 45 T > G (rs2241766) of the AdipoQ gene and T2D was carried out based on a cross-sectional study in the Liangshan area, Sichuan province in Southwestern China. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used to test for the presence of SNP + 45 T > G (rs2241766) in the AdipoQ gene. Distributions of genotypes variants (TT/GG/TG) were not significantly different between T2D cases and controls both in Yi and Han people in China (p > 0.05). The allele frequencies (T/G) demonstrated a non-significant association with T2D, displaying OR of 1.1 (95 % CI: 0.8, 1.6) in Yi people and OR of 1.0 (95 % CI: 0.7, 1.4) in Han people. The SNP + 45 (rs2241766) of the AdipoQ gene is not associated with T2D neither in Yi nor in Han people in southwestern China.