Analysis Of Gene Polymorphisms Research Articles

Aromatase Gene Polymorphism (rs2470152) in Polycystic Ovary Syndrome Patients of Eastern Uttar Pradesh

Introduction: Polycystic Ovary Syndrome (PCOS) is the most common endocrine disorder occurring in fertile age women. Its prevalence is increasing and varies day by day in the present population depending on the diagnostic criteria. The diagnostic features of PCOS are known at least but the causative factors which directly or indirectly play a part in it are yet not known. Few studies have demonstrated that aromatase gene with many factors (hormonal, environmental etc.,) may play a role together for the causes of PCOS. Aim: The purpose of this study was to characterise the salient features, frequency of PCOS in Eastern Uttar Pradesh population and aromatase gene polymorphism (rs2470152) analysis with Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDH) as reference gene. Materials and Methods: It was a pilot study where participants were recruited from SS Hospital, BHU between January 2018-2019. Participants completed a questionnaire with proforma and had to undergo physical examination before inclusion in the study. Single Nucleotide Polymorphisms (SNP) analysis was done for aromatase gene by PCR-RFLP. Allele and genotype distribution among groups were evaluated using the chi-square test or Fisher’s-Exact test. Two-tailed p-values less than 0.05 were considered statistically significant.Results: The data indicated that the prevalence of PCOS was high in reproductive age group and hormone profiles differ in different participants, with features of PCOS. With this it was found that aromatase gene was expressed in both control and PCOS patients, but the aromatase gene polymorphism was not significantly related to PCOS. Conclusion: PCOS was increasingly high in reproductive women of eastern Uttar Pradesh population. Its diagnostic criteria have many parameters that differ from individual to individual. The aromatase gene polymorphism is not found significantly associated with PCOS in the Eastern Uttar Pradesh population.

Association of Calcineurin B (PPP3R1) Functional Gene Polymorphism in South Indian Children with Idiopathic Mental Retardation

The present study aims to evaluate the possible association of PPP3R1 gene polymorphism (CnB 5I/5D) in clinical presentation of mental retardation (MR). A total of 100 children with idiopathic mental retardation in the age group of 5-16 years from both the sexes were recruited in the study considering age and sex matched healthy controls. Both cases and controls were genotyped by Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP) method for a single nucleotide polymorphism in PPP3R1 gene. The psychometric analysis of 100 MR children indicated that 3% of the children had borderline degree of retardation in which 42% of them were mild, 25% of them were moderate, 30% of them had severe degree of retardation. All the subjects included in the study were categorized based on their clinical and dysmorphic features. Among them 54% had behavioural disorders, 9% had cerebral palsy, 8% had microcephaly, 18% had convulsions and 11% had epilepsy. A significant association was observed for genetic variation at PPP3R1 (CnB 5I/5D) and MR [p < 0.04]. The results revealed that PPP3R1 (CnB 5I/5D) gene polymorphism is associated with MR. Insilico analysis of gene polymorphism i.e., CnB 5I/5D showed absence of TBP binding and may be responsible for low levels of calcineurin. Since calcineurin is involved in biosynthesis and release of neurotransmitter, the low levels of calcineurin and the associated gene polymorphism may be involved in causation of mental retardation.

Clinical Outcomes and Safety of Apatinib Mesylate in the Treatment of Advanced Non-Squamous Non-Small Cell Lung Cancer in Patients Who Progressed After Standard Therapy and Analysis of the KDR Gene Polymorphism.

PurposeThis study investigated the clinical outcomes and safety of apatinib mesylate in the treatment of advanced non-squamous non-small cell lung cancer (NSCLC) in patients who progressed after standard therapy, and analyzed the kinase insert domain receptor (KDR) gene polymorphism.MethodsA total of 135 patients with advanced non-squamous NSCLC who received apatinib mesylate were included. Objective response rates were evaluated. Subsequently, progression-free survival (PFS) and overall survival (OS) were assessed and safety data were recorded. Additionally, peripheral blood and biopsy cancer tissue specimens were collected from the patients with NSCLC for the genotyping of the genetic polymorphism and mRNA expression of the KDR gene, respectively. Analysis on the association between genotypes and prognosis was conducted.ResultsThe objective response rate of the 135 patients with NSCLC was 18.52%, disease control rate was 65.19%, median PFS was 3.95 months, and median OS was 10.05 months. Regarding the KDR gene polymorphism analysis, the distribution of the 4397T>C polymorphism genotypes was in accordance with the Hardy–Weinberg Equilibrium (P=0.868). Moreover, the prognosis analysis indicated that the median PFS of patients with the CC/TC and TT genotypes was 2.80 and 4.80 months, respectively (P=0.002). Furthermore, the median OS of patients with the two genotypes was 9.10 and 10.56 months, respectively (P=0.041). The multivariate Cox regression analysis showed that the TC/CC genotypes were an independent factor for PFS (odds ratio: 1.72, P=0.009). There was no correlation between the polymorphism and adverse reactions. Additionally, the mRNA expression analysis suggested that the mRNA levels of KDR in cancer tissues were significantly different between the TT and TC/CC genotypes (P<0.001).ConclusionThe clinical outcomes of treatment with apatinib mesylate for advanced non-squamous NSCLC in patients who progressed after standard therapy may be influenced by the KDR 4397T>C polymorphism through mediation of the mRNA expression of KDR.

An analysis of association FGB and eNOS3 genes polymorphisms with intracranial hemorrhagic and atherothrombotiс ischemic stroke

European Stroke Organisation (ESO) in cooperation with the Stroke Alliance for Europe (SAFE) prepared a 2018 – 2030 European Stroke Action Plan. One of priority items of this plan is taking to account human polygenetic risk profiles. NO-synthase3 (eNOS3) and beta-fibrinogen (FGB) polymorphisms are clinically significant for cardiovascular diseases and ethnically different. Objective: to estimate the association оf polymorphisms Т-786С, G894T 4b/4a of eNOS3 gene and С-148Т polymorphism of FGB gene with a risk of ischemic atherothrombotiс stroke and intracranial hemorrhagic stroke of Ukrainian people. Materials and methods. 102 patients with atherothrombotiс ischemic stroke, 56 patients with intracranial hemorrhagic stroke and 102 healthy control subjects were included in the study. Single nucleotide polymorphisms were detected by polymerase chain reaction followed by restrictases digestion and VNTR polymorphism gene was determined by allele-specific PCR method. Results. The study revealed association of C-148T polymorphism eNOS3 gene in dominant (OR = 2,276; 95 % CI:1,298– 4,152) and multiplicative (OR = 2,322; 95 % CI:1,322–4,080) models of analysis with a risk of ischemic atherothrombotiс stroke. Intracranial hemorrhagic stroke manifestation associated with VNTR 4b/4a of eNOS3 gene polymorphism in codominant інтракраніального геморагічного інсульту, як показали кодомінантна (OR=2,509; 95 % CI:1,049-4,080), домінантна (OR = 2,977; 95 % CI:1,344–6,596) та мультиплікативна (OR=3,037; 95 % CI:1,529–6,030) моделі обрахунку. Комбінація генотипів 894GТ та 4b/4a гена eNOS3 із генотипом -148СТ гена FGB збільшувала, а комбінація генотипу -148СС гена FGB із генотипом -786СС гена eNOS3 зменшувала ризик розвитку ішемічного атеротромботичного інсульту. Висновки. Генетичне дослідження до маніфестації хвороби, особливо при спадковому обтяженні, може стати суттєвим інструментом у розробці індивідуальних профілактичних заходів, направлених на попередження розвитку гострих порушень мозкового кровообігу. Ключові слова: поліморфізм, бета фібриноген, NO-синтаза 3, ішемічний інсульт, геморагічний інсульт. Для цитування: Цимбалюк ВІ, Васильєва ІГ, Костюк МР, Чопик НГ, Галанта ОС, Цюбко ОІ, Олексенко НП, Дмитренко АБ, Макарова ТА, Шуба ІМ. Аналіз асоціації поліморфізмів генів FGB та eNOS3 із ризиком розвитку інтракраніального геморагічного та атеротромботичного ішемічного інсультів. Журнал Національної академії медичних наук України. 2019;25(4):389–96.

Analysis of rpoB polymorphism and PCR-based approaches for the identification of Leuconostoc mesenteroides at the species and subspecies level

Leuconostoc mesenteroides includes the subsp. cremoris, subsp. dextranicum, subsp. mesenteroides and subsp. jonggajibkimchii, but the identification at the subspecies level using current phenotypic and/or genotypic methods is still difficult.In this study, a polyphasic approach based on the analysis of rpoB gene polymorphism, Multiplex-PCR and phenotypic tests was optimised and used to identify a collection of Leuc. mesenteroides strains at the species and subspecies levels. The annotation of published Leuc. mesenteroides genomes was also revised.A polymorphic region of rpoB gene was effective in separating Leuc. mesenteroides strains at the species (rpoB-species-specific-PCR) and subspecies (phylogenetic comparison) levels. Multiplex-PCR discriminated the subsp. mesenteroides from subsp. cremoris, but strains of uncertain attribution were found among subsp. dextranicum and subsp. jonggajibkimchii. Most of phenotypic features were not suitable for subspecies discrimination.Our assays may provide a rapid and reliable identification of subsp. mesenteroides and subsp. cremoris strains in fermented foods. The discrimination of subsp. dextranicum and subsp. jonggajibkimchii suffered from several limitations (e.g. low number of available strains and genomes, phenotypic profile close to subsp. mesenteroides, discrepancy between genotypic and phenotypic traits) and further investigations are needed to clarify their delineation and taxonomical position.

Analysis of HCRTR2, GNB3, and ADH4 Gene Polymorphisms in a Southeastern European Caucasian Cluster Headache Population.

Studies point to an increased hereditary risk of cluster headache. HCRTR2 gene rs2653349 and ADH4 gene rs1800759 polymorphisms have been associated with cluster headache susceptibility. Also, GNB3 rs5443 polymorphism, associated with increased signal transduction via GPCRs, seems to influence triptan treatment response. DNA from 114 cluster headache patients and 570 non-related controls, representing a general Southeastern European Caucasian (SEC) population, was extracted from buccal swabs and genotyped using real-time PCR. Gene distribution for the rs2653349 was GG = 79.8%, GA = 18.4%, and AA = 1.8% for patients and GG = 79.1%, GA = 19.1%, and AA = 1.8% for controls. The frequency of the mutated A allele was 11.0% for patients and 11.3% for controls. The frequencies for rs5443 were CC = 44.7%, CT = 44.7%, and TT = 10.5% for patients and CC = 43.9%, CT = 42.6%, and TT = 13.5% for controls. The frequency of the mutated T allele was 32.9% for patients and 34.8% for controls. A 2.7-fold more frequent appearance of the mutated T allele was observed in patients with better triptan treatment response, although not statistically significant. For rs1800759, the frequencies were CC = 36.0%, CA = 43.0%, and AA = 21.0% for patients and CC = 34.0%, CA = 50.2%, and AA = 15.8% for controls. The frequency of the mutated A allele was 42.5% and 40.9% for patients and controls, respectively. The mutated T allele of GNB3 rs5443 polymorphism was more prevalent in patients with better triptan treatment response, indicating a possible trend of association between this polymorphism and triptan treatment response in SEC population. According to our observation, no association of HCRTR2 rs2653349 and ADH4 rs1800759 polymorphisms and cluster headache in SEC population could be documented.

Determination of SIRT1 rs12778366, FGFR2 rs2981582, STAT3 rs744166, and RAGE rs1800625 Single Gene Polymorphisms in Patients with Laryngeal Squamous Cell Carcinoma.

Purpose To determine the frequency of the genotype of signal transducer and activator of transcription protein 3 (STAT3) rs744166, sirtuin (SIRT1) rs12778366, fibroblast growth factor (FGFR2) rs2981582, and advanced glycosylation end product-specific receptor (RAGE) rs1800625 gene polymorphisms in patients with laryngeal squamous cell carcinoma (LSCC). Methods A total of 944 subjects were evaluated, which includes 144 patients with LSCC and 800 healthy controls. The genotyping of STAT3 rs744166, SIRT1 rs12778366, FGFR2 rs2981582, and RAGE rs1800625 was carried out using the RT-PCR. Results The analysis of STAT3 rs744166, SIRT1 rs12778366, and FGFR2 rs2981582 gene polymorphisms did not reveal any differences in genotype distribution between the patients with LSCC and the control subjects. However, statistical analysis revealed that genotypes (AA, AG, and GG) of rs1800625 in RAGE gene were distributed statistically significantly differently between patients and controls (61.1%, 30.6%, and 23.6% vs. 72.5%, 25.8%, and 1.8%, respectively; p < 0.001). Additionally, statistical significance was observed in allele distribution between these two groups, i.e., allele G at rs1800625 was more frequently observed in the patient group than in controls (23.6% vs. 14.6%; p < 0.001). Conclusion RAGE rs1800625 gene polymorphism may play a significant role in laryngeal squamous cell carcinoma development.

PREVALENCE OF GLUTAMATE CARBOXYPEPTIDASE II C1561T, REDUCED FOLATE CARRIER 1 A80G, AND METHIONINE SYNTHASE A2756G GENE POLYMORPHISMS IN PATIENTS WITH TYPE 2 DIABETES MELLITUS AMONG SOUTH INDIANS

Objective: Glutamate carboxypeptidase II (GCPII), reduced folate carrier 1 (RFC1), and methionine synthase (MTR) genes involved in the folate metabolic pathway may play a key role in the pathogenesis of diabetes and its complications. The present study aimed to investigate the prevalence of genetic polymorphisms of GCPII C1561T, RFC1 A80G, and MTR A2756G in individuals with type 2 diabetes mellitus (T2DM) among South Indians.&#x0D; Methods: The study subjects consisted of 100 healthy individuals and 200 patients with T2DM. Genetic polymorphisms (GCPII C1561T, RFCI A80G, and MTR A2756G) in the folate metabolic pathway were analyzed by polymerase chain reaction-restriction fragment length polymorphism method. Statistical analysis was performed to test the level of significance.&#x0D; Results: With regard to GCPII C1561T and MTR A2756G gene polymorphisms, significant differences were not found when diabetic patients (with and without complications) and controls were compared according to different statistical models (dominant, recessive, and overdominant) p&gt;0.05. A case–control genetic association analysis of RFC1 A80G gene polymorphism has shown that there was 3.7-fold increased risk for patients without complications and 4.9-fold increased risk for diabetic patients with complications.&#x0D; Conclusions: Our findings suggest that the GCPII C1561T and MTR A2756G gene polymorphisms were not significantly associated with diabetes and its complications. Whereas, the RFCI A80G gene polymorphism involved in folate metabolism confers increased risk for diabetes and its complications in South Indian population.

The Brain-Derived Neurotrophic Factor (BDNF) gene Val66Met (rs6265) polymorphism and stress among preclinical medical students in Malaysia.

ObjectiveThis study aimed to determine the allelic and genotypic association of the Val66Met (rs6265) polymorphism in the BDNF gene with stress levels in preclinical medical students of Universiti Sultan Zainal Abidin (UniSZA), Terengganu, Malaysia.MethodsIn this cross-sectional study, we recruited all 122 preclinical medical students. The validated depression anxiety stress scales-21 (DASS-21) questionnaire was distributed and blood samples were collected from each subject for DNA extraction. Genotyping analysis of the BDNF gene (Val66Met) polymorphism was performed via an optimised polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.ResultsA total of 105 subjects agreed to participate in this study. Indian students were found to more likely have the Val/Val genotype, whereas Malay students were more likely to have the Met/Met genotype (p = 0.027). Individuals carrying any one of the three BDNF genotypes (Val/Val, Val/Met and Met/Met) differed significantly from each other in terms of their perception of stress (p = 0.010); students carrying the Val/Val genotype (M = 10.6) perceived significantly lower stress than students carrying the Val/Met (M = 14) and Met/Met (M = 15.1) genotypes.ConclusionIn our study, the Met-allele was associated with higher stress levels. To the best of our knowledge, this is the first study investigating this stress-related gene in medical students. The findings from this study should trigger more investigators to focus on the impact of stress on genetically predisposed medical students.

Molecular Analysis of Leptin Gene Polymorphism in Achai, Sahiwal Cattle and Nili-ravi Buffalo Breeds of Pakistan

Pakistan is blessed with rich sheep genetic resources and being a source of milk, meat and wool sheep breeds are reared across the country. Despite its great economic importance very limited work has been done in Pakistan on sheep genetic exploration. Leptin hormone plays important role in milk yield, body weight, energy balance, feed intake, immune function and fertility performance in animals. The current study was carried out to investigate genetic polymorphism in exon III of Leptin gene (LEP) in indigenous animal breeds (Nilli-ravi buffalo, Sahiwal and Achai cattle) of Pakistan using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). PCR-RFLP analysis revealed that all the three studied animals breeds were polymorphic for i>LEP gene (having all the three genotypes AA, AB and BB) with frequency of 60%, 33% and 7% in Nili-ravi buffalo, 55%, 41% and 4% in Achai cattle and 52%, 45% and 3% in Sahiwal cattle breed. The genotype BB is highly desirable in cattle and buffalo breeds but its frequency is very low in our indigenous population. Studying genetic polymorphism of milk protein is important due to its application in dairy industry and these in formations could further be utilized for future breeding programs particularly for the enrichment of the rare genotype.

Hemostasis-related gene polymorphisms and their epistatic relationship in women with idiopathic infertility.

: A numerous factor can cause infertility, but around one of four reproductive failure cases remain unexplained and diagnosed as idiopathic infertility. In the past few decades, analysis of gene polymorphisms takes a significant place in pathogenesis of infertility. The aim of this study was to evaluate the possible role of hemostasis-related gene polymorphisms in unexplained infertility. The study includes 117 female patients with idiopathic infertility and 130 fertile women with at least one born child. Eight polymorphisms important for hemostasis (ITGB3 1565T>C, FV 1691G>A, FII 20210G>A, MTHFR 677C>T and 1298A>C, ATIII 786G>A, PAI-14G/5G and ACE I/D) were genotyped by real-time PCR system. The frequencies of alleles and genotypes of examined polymorphisms were analyzed in SPSS statistical program, whereas gene interactions were identified using the GMDR software. Examination of etiological factors has shown that family history is a significant factor in assessing individual risk for infertility. The alleles and genotypes frequency of FV 1691G>A and FII 20210G>A polymorphisms were statistically different between control and patient group leading to a greater risk for infertility. The analysis of epistatic relationship between examined hemostasis-related gene polymorphisms identified more complex high-risk genotypes associated with infertility. Our results suggest that positive family history could be important predictive factor for fertility problems, pointing to the potential hereditary basis of this condition. Polymorphisms FVL and FII prothrombin are independent risk factors for idiopathic infertility, whereas multilocus interactions approach should be taken into consideration for the future research.

Association of MTHFR C677T Polymorphism with Preeclampsia in North East of Iran (Khorasan Province)

Background: Preeclampsia (PE) is one of the main causes of fetal and maternal mortality. The analysis of candidate gene polymorphisms can improve our understanding of the mechanisms underlying pathogenesis of PE. Present study is aimed at investigating the association between MTRR c.66A > G, MTHFR c.677C > T, MTHFR c.1298A > C, and MTR c.2756A > G polymorphisms and PE in Iranian women. Methods: About 117 women with history of PE and 103 healthy women with a pregnancy not complicated by PE were selected. The genomic DNA was extracted from peripheral blood. Single-nucleotide polymorphisms were genotyped using Real-Time PCR. Results: There was a significant difference between MTHFR c.677C > T polymorphism with PE (p = 0.045). The frequency of C/T heterozygous genotypes were (58% vs. 36%) in the case and control groups, respectively. There were no statistically significant differences between other genetic polymorphisms. Conclusions: The results indicated that the MTHFR c.677C > T polymorphism may be associated with development of PE in Iranian women.

Polymorphism of β-amyrin synthase gene (β-AS) influence the accumulation of triterpenes in licorice

Licorice is one of the most-frequently-used Chinese herbs. Glycyrrhizic acid (GA), as the most important marker component in licorice, is biosynthesized by mevalonic acid (MVA) pathway and regulated by many key enzymes. Among them, β-amyrin synthase (β-AS) is responsible for the triterpene skeleton formation. In this paper, we tried to find out the influence of β-AS gene polymorphism on the GA biosynthesis. The contents of 18α-glycyrrhizic acid (18α-GA) and 18β-glycyrrhizic acid (18β-GA) in 60 licorice samples were assayed by HPLC. For the β-AS gene polymorphism analysis, six samples with high GA content and seven samples with low GA content were selected. Thirteen β-AS cDNA sequences were obtained and eleven haplotypes were determined. The full length of these β-AS cDNA sequences is 2289 bp, with a complete open reading frame (ORF), encoding 762 amino acid residues. Haplotype-3 was the major haplotype in the group with high GA content, while haplotype-8 was the major haplotype in the group with low GA content. The missense mutation sites between haplotype-3 and haplotype-8 were G/C at 104 bp and 106 bp, resulting in the mutations of serine/threonine at the 35th amino acid residue site and alanine/proline at the 36th amino acid residue site. The yeast expression vectors, GS115-BAS-3 and GS115-BAS-8, containing haplotype-3 or haplotype-8 were constructed, and later transformed into Pichia pastoris GS115 by electrotransformation, respectively. The catalytic efficiency of protein BAS-3 and BAS-8 expressed in the different recombinant P. pastoris GS115 strains were analyzed by GC–MS. It was showed that compared with BAS-8, BAS-3 had a higher catalytic activity. The relative expression analysis showed that there was a positive correlation between the expression level of β-AS gene and the content of GA. We hope this paper will provide a basis for functional gene studies involved in the biosynthetic pathway of GA and high-quality cultivated licorice selection in the future.

MOLECULAR FEATURES OF BORTEZOMIB-INDUCED NEUROPATHY IN PATIENTS WITH MULTIPLE MYELOMA

Background. The regimens of therapy with bortezomib have significantly improved the survival among patients with multiple myeloma (MM). However, the development of peripheral polyneuropathy (PP) resulting from treatment using proteasome inhibitors is still an undesirable event. Risk factors for PP in MM patients include old age, previous neuropathy and use of neurotoxic drugs. Recent studies have established the presence of a genetic component in the mechanism of developing bortezomib-induced neurotoxicity. However, there are conflicting opinions on the role of genetic characteristics in predicting the risk of treatment-induced neuropathy development.Aim. To identify the risk group of bortezomib-induced PP based on the analysis of gene polymorphism of the immune response in patients with newly-diagnosed MM.Materials and methods. A study of the association of 20 polymorphic loci of 14 immune response genes in 46 MM patients was conducted using a candidate gene identification approach. All the patietns were receiving VCD therapy with bortezomib.Results. The distribution of single nucleotide polymorphisms was compared in groups of patients with the presence and absence of PP. It is found that homozygous carriers of the wild type allele of the genes TLR6 (Ser249Pro) (p = 0.006), IL1β (G-1473C) (p = 0.04), IL4 (C-589T) (p = 0.04), as well as haplotype carriers with the mutant allele of the gene IL10 (G-1082A) (p = 0.04) and with the wild type allele gene IL2 (T-330G) (p = 0.01) were significantly more frequent among PP patients.Сonclusion. Our results have confirmed the contribution of the genetic component to the risk of developing bortezomibinduced neuropathy. These findings can be used for individualization of therapeutic approaches to the treatment of MM patients.

Analysis of VEGF gene polymorphisms and serum VEGF protein levels contribution in polycystic ovary syndrome of patients.

Vascular endothelial growth factor (VEGF) is a well-known factor in reproductive function and contributes to the pathogenesis of polycystic ovary syndrome (PCOS). Genetic variations in VEGFA gene were suggested to contribute alterations in VEGF secretion and PCOS. This study evaluated the association of VEGFA SNPs with altered VEGF secretion level and PCOS among ethnically-matched control women. This prospective case-control study was conducted from 2016 to 2018 and comprised of 55 women with PCOS and 52 control subjects. ELISA was used to measure VEGF levels; and various other related bio chemicals whereas the genotyping of VEGFA variants was performed through the analysis of nine SNPs of VEGF. PRL, E2, PRGE testosterone and glucose level were found to be insignificantly different. The levels of FSH, LH, LH/FSH, TT, insulin, SHBG and HOMA-IR were significantly higher in the study group. Among the nine tested variants of VEGF SNPs, two SNPs rs3025020 and rs833061, consisted of TT (Recessive and Dominant homozygous, respectively) which were marginally higher in test. The SNP rs1570360 had significantly higher GG allele (32.73%) which was recessive homozygous. There was no significant difference observed in genotype frequencies related to higher value of VEGF. The genotype frequencies for the studied SNPs were in alignment with Hardy-Weinberg equilibrium (HWE). The mean serum VEGF levels got significantly increased in PCOS group. No significant association was found between VEGF genotypes and its serum levels. VEGF levels in rs699947 (AA-major homozygous), rs3025039 (CC-major homozygous) and rs833061 (TT & CC-major & minor homozygous) genotypes were significantly higher in PCOS. The study results evidently proved that the allelic variants in genes may be a factor for PCOS and VEGF serum levels with respect to few SNP variants only. These findings indicated that VEGF may be involved in PCOS status and confirmed the previous association between genetic variants in VEGF, serum level of VEGF protein and PCOS.

Development of Novel Genotyping Protocol and Its Application for Genotyping of Alcohol Metabolism-related Genes

A new single nucleotide polymorphisms (SNP) genotyping method has been developed and validated using biological specimens directly as templates for TaqMan PCR without general DNA extraction and purification procedure from dried saliva samples attached on water-soluble papers. This new method can set up at ease and complete PCR analysis including data interpretation in under two hours with additional advantages of application for large-scale clinical research, diagnostics, and epidemiological studies at low cost. Specifically, SNP genotyping of alcohol metabolism-related genes ADH1B (rs1229984) and ALDH2 (rs671) were demonstrated by TaqMan PCR assay using dried saliva samples in the present investigation. In this protocol, by simplifying experimental operations and improving efficiency, omitting and simplifying the time and laborious DNA purification process, it is possible to shorten the experiment time and reduce the risk of human error such as contamination. Furthermore it became possible with great cost reduction. We succeeded in dramatically improving the judgment rate and accuracy of SNP genotyping by the master mix reagent for commercial available real-time TaqMan PCR. Moreover, it becomes possible to stably introduce template DNA into the reaction system, and it will be possible to apply it to copy number variation (CNV) by TaqMan probe method. The SNP analysis process using this optimized water-soluble paper will be applied to gene polymorphism analysis of drug metabolizing enzyme gene CYP, etc., to help efforts to realize personalized medicine.

Analysis of IVS8 CFTR gene polymorphism in asthmatic children in a Tunisian population

ObjectiveAsthma is a multifactorial disease of genetic origin; its clinical expression depends largely on acquired factors, often related to the environment. It is defined as a chronic inflammatory condition of the airways with mucus obstruction, a feature it shares with cystic fibrosis (CF). Material and methodsThe present work concerns a study, for the first time in Tunisia, of the genotypic and allelic distribution of IVS8 TGmTn repeat motifs in intron 8 of the CFTR gene in an asthmatic population. TGmTn repeat analysis was performed for 100 asthmatic subjects and 103 controls using a sequencing technique. ResultsThe results showed the predominance of the T7 allele in both patients and controls, as for the TG11 allele, which represents the major allele of the two groups studied. Our results also showed a significant difference in distribution of the TG12 allele. In addition, a haplotype study showed predominance of the TG11T7 haplotype in both groups, which is in agreement with the data in the literature. ConclusionOur study is one of the first to be carried out in the Tunisian asthmatic population. The results obtained will provide a better understanding of the molecular basis of this multifactorial disease.

In the search of a ‘fitness gene’: an analysis of ACTN gene polymorphisms in serving soldiers

BackgroundGenetic polymorphisms in the exon 15 and exon 16 of the ACTN3 gene are believed to be associated with athletic performance. Paratroopers are some of the fittest soldiers in the Indian Armed Forces. This study was taken up to assess if there was a significant difference in the genetic profile between paratroopers and non-paratroopers. MethodPolymerase chain reaction (PCR) followed by restriction length fragment polymorphism (RFLP) was used to analyse the genetic polymorphisms in the exon 15 and 16 of the ACTN3 gene. ResultsThere was a significant difference between paratroopers and non-paratroopers in the polymorphic loci at codon 15 and 16. ConclusionsThe study suggests that there is a significant difference in the genotype between paratroopers and non-paratroopers. It is likely that the differences in muscle fibres as a result of these genotypic changes confer a ‘survival advantage’; people with a homozygous genotype are more likely to pass the harsh probation and qualify for the Parachute Regiment.

Interleukin-6 serum level and gene polymorphism in keloid patients

The formation of keloid is associated with accumulation of extracellular matrix (ECM) formed mainly of collagen and fibronectin. Persistent deregulated IL-6 synthesis causes the development of various diseases. This study aim to investigate interleukin 6 (IL-6) serum level and gene polymorphism in a sample of Egyptian patients having keloid. This study was carried out on 90 subjects; 60 patients with keloid, and 30 age and sex matched apparently healthy control. All subjects underwent full history taking, clinical examinations, weight and length measuring to calculate BMI, dermatological examination, analysis of IL6-572 gene polymorphism using REFLP- PCR and IL-6 serum level using ELISA.IL-6 serum levels were significantly higher in keloid patients than control group (75.54±39.18) vs (19.17±6.06), (p &lt;0.001). The higher serum levels of IL-6 were associated with GG genotype (104.84±19.12) followed by CG (57.64±35.38) genotype (P&lt;0.001). GG genotype was significantly higher in keloid patients and increased the risk for keloid development by nearly14 folds (p&lt;0.001, OR (95%CI) =13.81). CG genotype was significantly observed in keloid patients and increased the risk for keloid development by about 4 times (p=0.010, OR (95%CI) =4.27). G Allele significantly increased the risk for keloid development by about 5 folds (P &lt;0.001 OR =5.11). In conclusion, there was a great association between IL-6 572 gene polymorphism and its serum level in patients with keloid specifically who have family history.

Analysis of Prion Protein Coding Gene Polymorphisms in Palestinian Native Sheep Breeds

Prion protein coding gene (PRNP) is the genetic locus correlated with the greatest impact on classical scrapie susceptibility in sheep. At codons 136, 154, and 171 of PRNP alanine/arginine/glutamine (ARQ) and valine/arginine/glutamine (VRQ) haplotypes, in turn, are related to susceptibility to classical scrapie while alanine/arginine/arginine ARR haplotype is correlated with resistance. The aim of the present study was to genotype the Palestinian native sheep breeds for detection of genetic resistance. A total of 38 healthy sheep from Awassi and Assaf breeds were randomly sampled. Genomic DNA was isolated from blood samples. After PCR amplification and DNA sequencing, ARQ, ARR, ARH, AHQ, ARL and VRQ alleles and ARR/ARQ, ARQ/ARQ, ARQ/ARL, ARH/ARQ, ARH/ARL, AHQ/ARQ and ARQ/VRQ genotypes were detected in PRNP gene. ARQ allele was found as a predominant allele in this study with the frequency of 0.76 for Awassi and Assaf breeds while the uncommon allele ARL was identified at low frequencies in both breeds. In addition, two different polymorphisms were recognized (V12I and L23H) at different codons of PRNP. Results have indicated that most of the genotypes belong to risk group 3. The careful dissemination of ARR/ARR sheep is suggested to increase resistant allele frequencies in Assaf and Awassi breeds.