Differences In Genotype Frequencies Research Articles

Різноманіття Ppd-1 генотипів сортів ярої та озимої м’якої пшениці (Triticum aestivum L.) України

Ancient and modern 183 varieties of winter and 23 spring types of development of bread wheat (Triticum aestivum L.) selected Ukrainian state institutions and private companies are characterized by alleles of Ppd-D1, Ppd-B1, and Ppd-A1 genes. Allele-specific molecular markers, proposed in the scientific literature, were used to identify carriers of the Ppd-D1a, Ppd-D1b, Ppd-D1c, Ppd-D1d, Ppd-B1a, Ppd-B1c, Ppd-A1b alleles. According to the results of PCR analysis, the most widespread among the studied winter cultivars was observed in the dominant allele Ppd-D1a (91.9 %) with a range from 80.0 % in the sampling of varieties of the Northeast (Kharkiv, Sumy) to 95.0 % in southern cultivars (Odesa, Kherson), and in spring – recessive Ppd-D1c (43.5 %). The share of carriers of various recessive alleles of the Ppd-D1 gene among spring varieties is 73.9 %, and among winter – 8.1 % and, except for Borovitsa and Talisman consists of cultivars created by the late 60 – early 70 years of last century. The frequencies of the Ppd-B1a and Ppd-B1c alleles are quite small. The Ppd-B1a allele was found only in three spring varieties, and the Ppd-B1c allele in 5 winter varieties and spring wheat Struna Mironivska, except for the latter cultivar, in all cases found together with the Ppd-D1a allele. The Ppd-A1 gene was present in a recessive state in all studied sorts. Seven different homozygous Ppd-1 genotypes have been determined in the studied cultivars. Samples of winter and spring varieties differ significantly in the quantity and frequency of specific Ppd-1 genotypes. The presence of varieties with monogenic dominant Ppd-D1a or Ppd-B1c control of traits and digenic dominant Ppd-D1a Ppd-B1a genotypes has been marked in spring wheat, as well as monogenic dominant for Ppd-D1a and digenic dominant for Ppd-D1a in winter wheat varieties. In spring cultivars the share of carriers of recessive alleles of Ppd-1 genes is several times higher (69.6 %) than in winter varieties; conversely, the samples of winter varieties have significantly more dominant alleles (91.9 %). Such differences in genotype frequencies are due to the timing of sowing and duration of the natural day at the latitude of the growing region during the growing season of winter and spring varieties.

Genealogical analysis of European bison population revealed a growing up population despite very low genetic diversity.

In 1919, the European bison population became extinct in the wild. The rescue of the lowland subspecies and the whole species was achieved mainly thanks to individuals from the Białowieża Forest (Polish-Belarusian border). There are currently two breeding lines-the lowland (purebred B. b. Bonasus) founded by 7 individuals and the lowland-Caucasian (hybrids of B. b. Bonasus and B. b. caucasicus) founded by 12 individuals. This genealogical study was conducted on 15,071 individuals recorded in the pedigree book between 1881 and 2020. Its objective was to determine the level of genetic variability and inbreeding almost 100 years after the rescue measures were initiated. The completeness of the pedigree of the reference population was 77% in the fifth generation backwards. A maximum of 23 generations can be traced back in the pedigree. The average inbreeding coefficient and the mean average relatedness of the reference population were very high, about 17% and 16% respectively. No significant amount of new inbreeding was discovered. The reference population has lost 9.11% of the total genetic diversity compared to the population of founders. A male of the Caucasian subspecies Kaukasus was discovered among the ancestors of the lowland lineage reference population. The effective population size calculated based on the increase in inbreeding was 23.93 individuals, based on complete generations equivalent it was 16.1 individuals. Wright's F-statistics showed very small differences in genotypic frequencies between individuals within the two lineages in the reference population (FIS = 0.10), between individuals and the total population (FIT = 0.04) and low differentiation between lineages (FST = 0.06). The population of the European bison from the Białowieża Forest is generally very uniform but still shows good fitness.

Importance of selected ABCB1 SNPs for the level of severity of depressive symptoms and effectiveness of recurrent depressive disorder therapy

The expression level of mRNA and also the function of P-gp are strictly connected with the polymorphic nature of the ABCB1 gene. In this study, we evaluated the association between promoter SNP, i.e. T-129C, three other SNPs investigated earlier and ABCB1 expression in the depression group. To assess the additive significance of these SNPs on clinicopathological features a mathematical model was also built.102 patients suffering from recurrent depressive disorder (rDD) and 94 healthy individuals from a local blood bank were enrolled in this study. ABCB1 gene polymorphism was identified by the RFLP method. The relative level of ABCB1 expression was measured by real-time PCR.For SNP T-129C no statistically significant differences in allele and genotype frequencies between depression and control groups were found (p = 0.3176). There was no statistically significant association between the expression value and 4 studied SNPs in ABCB1 (T-129C, C1236T, G2677T/A and C3435T) or the investigated clinicopathological features. Furthermore, a correlation between the initial HDRS score (lower than 23) and presence of at least 1236 T allele was observed, in particular in combination with 3435 T or 2677 T/A. Mutated allele of each SNP was also significantly associated with declined response to antidepressant therapy, both individually and in combination with others.Results of this study suggest that T-129C does not play an important role in the rDD development. The influence of the studied SNPs on ABCB1 gene expression is still unknown. However, the additive impact of 3 most frequently studied SNPs of ABCB1 on the course of depression and effectiveness of its treatment was confirmed.

Association of Nogo-A Gene Polymorphisms with Cerebral Palsy in Southern China: A Case-Control Study

Cerebral palsy (CP) is a motor and postural disorder syndrome caused by the nonprogressive dysfunction of the developing brain. Previous studies strongly indicated that the Nogo-A gene might be related to the pathogenesis of CP. The objective of this research was to explore the relationship between Nogo-A polymorphisms (rs1012603, rs12464595, and rs2864052) and CP in Southern China. The Hardy-Weinberg equilibrium (HWE) testing, allele and genotype frequencies analysis, and haplotype association analysis were applied to the genotyping of 592 CP children and 600 controls. The results showed that the allele and genotype frequencies of rs1012603 of CP group were significantly different from the control group. The haplotype “TTGGG” was significantly associated with an increased risk of CP. The allele frequencies of rs1012603 were significant differences between CP with spastic diplegia, female CP cases, and controls. Furthermore, significant differences in allele and genotype frequencies were also noticed between GMFCS I of CP and controls for rs1012603, and significant differences in allele and genotype frequencies were observed between the ADL (>9) of CP and controls for rs1012603 and rs12464595. This study showed that the SNPs rs1012603 of Nogo-A were significantly correlated with CP, and the correlations were also found in spastic diplegia, GMFCS I of CP, ADL (>9) of CP, and female subgroups, indicating that Nogo-A might mainly affect mild types of CP and there might be sex-related differences.

Association between Interleukin-6 rs1800795 Polymorphism and Serum Interleukin-6 Levels and Full-Term Neonatal Sepsis

Abstract Objective Cytokines are involved in the pathogenesis of sepsis. Association between IL-6 rs1800795 G/C polymorphism and the risks of sepsis is controversial. The aim of this study was to investigate the association of IL-6 rs1800795 G/C gene polymorphism with full-term neonatal sepsis and to determine its effect on the serum IL6 levels in these infants by a prospective study. Methods The study included 200 full-term neonates from January 2019 to December 2020: 100 with sepsis (sepsis group), 47 with culture proven sepsis, and 53 with clinical sepsis, and 100 without infection (control group). The concentrations of IL-6 in serum were determined using enzyme-linked immunosorbent assay (ELISA). The polymorphisms of IL-6 rs1800795 G/C were analyzed to compare the genotypic and allelic frequencies in the groups by using the first-generation sequencing (Sanger sequencing). The association was studied between IL-6 rs1800795 G/C polymorphisms and serum IL-6 levels, and neonatal sepsis. The relationships between IL-6 rs1800795G/C polymorphisms and sepsis and serum IL-6 levels were separately analyzed by logistic regression and analysis of variance. Results There were no significant differences in genotypic frequencies and allelic frequencies of IL-6 rs1800795(G/C) in the groups (p >0.05). There were no relations between IL-6 rs1800795G/C polymorphisms and sepsis and serum IL-6 levels by statistical analysis (p >0.05). Conclusion IL-6rs1800795G/C may not be genetic risk factors for full-term neonates; There was no association between serum IL-6 levels and IL-6 rs1800795G/C polymorphisms.

Sex-specific genetic association of brain and muscle Arnt-like protein-1 (BMAL1) and obesity in Chinese youth

BackgroundThe circadian clock gene brain and muscle Arnt-like protein-1 (BMAL1) regulates energy metabolism, adipocyte proliferation and differentiation, glucose metabolism, and other functions. This study aimed to examine the association of potential polymorphisms in BMAL1 with obesity among Chinese youth. MethodsA total of 2973 participants were included in this study. According to the body mass index obesity standard of China, 208 subjects were defined as experiencing general obesity. According to the waist-to-hip ratio obesity standard, 335 participants were defined as experiencing central obesity. Four single nucleotide polymorphisms (SNPs) (rs9633835, rs6486121, rs7107287, and rs12364562) were genotyped using TaqMan probe techniques. ResultsThere was no significant difference in the either genotypic or allelic frequencies between the non-general and general obesity groups, while a positive association was observed between BMAL1 rs6486121 variant and central obesity risk (CC＋CT vs. TT: OR:2.139, 95% CI:1.164–3.930; P = 0.014) after adjusting for covariates. Stratification analyses revealed significant associations with central obesity risk for rs6486121 polymorphism in women according to the additive model (CC vs. CT vs. TT: OR：1.409; 95 % CI: 1.029–1.930; P = 0.032). Haplotype analysis showed that only paired haplotypes, including rs9633835G with rs6486121T, had a significant effect on central obesity with OR (95%CI) was 1.035 (1.011–1.060) and P = 0.004. Conclusionour findings suggest that BMAL1 polymorphisms are significantly associated with central obesity and sex-specific genetic effects on BMAL1-mediated genetic susceptibility to obesity.

Relationship between KIR genotypes and HLA-ligands with SARS-CoV-2 infection in the Saudi population

AimTo ascertain whether killer cell immunoglobulin-like receptors (KIR) genes polymorphisms and HLA-I ligands are associated with COVID-19 in Saudi Arabia. MethodsEighty-seven COVID-19 patients who tested positive for SARS-CoV-2 and onehundred and fourteen healthy controls were enrolled in this study for genotyping of the 16 KIR genes, HLA-C1 and -C2 allotypes and HLA-G 14-bp indels polymorphisms using the sequence specific primer polymerase chain reaction (SSP-PCR) method. KIR genotype frequency differences and combination KIR-HLA-C ligand were tested for significance. ResultsFramework genes KIR2DL4, KIR3DL2, KIR3DL3, and KIR3DP2 were present in all individuals. The frequencies of KIR2DL2 and KIR2D4 were higher in COVID-19 positive patients than in healthy individuals. The frequencies of the combination KIR2DL2-HLA-C2 was also significantly higher in patients affected by COVID-19 compared with healthy controls. ConclusionIt was found that the inhibitory KIR2DL2 gene in isolation or combined with its HLA-C2 ligand could be associated with susceptibility to COVID-19 in the Saudi population.

Impact of SLC23A1 and SLC23A2 Polymorphisms on the Risk for Preeclampsia in a Chinese Han Population.

Solute carrier family 23 member 1 (SVCT1) and solute carrier family 23 member 2 (SVCT2), encoded by SLC23A1 and SLC23A2, may be associated with preeclampsia (PE). The purpose of this study was to investigate the association between polymorphisms of SLC23A1 and SLC23A2 and PE in Chinese Han population. The primers and double-labeled probes were designed according to the SNPs of rs10063949 in SLC23A1, rs6133175 and rs1279683 in SLC23A2. Genomic DNA was extracted from peripheral blood of 2,066 subjects (1,029 with PE and 1,037 without PE), and Taqman real-time PCR was used to detect the three SNPs. We observed a significant difference in genotypic frequency of the SLC23A2 rs6133175 polymorphism (χ2=8.08, p=0.02) between PE patients and controls, while no significant differences were found in the allelic frequencies (χ2=1.45, p=0.23). Then we fractionized these samples into the dominant model of the allele G (GG/AG+AA group) or the recessive model of the A allele (AA/AG+GG group), and observed a significant difference under the recessive model of the A allele (p=0.01, OR=0.71, 95% CI 0.55-0.92). Furthermore, there were no significant differences in the genotypic and allelic frequencies of rs10063949 and rs1279683 between PE patients and controls (for rs10063949, χ2=2.96, p=0.23 by genotype, χ2=2.11, p=0.15 by allele; for rs1279683, χ2=1.52, p=0.47 by genotype, χ2=0.64, p=0.44 by allele). We first found that SLC23A2 rs6133175 may be the certain genetic polymorphisms modulating their effects in the development of PE in a Chinese Han population and the AG or GG genotypes may be a risk factor for PE.

검도 선수군의 운동 수행능력에 영향을 미치는 유전자 다형성의 탐색

It has been widely recognized that multiple genetic as well as environmental factors contributes to the inter-individual differences of the athletic performance, and advances in genetics and genetic engineering fields allow us to search for the useful genetic markers influencing sports talents. The purpose of this study was to identify causative genes that may contribute to the athletic performance of kendo discipline. A total of 98 unrelated male individuals were participated in this study, and they divided into controls(n=43) and kendo players(n=55), respectively. Also, the genetic polymorphisms in a total of six candidate genes(AMPD1(C34T, rs17602729), MCT1(T1470A, rs1049434), BDNF(Val66Met, G/A, rs6265), DRD(-521C/T, rs1800955), AGTR2(C/A, rs11091046) and ACE2(C/T or G/A, rs1978124) genes) were genotyped by using SNaPshot method in both groups. Among genetic polymorphisms studied, there were the significant differences in both genotype and allele frequencies of the -521C/T polymorphism in DRD4 gene between both groups, respectively(p.05). Especially, the frequencies of TT genotype and T allele in this genetic polymorphism were more higher in kendo players than in controls, respectively. Therefore, it is likely that the -521C/T polymorphism in DRD4 gene may be one of genetic markers influencing athletic performance from a psychological point of view in the case of kendo players. However, sample size in this study is modest, and athletic performance is fundamentally under the influence of many genes, further studies by using larger smaple size and more candidate genes will be required in order to get a better understanding on innate talent of kendo discipline.

Investigating the Association of Poly (ADP-Ribose) Polymerase-1 (PARP-1) and Nuclear Factor-κB (NF-κB) Polymorphisms with Vitiligo Susceptibility

Background: Poly (ADP-ribose) polymerase-1 (PARP-1) is a co-activator of nuclear factor-κB (NF-κB) and is also strongly activated by DNA damage. PARP has also been found to be associated with several autoimmune disorders. Vitiligo is a polygenic, multifactorial, acquired skin disorder caused due to loss of epidermal melanocytes. Among others, genetic and immunological factors are associated with vitiligo pathogenesis. Aim: To investigate the association of PARP1 exon 17 (rs1136410; V762A) and promoter CA microsatellite repeat (rs1136410) polymorphisms, and NF-κB promoter -94 indelATTG (rs28362491) polymorphism with vitiligo pathogenesis in Gujarat population. Methods: Genotyping of PARP1 17T/C (rs5030870) polymorphism was done by PCR-RFLP.PARP1 CA microsatellite and NF-κB-94 indel (rs28362491) polymorphisms were genotyped by Real-Time PCR. Anti-PARP antibody levels were assessed by ELISA. Results: The results suggested no significant difference in allele and genotype frequencies of PARP1 17 T/C (p=0.5094 and p=0.4201, respectively), PARP1 CA microsatellite polymorphisms (p=0.9519 and p=0.9338, respectively) and NF-κB-94 ATTG indel polymorphism (p=0.1482 and p=0.3784, respectively) in patients as compared to controls. Conclusion: This study suggests no association of PARP1 17 T/C, PARP1 CA microsatellite and NF-κB-94 ATTG indel polymorphisms with vitiligo susceptibility in Gujarat population. Additionally, anti-PARP1 antibody levels were not significantly different among patients and controls. These findings suggest the need for additional studies to explore the role of PARP1 in vitiligo pathogenesis. Keywords: Vitiligo, poly (ADP-ribose) polymerase-1(PARP-1), nuclear factor-κB (NF-κB), polymorphisms, Autoimmunity

An association study of IL2RA polymorphisms with cerebral palsy in a Chinese population

BackgroundCerebral palsy (CP), the most common physical disability of childhood, is a nonprogressive movement disorder syndrome. Eighty percent of cases are considered idiopathic without a clear cause. Evidence has shown that cytokine abnormalities are widely thought to contribute to CP.MethodsAn association between 6 SNPs (rs12244380, rs2025345, rs12722561, rs4749926, rs2104286 and rs706778) in IL2RA (interleukin 2 receptor subunit alpha) and CP was investigated using a case–control method based on 782 CP cases and 778 controls. The allele, genotype and haplotype frequencies of SNPs were assessed using the SHEsis program. Subgroup analyses based on complications and clinical subtypes were also conducted.ResultsGlobally, no differences in genotype or allele frequencies for any SNPs remained significant after Bonferroni correction between patients and controls, except rs706778, which deviated from Hardy–Weinberg equilibrium and was excluded from further analyses. However, subgroup analysis revealed a significant association of rs2025345 with spastic tetraplegia (P genotype = 0.048 after correction) and rs12722561 with CP accompanied by global developmental delay (P allele = 0.045 after correction), even after Bonferroni correction.ConclusionsThese findings indicated that genetic variations in IL2RA are significantly associated with CP susceptibility in the Chinese Han population, suggesting that IL2RA is likely involved in the pathogenesis of CP. Further investigation with a larger sample size in a multiethnic population is needed to confirm the association.

Association of rs2910164 in miR-146a with type 2 diabetes mellitus: A case-control and meta-analysis study.

ObjectiveSeveral studies have shown that miR-146a rs2910164 (C > G) is associated with type 2 diabetes mellitus (T2DM) susceptibility, but the results are still controversial. This study is divided into two parts, and one is to explore the relationship between miR-146a rs2910164 polymorphism and the genetic susceptibility of T2DM in Chinese Han population. Second, a meta-analysis on the basis of a larger sample size was used to determine whether this is a susceptibility gene for T2DM.MethodsA case–control study including 574 T2DM patients and 596 controls was used to evaluate the association of miR-146a rs2910164 polymorphism with the risk of T2DM in Chinese Han People. Then, we systematically searched studies investigating the correlation between miR-146a rs2910164 polymorphism and T2DM susceptibility published before April 2022 from PubMed, Web of Science, Wanfang, and China National Knowledge Infrastructure database, and a meta-analysis including six studies was carried out. The results were expressed by odds ratio (OR) and its 95% confidence interval (95% CI).ResultsIn a case–control study, we found that there were no statistical differences in genotype frequencies between T2DM and control group. Subgroup analysis showed that, compared with the CC genotype, CG + GG genotype was associated with a decreased risk of T2DM in the subgroup of individuals ≥ 65 years old (OR = 0.75; 95% CI: 0.58–0.98; P adjusted = 0.032) and BMI < 18.5 (OR = 0.16; 95% CI: 0.03–0.89; P adjusted = 0.037). In overall meta-analysis, significant heterogeneity was detected. No significant association between miR-146a rs2910164 polymorphism and T2DM was observed in all genetic models under random effects models. Subgroup analysis revealed that there was a significant difference in genotype frequencies between the T2DM and control group in recessive model (CC vs. CG + GG: OR = 1.79; 95% CI: 1.08–2.96; PQ = 0.307, I 2 = 4.0%) and homozygote model (CC vs. GG: OR = 1.79; 95% CI: 1.07–3.00; PQ = 0.216, I 2 = 34.7%) in Caucasians.ConclusionThe results of our study demonstrate that the miR-146a rs2910164 polymorphism might have ethnicity-dependent effects in T2DM and may be related to T2DM susceptibility in Caucasians.

Cranial and extracranial giant cell arteritis do not exhibit differences in the IL6 -174 G/C gene polymorphism.

Since interleukin-6 (IL-6) is a pivotal proinflammatory cytokine implicated in the pathogenesis of giant cell arteritis (GCA), we aimed to determine the potential association of the functional IL6 -174 G/C polymorphism with GCA as well as if the single base change variation at the promoter region in the human IL-6 gene may account for differences in the clinical spectrum of GCA between cranial and extracranial large vessel vasculitis (LVV)-GCA. The IL6 -174 G/C polymorphism (rs1800795) was genotyped in 191 patients with biopsy-proven GCA who had typical cranial manifestations of the disease, 109 patients with extracranial LVV-GCA, without cranial ischaemic manifestations of GCA, and 877 ethnically matched unaffected controls. A comparative study was carried out between patients with cranial and extracranial LVV-GCA and controls. No significant differences in genotype and allele frequencies of IL6 -174 G/C polymorphism were found between the whole cohort of GCA patients and healthy controls. It was also the case when cranial and extracranial LVV-GCA were compared or when each of these subgroups was compared to controls. Moreover, no significant results in genotype and allele frequencies of IL6 -174 G/C polymorphism were disclosed when the whole cohort of GCA patients were stratified according to the presence of polymyalgia rheumatica, severe ischaemic manifestations, including permanent visual loss and peripheral arteriopathy, and HLA-DRB1*04:01 status. Our results show that the IL6 -174 G/C polymorphism does not influence the phenotypic expression of GCA.

Genetic Polymorphisms in MicroRNA-196a2 and the Risk of Human Abortion Related to Mycoplasma hominis.

Mutations in some miRNAs are associated with human recurrent pregnancy loss (RPL). In parallel, Mycoplasma spp. are one of the most common infections in pregnant women. The objective of this study was to identify the relationship between miRNA196a-2 gene polymorphism and Mycoplasma hominis (M. hominis) infection as a possible cause of human abortion. A total of 160 cervical swab specimens were collected from women (80 samples with at least one abortion as case, and 80 samples without abortion as control). A PCR-based method using 16S rRNA gene and tetra primer amplification refractory mutation system-polymerase chain (Tetra-ARMS-PCR) were used to identify the presence of M. hominis infections and miRNA196a-2 genotypes of studied women, respectively. Results showed that 22.5% of women with abortion and 7.5% of women without abortion were infected with M. hominis, thereby suggesting a significant difference between the two groups (P < 0.05). Tetra-ARMSPCR indicated that no significant difference in frequency of genotypes existed between women experimenting abortion and control group. Independently to the presence of M. hominis infection, a significant difference (P < 0.05) was observed in genotypic frequencies of miRNA196a-2 between RPL women and those with one abortion. Estimation of the Odds Ratios indicated that the chance of recurrent abortions in TT genotypes of miRNA196a-2 was about three times more likely than CC in non-infected individuals and about five times more likely than CC in M. hominis-infected patients. Our results proposed the role of miRNA196a-2 genotypes in RPL either in M. hominis-infected or non-infected individuals.

Association of THBS1 genetic variants and mRNA expression with the risks of ischemic stroke and long-term death after stroke.

BackgroundThrombospondin-1 (THBS1) derived from platelets and acted as a critical mediator of hemostasis promoting platelet activation in thrombus formation. The biological connection of genetic variants and mRNA expression of THBS1 with ischemic stroke (IS) warrants further validation with population-based evidence.ObjectiveTo evaluate the association of single nucleotide polymorphisms (SNPs) and mRNA expression of THBS1 with the risks of IS and long-term death after stroke.MethodsA case-control study consisted of 4,584 IS patients recruited from five hospitals in Jiangsu, China, and 4,663 age-gender-matched controls free of IS. A cohort study enrolled 4,098 participants free of stroke and lasted from 2009 to 2022. Early collected 3158 IS patients aged between 35 and 80 years were followed up an average of 5.86-year to follow up their long-term death outcomes. Two tagSNPs of the THBS1 gene, rs2236471 and rs3743125, were genotyped in all subjects and THBS1 mRNA expression of peripheral leukocyte was measured using RT-qPCR in 314 IS cases and 314 controls.ResultsThere is no significant difference in genotype and haplotype frequencies of rs2236741 and rs3743125 between IS cases and controls (all P > 0.05). Furthermore, the cohort studies did not observe significant associations between THBS1 variants and the risk of IS incidence or long-term death after IS (all P > 0.05). The THBS1 mRNA expression level (2–Δ Δ CT) in IS cases was approximately equal to that in controls (1.01 vs. 0.99, P = 0.833). In addition, THBS1 mRNA expression had no significant association with all-cause death, stroke death, and IS death of IS patients (all P > 0.05).ConclusionTherefore, our study suggested that there is no significant association of THBS1 polymorphisms and mRNA expression level with the risk of IS and long-term death after IS.

Methylenetetrahydrofolate reductase (MTHFR) 677C>T polymorphisms in breast cancer: A Filipino preliminary case-control study

Single nucleotide polymorphisms (SNP) present in folate metabolic enzymes, such as methylenetetrahydrofolate reductase (MTHFR), affect DNA synthesis and methylation processes that can lead to cancer development. Several studies suggest that MTHFR SNP is associated with breast cancer risk, particularly among Asian populations. Thus, this study determined the association of MTHFR 677C>T SNP with breast cancer risk in selected Filipino population. DNA samples from breast cancer cases (n = 100) and clinically healthy controls (n = 100) were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The differences in MTHFR genotype and allele frequencies were evaluated by computing for the odds ratio (OR) with a 95 % confidence interval (CI). The CT genotype (OR: 0.775, 95 % CI: 0.35–1.71, p = 0.53), T allele (OR: 0.703, 95 % CI: 0.34–1.48, p = 0.35), and presence of at least one T allele (ORCT+TT: 0.729, 95 % CI: 0.33–1.60, p = 0.43) were not associated with breast cancer risk. Based on the SNP interaction with other risk factors, no significant difference (p > 0.05) was observed for the tumor characteristics, menarche age, and menopause age. Interestingly, a decreased risk (OR: 0.342, 95 % CI: 0.14–0.84, p = 0.019) was observed for the CC genotype in individuals who consumed dietary fibers. Meanwhile, there was an increased risk for passive smokers with the CC genotype (OR: 6.31, 95 % CI: 2.68–14.9, p < 0.001). Overall, the MTHFR 677C>T was not significantly associated with breast cancer risk in a selected Filipino population. Since this study involved a relatively small number of participants, increasing the number of samples is recommended for a more conclusive test of association of MTHFR 677C>T with breast cancer risk in Filipinos.

Status of tick-borne haemoprotozoan infection in south Indian sheep in association with variation in Ovar-DRB1 gene

A study was carried out to detect Babesia and Theileria spp. in native sheep of Andhra Pradesh, south India and determine the association of Ovar-DRB1 alleles with resistance/ susceptibility to natural infection of these species using 249 blood samples collected from different breeds (Nellore breed, Gaddabolli, Vizianagaram and Macherla brown). Initial blood smear examination revealed 12.9% (32/249) prevalence of Theileia spp. Further Babesia/Theileria genus specific PCR amplified only 430 bp 18 S rRNA specific to Theileria spp. in 34.9% (87/249) of sheep samples. None of the samples yielded amplification specific for Babesia spp. Species specific differentiation of theileriosis samples revealed that 76 were found to be positive for T. luwenshuni and eleven were positive for mixed infection with T. luwenshuni and T. ovis. Age was found to be significantly (P < 0.05) associated with positivity for theileriosis being high in adult sheep, while gender, breed and zone were not associated with the disease occurrence. Amplification and characterization of Ovar-DRB1 exon 2 by PCR-RFLP from DNA samples of healthy and infected sheep generated three genotypes ‘aa’, ‘ab’ and ‘bb’ and two alleles ‘a’ and ‘b’. The overall frequency of ‘a’ and ‘b’ allele was 0.83 and 0.17 (P < 0.01) and the polymorphic information content varied from 0.22 to 0.26 among the different sheep populations. The χ2 differences of genotype and allele frequencies between different breeds was no significant (P > 0.05). Except for Gaddabolli and Nellore sheep populations the observed heterozygosity value deviated from that of the expected heterozygosity. The χ2 test of independence revealed an association (P < 0.05) between genotypes and infection status in sheep. The frequencies of sheep carrying ‘b’ allele (‘ab’ and ‘bb’ genotypes) were higher in the healthy group compared to the theileriosis sheep, which implied that there was an association between ‘b’ allele and theileriosis resistance. This is the first study demonstrating the association between Ovar-DRB1 alleles and resistance/susceptibility to theileriosis.

Polymorphisms of TNF-alpha (− 308), IL-1beta (+ 3954) and IL1-Ra (VNTR) are associated to severe stage of endometriosis in Mexican women: a case control study

BackgroundEndometriosis is an estrogen-dependent and chronic inflammatory disease affecting up to 10% of women. It is the result of a combined interaction of genetic, epigenetic, environmental, lifestyle, reproductive and local inflammatory factors. In this study, we investigated whether single nucleotide polymorphisms (SNPs) mapping to TNF-alpha (TNF, rs1800629) and IL-1beta (IL1B, rs1143634) and variable number tandem repeat polymorphism mapping to IL1-Ra (IL1RN intron 2, rs2234663) genetic loci are associated with risk for endometriosis in a Mexican mestizo population.MethodsThis study included 183 women with confirmed endometriosis (ENDO) diagnosed after surgical laparoscopy and 186 women with satisfied parity and without endometriosis as controls (CTR). PCR/RFLP technique was used for genotyping SNPs (rs1800629 and rs1143634); PCR for genotyping rs2234663.ResultsWe found no statistical differences in age between groups nor among stages of endometriosis and the CTR group. We observed no difference in genotype and allele frequencies, nor carriage rate between groups in none of the three studied polymorphisms. The prevalence of TNF*2-allele heterozygotes (p = 0.025; OR 3.8), TNF*2-allele (p = 0.029; OR 3.4), IL1B*2-allele heterozygotes (p = 0.044; OR 2.69) and its carriage rate (p = 0.041; OR 2.64) in endometriosis stage IV was higher than the CTR group. Surprisingly, the carriage rate of IL1RN*2-allele (ENDO: p = 0.0004; OR 0.4; stage I: p = 0.002, OR 0.38; stage II: p = 0.002, OR 0.35; stage III: p = 0.003, OR 0.33), as well as the IL1RN*2-allele frequencies (ENDO: p = 0.0008, OR 0.55; I: p = 0.037, OR 0.60; II: p = 0.002, OR 0.41; III: p = 0.003, OR 0.38) were lower than the CTR group. Women with endometriosis stage IV (severe) had frequencies more alike to the CTR group in the IL1RN*2 allele frequency (31.2% vs. 27.2%) and carriage rate (37.5% vs. 41.9%).ConclusionAlthough these polymorphisms are not associated with the risk of endometriosis, Mexican mestizo women with severe stage of endometriosis have higher frequencies of TNF*2-, IL1B*2- and IL1RN*2-alleles, which may explain a possible correlation with disease severity rather than predisposition or risk.

The Effect of Selected Polymorphisms of the ACTN3, ACE, HIF1A and PPARA Genes on the Immediate Supercompensation Training Effect of Elite Slovak Endurance Runners and Football Players.

We aimed to evaluate the effect of selected polymorphisms of the ACTN3, ACE, HIF1A and PPARA genes on the immediate supercompensation training effect of elite Slovak endurance runners and football players compared with a sedentary control group. Adaptation effect levels were evaluated by 10 s continuous vertical jump test parameters measured by Optojump. Genetic polymorphisms were determined by PCR and Sanger sequencing. We found significant differences in the effect of PPARA genotypes in the experimental group. C allele genotypes represented an advantage in immediate supercompensation (p < 0.05). We observed a significant combined effect of multiple genes on immediate supercompensation (p < 0.05): the RR genotype of the ACTN3 gene, the ID genotype of the ACE gene, the Pro/Pro genotype of HIF1A, and the GC and GG genotypes of PPARA genes. In the control group, we found a significant effect (p < 0.05) on immediate supercompensation of the II genotype of the ACE gene and the Pro/Ser genotype of the HIF1A gene. We found significant differences in genotype frequency of ACE (p < 0.01) and PPARA (p < 0.001) genes. We confirmed that individual genetic polymorphisms of ACTN3, ACE, HIF1A and PPARA genes have a different effect on the level of immediate supercompensation of the lower limbs depending on the training adaptation of the probands and the combination of genotypes.

Cranial and extracranial large-vessel giant cell arteritis share a genetic pattern of interferon-gamma pathway.

Two main different clinical phenotypes of giant cell arteritis (GCA) have been described, the classic cranial pattern and the extracranial large-vessel (LV) pattern. Since interferon gamma (IFNG) has shown to be a pivotal cytokine in the pathophysiology of GCA, our aim was to evaluate for the first time the influence of IFNG and IFNG receptor 1 (IFNGR1) polymorphisms in the different clinical phenotypes of GCA. Two IFNG polymorphisms (rs2069718 G/A and rs1861493 A/G) and one polymorphism in IFNGR1 (rs1327474 G/A) were genotyped in 191 patients with biopsy-proven cranial GCA, 109 with extracranial LV-GCA and 490 healthy controls. A comparative study was conducted between patients with cranial and extracranial LV-GCA. No significant differences in genotype, allele, and haplotype frequencies of IFNG polymorphisms were found between GCA patients with the classic cranial pattern and the extracranial LV-GCA pattern. Similar results were found for genotype and allele frequencies of IFNGR1 polymorphism. It was also the case when patients with extracranial LV-GCA were compared with healthy controls. Our results show that IFNG and IFNGR1 polymorphisms do not influence the clinical phenotype of expression of GCA. Classic cranial GCA and extracranial LV-GCA seem to share a genetic pattern of IFNG pathway.