Academic literature on the topic 'Genotype pattern association'

Bovine tuberculosis (bTB) is a global zoonotic disease that has detrimental economic impacts worldwide. The NOS2A gene plays a key role in immunological control of many infectious diseases. However, research on the association between NOS2A polymorphisms and bTB infection in Holstein cattle reared on the Yunnan-Guizhou plateau of China is scarce. This study investigated a possible linkage between NOS2A polymorphisms and risk of developing bTB in Chinese Holstein cattle. The NOS2A gene was genotyped in 144 bTB-infected Holstein cows and 139 healthy controls were genotyped through nucleotide sequencing. Ten single-nucleotide polymorphisms (SNPs) were detected, six of which were associated with susceptibility/resistance patterns of bTB. Furthermore, the C/T genotypes of 671 and 2793, and T/T genotype of E22 (+15) were significantly associated with susceptibility risk; the G/A genotype of 2857, T/T genotype of E9 (+65), and C/C genotype of E9 (+114) probably increased resistance to bTB. In addition, the haplotypes of NOS2A-2 and NOS2A-9 were risk factors for bTB susceptibility, while the NOS2A-5 and NOS2A-8 haplotypes were contributing protective variants against tuberculosis. There is a significant association between variation in SNPs of NOS2A and tuberculosis susceptibility/resistance pattern. These findings suggest that substitution of genetic selection would be helpful for eradicating bTB. However, further investigation is required to study the underlying mechanism through which NOS2A polymorphisms affect bTB infection.

BACKGROUND & OBJECTIVE: primary Hepatitis C is a serious public health problem and is the cause of liver cirrhosis, hepatocellular carcinoma (HCC), and numerous end-stage liver disease manifestations. The management of hepatitis C is to preclude liver cirrhosis, lessen the risk of hepatocellular carcinoma or hepatoma, and curing the extra hepatic diseases. Initially, interferon was the cornerstone for treating hepatitis C, but due to its cumbersome complications, route of administration, and limited treatment access, many patients showed noncompliance. New therapies for chronic hepatitis C have been introduced based on direct antiviral effects. Several genotypes of hepatitis C have been discovered and they are responsive to different antiviral therapies. Our objective was to assess the genotypic distribution of HCV in our local setup and their pattern of response to different combination of anti-viral therapies by assessing the sustained viral response (SVR) after 12 weeks post-treatment. To determine the most prevalent genotype of hepatics C virus in our population and pattern of the response of multiple genotypes to different antiviral regimens. METHODOLOGY: It is a cross-sectional study conducted for duration of six months and recruited those patients whose polymerase chain reaction (PCR) was found positive for hepatitis C virus at Islamabad Diagnostic Center. We analyzed 100 patients, both children and adults. Patients were assessed for different genotypes and then different combinations of antiviral treatments were administered. Their clinical data, hematological parameters and viral load before and after treatment were also analyzed. RESULTS: In a total of 100 positive hepatitis C virus-infected patients, 55% were females and 45% males. The frequencies of genotypes observed were 91 %, 06%, and 03% of genotype 3, 1a, and 1b respectively. 51 out of 91 patients with type 3 genotype, who were on antiviral therapy of sofosbuvir and ribavirin, all of them achieved SVR. 30 out of 91 patients with type 3 genotype were treated with sofosbuvir alone, the percentage of failure to achieve SVR in them was 6.7%. Treatment failure percentage of 10% was observed when a combination of Interferon (INF) alpha and ribavirin was used in type 3 genotype. Remaining six patients with type 1a and three patients of type 1b genotype achieved SVR with different regimens used. CONCLUSION: Although the increased load of HCV in our setup is an alarming situation the prevalence of type 3 genotype is a blessing in disguise. The success of sustained viral response after various combinations of direct antiviral therapy and interferon-free treatment is hope for the ultimate cure of the disease and avoidance of debilitating side effects related to interferon.

Arbuscular mycorrhiza (AM) is a widespread symbiotic association between plants and Glomeromycota fungi, that brings nutritional-derived benefits for phytobiont. Influence of plant breeding on arbuscular mycorrhiza susceptibility is a topic of current interest that can have many practical implications. Insights into whether new cultivars have a lower mycorrhizal potential, are critical for optimization of AM use. Aim of this research was to conduct a comparative assessment of AM colonization across a phenophase gradient in two Iris sibirica genotypes: one displaying the wild traits versus a modern reblooming cultivar with double flowers. Analysis showed that both Iris sibirica genotypes developed Paris-morphotype. Results indicated that on average the genotype with simple flowers had a higher AM colonization frequency (84.44±2.15) compared to the new cultivar with double flowers (52.22±6.09). Significant influence was exercised both by genotype (p<0.001) as well as by phenophase (p=0.0013), over colonization frequency. The genotypes displayed contrasting colonization dynamics: highest AM frequency level occurred in spring for the genotype with simple flowers, and in autumn for the one with double flowers. Results suggest that host metabolic state has regulating role over functionality of established AM-symbiotic association according to plant nutritional requirements, while fungi might also respond to increased or decreased carbon flux in the plant, associated with geophyte phenology.

Introduction: Type 2 diabetes mellitus (T2DM) is a metabolic, multifactorial disease caused by genetic, dietary and environmental interactions with alterations in the pattern of cytokine expression. Association between interleukin (IL)-10 polymorphism and T2DM is not known in Black Af-ricans. This study therefore investigates the relationship between IL-10 -1082A/G polymorphism and risk of T2DM in Southwest Nigeria. Methods: 100 patients with T2DM and 105 healthy controls were enrolled. Anthropomet-ric indices were measured and fasting blood sample was obtained from all subjects. Plasma glucose and lipid profile were estimated by standard laboratory procedures. IL-10 (-1082A/G) gene polymorphism was genotyped using Allele Refractory Mutation detection System-Polymerase Chain Reaction (ARMS-PCR) technique. Odds ratio analysis (95%CI) was used to determine association between genotype and diabetes mellitus in studied subjects. Results: T2DM patients had the highest frequency of IL 10 -1082G/G genotype (58.3%) while -1082AG frequency was highest (63.1%) in non-diabetics. Non- significant associations between IL 10 -1082 gene polymorphism and T2DM risk (for AG genotype: OR=0.95, 95%CI =0.19-4.2, p = 0.95; for GG genotype: OR=0.49, 95%CI = 0.10-2.41, p = 0.38) were recorded. Fasting plasma glucose, 2hours post-prandial, total cholesterol and triglyceride were all significantly elevated in IL 10 -1082G/G than AG and AA genotypes in T2DM subjects (p<0.001). Expression of A allele was higher in controls than DM patients . Conclusion: This case-control study did not find a significant association between IL 10-1082A/G polymorphism and T2DM; however further studies with larger sample size and IL-10 plasma level meas-urement will be recommended to validate this observation.

SUMMARYThis study reports the epidemiology of respiratory syncytial virus (RSV) in hospitalized children in Cyprus over three successive seasons (2010–2013) and the association between prevalent genotypes and disease severity. RSV infections had a circulation pattern from December to March. Most RSV-positive children (83%) were aged <2 years. Genotyping of RSV isolates showed that during the first winter season of the study (2010–2011), the only RSV genotype circulating was GA2 (RSV-A), followed by genotype BA (RSV-B) in the next winter season with only few sporadic cases of GA2. During the last winter season of the study (2012–2013) the newly emerged RSV genotype ON1 (RSV-A) was virtually the only circulating genotype. Children infected with genotype ON1 suffered a significantly milder illness compared to infections with genotypes GA2 and BA with a higher percentage of BA-infected children requiring oxygen. Our findings are in contrast to the majority of published reports that suggest RSV-A causes more severe illness than RSV-B. Therefore, further investigation of the association between RSV genotypes and disease severity is required, as it might affect treatment strategies in the future.

The speciality of the modern methodology in breeding is using the molecular information, received during genome analysis. This methodology can significantly accelerate the improvement of productivity traits and it is particularly useful in relation to the traits with low coefficient of inheritance while classic methods are not effective enough. The reproductive traits are one of the most important in pig farming, estrogen receptor 1 gene (ESR1) is involved in their control. Meanwhile, the use of ESR1 locus polymorphism in the marker-assisted selection needs to determine the extent of its association with the reproductive traits of animals in those populations where it is planned to conduct such selection. Implementation of marker-assisted selection in Large White and Mirgorod breeds for improving the reproductive traits is an actual task, but a necessary step in this work is the associative analysis. The purpose of the work is to research the association of polymorphisms of ESR1 locus with some reproductive traits of sows of Large White breed (ULW-1 and ULW-3 lines) and sows of Mirgorod breed. Materials and methods of research. Experimental groups: 1) the sows of Large White breed, ULW-3 line, bred in "Bahmutskiy Agrarian Union" farm, Donetsk region; 2) the sows of Large White breed, ULW-1 line, bred in “Stepne” farm, Poltava region; 3) the sows of Mirgorod breed, bred in «Named after Dekabristy» farm, Poltava region. All the experimental animals were previously genotyped on RYR1 gene and had RYR1CC genotype. The animals were genotyped on estrogen receptor 1 locus with aid of PCR-RFLP analysis on PvuII-polymorphic restriction site in the third intron of the gene – DNA marker for estrogen receptor 1 gene. Associations between genotypes and the studied traits were calculated using ANOVA in Excel 2007. Results. ULW-3 sows with ESR1BB genotype turned out to have 1.36 more piglets in a litter (analysing data from 2nd-4th farrows) comparing to animals with ESR1AA genotype. There is a tendency for bigger amount of newborn piglets in the heterozygotes animals than in sows with homozygous ESR1AA. A similar pattern appears in the 1st farrowing, the sows with ESR1BB and ESR1AB genotypes had the advantage in the total number of piglets at birth. In the experimental group of ULW-1 sows statistically proven patterns were not found, there was only a tendency to slight predominance of sows with ESR1BB and ESR1AB genotypes comparing to individuals with ESR1AA genotype. In the experimental group of Mirgorod sows there was a tendency to have most part of individuals with heterozygous genotype. Analysis of prolificacy of ULW-3 sows due to their genotype for the estrogen receptor 1 gene confirmed the superiority of ESR1BB and ESR1AB genotypes comparing to ESR1AA sows. According to 2nd-4th farrows, sows with ESR1BB and ESR1AB genotypes had the advantage in prolificacy comparing to ESR1AA sows by 1.15 and 0.53 piglets, respectively. According to the 1st farrowing difference between genotypes was absent. ESR1/PvuII-polymorphism do es not influence on prolificacy of ULW-1 sows. According to the 1st farrowing the trend towards a higher level of prolificacy of Mirgorod sows with ESR1AA genotype was found, while difference in 2nd-4th farrows between the groups was absent. It was found that ESR1/PvuII-polymorphism impact on the total number of piglets at birth and prolificacy for ULW-3 sows is characterized by predominance of additive component with a little contribution of the dominant component, the similar trend is observed for ULW-1 sows. There is a complex nature of the impact of ESR1/PvuII-polymorphism on the reproductive traits of Mirgorod sows in the predominance of the dominant component. Conclusions. The impact of polymorphism in estrogen receptor 1 gene on the total number of piglets in the litter after the birth and prolificacy in ULW-3 sows was detected. ULW-3 sows with ESR1BB genotype have 1.36 more piglets in a litter (analysing data from 2nd-4th farrows) and 1.15 more comparing to animals with ESR1AA genotype. ESR1/PvuII-polymorphism was not associated with total number of piglets in a litter and prolificacy in ULW-1 sows and Mirgorod sows. The counted parameters of additive-dominant model indicate that ESR1/PvuII polymorphism impact on the total number of piglets at birth and prolificacy for ULW-3 sows is characterized by predominance of additive component with a little contribution of the dominant component.

Abstract Bone development and growth is a non-going, life-long process, varying greatly among individuals and much of this variation could be modulated by genetic factors. The purpose of this study was to evaluate the association between the polymorphisms in the TNF-a gene and skeletal class II malocclusion. Single nucleotide polymorphisms in TNF-a (rs1799724; rs1800629) gene were studied in 79 skeletal class II malocclusion and 102 skeletal class I malocclusion subjects from Straight Wire Group of Studies on Orthodontics and Functional Orthopedics for Maxillary from Rio de Janeiro, Brazil. The Genotyping of these selected polymorphisms was carried out by TaqMan real-time PCR using genomic DNA extracted from buccal cells. All allele and genotype frequencies were compared between the groups using the PLINK® software in a free, in a dominant and in a recessive model using a chi-square test (p≤0.05). There was no significant association of TNF-a (rs1799724; rs1800629) genotype and allele distribution with skeletal class II malocclusion. Regardless of the dominant or recessive genetic model, the preferential genotype associations for rs1799724 and rs1800629 was insignificant. In conclusion, no evidence of association is apparent between genetic polymorphisms involving TNF-a and skeletal class II malocclusion or the position of the maxilla and mandible in the postero-anterior direction.

Pathogens invading the mammary gland are recognized through a range of pattern recognition receptors (PRRs), residing on the plasma membrane of mammary epithelial cells. Toll-like receptor 2 (TLR2) signalling is responsible for recognition of Gram-positive bacteria, which are the most common mastitis-causing pathogens in goats. Somatic cell counts (SCC) in milk are routinely determined in goat dairy flocks and serve as an indicator of milk quality, which is highly correlated to intramammary infections. Recently, a single nucleotide polymorphism of the TLR2 was suggested to be associated with SCC in goat milk. To further test the suggested association, we genotyped 61 Slovenian Alpine goats included in the dataset. The effect of the genotype was analysed using the general linear model (GLM) procedure of SAS/STAT software. We found the TLR2 genotypes significantly (p = 0.0007) associated with milk SCC. Animals with the A/G genotype had significantly (p ≤ 0.05) lower SCC value in milk compared to the G/G genotype. Our data suggest that the A allele is the minor one and is associated with lower milk SCC. In the current study, we provide a validated PCR-RFLP based genotyping assay for the TLR2 SNP (rs650082970) and confirm its association with milk SCC. Further studies to confirm the association on a larger number of animals of different breeds and to explain functional consequences of the polymorphism in relation to SCC are encouraged.

Polymorphisms of DNA repair and genome integrity genes are associated with DNA repair capacity and elevated cancer risk. To establish an association between the pattern of polymorphism and the incidence of any type of cancer, studies across different populations are required. Polymorphic regions have been identified in the RAD51 repair gene in various cancer types; however, the influence of specific genetic variants on gastric cancer prevalence has not been empirically demonstrated. We conducted a case-control study with 76 gastric cancer patients and 78 healthy individuals from northeastern Anatolia to examine the association between polymorphism and gastric cancer. We genotyped the previously identified G135C polymorphism of RAD51 in all individuals and estimated the allele and genotype frequencies in the two groups. Our results indicated that the two groups differed both in allele and genotype frequencies. Additionally, a significant and elevated odd ratio (3.53) of gastric cancer for the C allele of RAD51 was observed. The genotypes GC and CC had also significant and high odd ratios (>3.75). Our results indicate that G135C polymorphism of the RAD51 gene was associated with an increased risk of gastric cancer in the examined population.

The present study was conducted to interpret Genotype main effect and GEI obtained by AMMI analysis and group the genotype having similar response pattern over all environments. Fifteen bread wheat genotypes were evaluated by RCBD using four replications at six locations in Ethiopia. The main effect differences among genotypes, environments, and the interaction effects were highly significant (P ≤ 0.001) for the total variance of grain yield. Results of AMMI analysis of mean grain yield for the six locations showed significant differences (P0.001) among the genotypes, environments and GEI. The environment had the greatest effect with the environmental sum of squares (35.28%) than the genotypes (33.46%) and GEI (31.45%) effect. The AMMI analysis for the IPCA1 captured 46.1% and the IPCA2 explained 28.6%. The two IPC cumulatively captured 74.7% of the sum of square the GEI of bread wheat genotypes, when the IPCA1 was plotted against IPCA2. The genotype ETBW8075, ETBW8070 and ETBW9470 were unstable as they are located far apart from the other genotypes in the biplot when plotted on the IPCA1 and IPCA2 scores. The ETBW8078, ETBW8459, Hidase and ETBW8311 were genotype located near to the origin of the biplot which implying that it was stable bread wheat genotypes across environments. There is closer association between Lemu and ETBW8065 which indicate similar response of the genotypes to the environment. The best genotype with respect to location Kulumsa was ETBW9470, ETBW8075 was the best genotype for Dhera, ETBW8070 was the best genotype for Holeta while ETBW9466 was the best genotype for Arsi Robe. Arsi Robe and Kulumsa is the most favorable environment for all genotypes with nearly similar yield response for grain yield.

Variations in gene expression have long been hypothesised to be the major cause of individual differences. An initial focus of this research thesis is to elucidate the genetic regulatory architecture of gene expression. Expression quantitative trait locus (eQTL) mapping analyses have been performed on expression levels of over 22,000 mRNAs from three tissues of a panel of recombinant inbred mice. These analyses are "single-locus" where "linkage" (i.e. significant correlation) between an expression trait and a putative eQTL is considered independently of other loci. Major conclusions from these analyses are: 1. Gene expression is mainly influenced by genetic (sequence) variations that act in trans rather than in cis; 2. Subsets of genes are controlled by master regulators that influence multiple genes; 3. Gene expression is a polygenic trait with multiple regulators. Single-locus mapping analyses are not designed for detecting multiple regulators of gene expression, and so observation of multiple-linkages (i.e. one expression trait mapped to multiple eQTLs) formed the basis of the second objective of this research project: to investigate the relationship between multiple-linkages and genotype pattern-association. A locus-pair is said to have associated genotype patterns if they have similar inheritance pattern across a panel of individuals, and these are attributed to one of fours sources: 1. linkage disequilibrium between loci located on the same chromosome; 2. non-syntenic association; 3. random association; 4. un-associated. To understand the validity of multiple-linkages observed in single-locus mapping studies, a newly developed method, bqtl.twolocus, is applied to confirm two-locus effects for a total of 898 out of 1,233 multiple-linkages identified from the three studies mentioned above as well as from seven publicly available eQTL-mapping studies. Combining these results with information of genotype pattern-association, a subset of 478 multiple-linkages has been deduced for which there is high confidence to be real.

Musculoskeletal disease covers a broad spectrum of conditions whose aetiology comprises variable genetic and environmental contributions. More recently it has become clear that, particularly early in life, the interaction of gene and environment is critical to the development of later disease. Additionally, only a small proportion of the variation in adult traits such as bone mineral density has been explained by specific genes in genome-wide association studies, suggesting that gene-environment interaction may explain a much larger part of the inheritance of disease risk than previously thought. It is therefore critically important to evaluate the environmental factors which may predispose to diseases such as osteorthritis, osteoporosis, and rheumatoid arthritis both at the individual and at the population level. In this chapter we describe the environmental contributors, across the whole life course, to osteoarthritis, osteoporosis and rheumatoid arthritis, as exemplar conditions. We consider factors such as age, gender, nutrition (including the role of vitamin D), geography, occupation, and the clues that secular changes of disease pattern may yield. We describe the accumulating evidence that conditions such as osteoporosis may be partly determined by the early interplay of environment and genotype, through aetiological mechanisms such as DNA methylation and other epigenetic phenomena. Such studies, and those examining the role of environmental influences across other stages of the life course, suggest that these issues should be addressed at all ages, starting from before conception, in order to optimally reduce the burden of musculoskeletal disorders in future generations.

Musculoskeletal disease covers a broad spectrum of conditions whose aetiology comprises variable genetic and environmental contributions. More recently it has become clear that, particularly early in life, the interaction of gene and environment is critical to the development of later disease. Additionally, only a small proportion of the variation in adult traits such as bone mineral density has been explained by specific genes in genome-wide association studies, suggesting that gene-environment interaction may explain a much larger part of the inheritance of disease risk than previously thought. It is therefore critically important to evaluate the environmental factors which may predispose to diseases such as osteorthritis, osteoporosis, and rheumatoid arthritis both at the individual and at the population level. In this chapter we describe the environmental contributors, across the whole life course, to osteoarthritis, osteoporosis and rheumatoid arthritis, as exemplar conditions. We consider factors such as age, gender, nutrition (including the role of vitamin D), geography, occupation, and the clues that secular changes of disease pattern may yield. We describe the accumulating evidence that conditions such as osteoporosis may be partly determined by the early interplay of environment and genotype, through aetiological mechanisms such as DNA methylation and other epigenetic phenomena. Such studies, and those examining the role of environmental influences across other stages of the life course, suggest that these issues should be addressed at all ages, starting from before conception, in order to optimally reduce the burden of musculoskeletal disorders in future generations.

Musculoskeletal disease covers a broad spectrum of conditions whose aetiology comprises variable genetic and environmental contributions. More recently it has become clear that, particularly early in life, the interaction of gene and environment is critical to the development of later disease. Additionally, only a small proportion of the variation in adult traits such as bone mineral density has been explained by specific genes in genome-wide association studies, suggesting that gene-environment interaction may explain a much larger part of the inheritance of disease risk than previously thought. It is therefore critically important to evaluate the environmental factors which may predispose to diseases such as osteorthritis, osteoporosis, and rheumatoid arthritis both at the individual and at the population level. In this chapter we describe the environmental contributors, across the whole life course, to osteoarthritis, osteoporosis and rheumatoid arthritis, as exemplar conditions. We consider factors such as age, gender, nutrition (including the role of vitamin D), geography, occupation, and the clues that secular changes of disease pattern may yield. We describe the accumulating evidence that conditions such as osteoporosis may be partly determined by the early interplay of environment and genotype, through aetiological mechanisms such as DNA methylation and other epigenetic phenomena. Such studies, and those examining the role of environmental influences across other stages of the life course, suggest that these issues should be addressed at all ages, starting from before conception, in order to optimally reduce the burden of musculoskeletal disorders in future generations.

Creativity is not a phenomenon that arises from the brain in isolation; it has an experiential, sociopolitical, and cultural context. Nonetheless, studies of the brain illuminate mechanistic aspects of human creativity with a clarity sufficient clearly to allow some predictions of the potential for creativity and have suggested ways in which it can be enhanced. This chapter briefly reviews associations between creativity and disease, focusing on rare case studies of people with neurodegenerative disease affecting the frontal lobe and executive processing. These suggest that impaired frontal activity can enhance more creative behaviors under some conditions, a hypothesis confirmed by direct testing with transient, noninvasive electrical interference with frontal lobe functions in healthy volunteers. The use of some drugs also has been associated with increased creativity. Improved performance on tests of creative cognition by people with Parkinson’s disease after treatment with L-dopa has highlighted roles for dopamine and norepinephrine in modulating cognitive flexibility. However, most of the recent advances in understanding brain mechanisms of creativity from functional brain imaging studies have highlighted that creativity is not localizable to one or a few brain regions, but instead engages coordinated activities across major systems in the brain, including the default mode network and executive control, salience, or attentional networks. With information on genotype and patterns of brain activity, neuroscientists may be able to classify people for their potential creativity.