Global distribution and prevalence of hepatitis C virus genotypes - Oxford Big Data Institute
© 2014 The Authors. Hepatitis C virus (HCV) exhibits high genetic diversity, characterized by regional variations in genotype prevalence. This poses a challenge to the improved development of vaccines and pan-genotypic treatments, which require the consideration of global trends in HCV genotype prevalence. Here we provide the first comprehensive survey of these trends. To approximate national HCV genotype prevalence, studies published between 1989 and 2013 reporting HCV genotypes are reviewed and combined with overall HCV prevalence estimates from the Global Burden of Disease (GBD) project. We also generate regional and global genotype prevalence estimates, inferring data for countries lacking genotype information. We include 1,217 studies in our analysis, representing 117 countries and 90% of the global population. We calculate that HCV genotype 1 is the most prevalent worldwide, comprising 83.4 million cases (46.2% of all HCV cases), approximately one-third of which are in East Asia. Genotype 3 ishttps://www.bdi.ox.ac.uk/publications/505902
HIV Genotype Assay in Gurgaon Sector 15, Gurgaon. View Prices, Labs & Book online only on | Practo
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HIV Genotype Assay in Gurgaon Sector 52, Gurgaon. View Prices, Labs & Book online only on | Practo
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HIV Genotype Assay in Gurgaon Sector 54, Gurgaon. View Prices, Labs & Book online only on | Practo
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HIV Genotype Assay in Chakkarpur, Gurgaon. View Prices, Labs & Book online only on | Practo
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PPT - PCR-Based Genotyping Methods PowerPoint Presentation - ID:6726805
PCR-Based Genotyping Methods. An introduction to PCR-RFLP/CAPS, and dCAPS. Common PCR-based Genotyping Methods for SNP Analysis. SNPs can have up to 4 alleles (A/C/G/T), but two alleles are most common . These methods can only positively detect one allele. PCR -RFLP / CAPS Slideshow 6726805 by tatiana-stanleyhttps://www.slideserve.com/tatiana-stanley/pcr-based-genotyping-methods
Missed abortion VIII. - O tom sa ťažko rozpráva - str. 127
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Missingness in the T1DGC MHC fine-mapping SNP data: association with HLA genotype and potential influence on genetic...
Aim: The absence or 'missingness' of single nucleotide polymorphism (SNP) assay values because of genotype or related factors of interest may bias association and other studies. Missingness was determined for the Type 1 Diabetes Genetics Consortium (T1DGC) Major Histocompatibility Complex (MHC) data and was found to vary across the region, ranging up to 11.1% of the non-null proband SNPs, with a median of 0.3%. We consider factors related to missingness in the T1DGC data and briefly assess its possible influence on association studies.. Methods: We assessed associations of missingness in the SNP assay data with human leucocyte antigen (HLA) genotype of the individual and with SNP genotypes of the parents. Within-cohort analyses were combined (over all cohorts) using (i) Mantel-Haenszel tests for two-by-two tables or (ii) by combining test statistics for larger tables and regression models. Mixed effect regression models were used to assess association of the SNP genotypes with affected status of ...http://researchrepository.murdoch.edu.au/id/eprint/8023/
Genotype, environment, and genotype by environment interactions determine quantitative resistance to leaf rust (Coleosporium...
Many inoculation studies of non-agricultural species have revealed genotypic differences in infection intensity (Burdon, 1980; Burdon & Marshall, 1981; de Nooij & van Damme, 1988; de Nooij et al., 1995; Ericson et al., 2002). Our results add to others that verify that genotype is also commonly a factor in determining infection intensity under conditions of natural disease spread (Fig. 1; Alexander, 1989; Schmid, 1994; Davelos et al., 1996). One way to attribute genotypic differences in infection intensity to genetic differences in resistance is to survey infection intensity of the same host genotypes over a number of locations and years. Evidence for resistance exists when the same genotypes have the lowest infection intensities across surveys. Our results show that genotypes 1 and 9 regularly have lower infection intensity, than other genotypes (Fig. 1). This approach to assessing resistance is robust to amoung-survey differences in initial pathogen density, genetic makeup and environmental ...http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2004.01082.x/full
PNPLA 3 I148M genetic variant associates with insulin resistance and baseline viral load in HCV genotype 2 but not in genotype...
Background: Hepatic steatosis in HCV patients has been postulated as a risk factor associated with a higher frequency of fibrosis and cirrhosis. A single genetic variant, PNPLA3 I148M, has been widely associated with increased hepatic steatosis. Previous studies of the PNPLA3 I148M sequence variant in HCV infected individuals have reported an association between this variant and prevalence of steatosis, fibrosis, and cirrhosis. To evaluate the impact of PNPLA3 I148M variant on metabolic traits and treatment response in HCV genotype 2 and 3 infected patients.. Methods. Three hundred and eighty-two treatment naïve HCV genotype 2 or 3 infected patients were included in a phase III, open label, randomized, multicenter, investigator-initiated trial (the NORDynamIC study), in which pretreatment liver biopsies were mandatory. PNPLA3I148M genotyping was performed in a total of 359 Caucasian patients.. Results: In HCV genotype 2 infected patients carrying the PNPLA3 148M allele, there was ...http://bora.uib.no/handle/1956/6663
Genetic and phenotypic variation
For example, there is 70% penetrance if only 700 individuals express red phenotype out of 1,000 HairredHairred individuals. If penetrance of a phenotype is not 100%, then it has reduced penetrance. Mechanisms of reduced penetrance are not always clear. Expressivity is another important concept in describing genotype-phenotype correlation. Expressivity describes the severity of a phenotype among individuals with the same genotype. For example, if a condition has variable expressivity then one individual might have mild symptoms while another might have severe symptoms (although they have the same genotype). If a trait has constant expressivity then individuals with the same genotype will have the same degree of symptoms.. Mechanisms of variable expressivity are not always clear. Although there is typically a clear genotype-phenotype correlation that associates a specific allele with a specific phenotype, this link is frequently muddled. Even individuals with identical genotypes can have different ...https://studentreader.com/JLM9L/genotypes-phenotypes/
Sofosbuvir and Velpatasvir for HCV Genotype 1, 2, 4, 5, and 6 Infection
Of the 170 million patients who are chronically infected with HCV worldwide, approximately half have HCV genotypes other than genotype 1, including about one third of patients with HCV in the United States.17 Currently approved regimens of direct-acting antiviral agents are not equally effective across all genotypes, which means that testing to determine genotype and subtype is required before treatment can be initiated.6,7 A single combination regimen that is effective in all patients regardless of HCV genotype would obviate the need for pretreatment testing, which is an obstacle to treatment in resource-limited settings and may limit treatment uptake outside of specialty clinics.18 In this international, randomized, double-blind, placebo-controlled phase 3 study, treatment with sofosbuvir-velpatasvir for 12 weeks resulted in high rates of sustained virologic response in patients with HCV genotype 1, 2, 4, 5, or 6, including those with cirrhosis and those who had received previous treatment and ...http://natap.org/2015/AASLD/AASLD_66.htm
Genotype - Conservapedia
The genotype refers to the entire set of genes in a cell, an organism, or an individual. A gene for a particular character or trait may exist in two allelic forms; one is dominant (e.g. A) and the other is recessive (e.g. a). Based on this, there could be three possible genotypes for a particular character. For instance, a genotype of AA delineates homozygous dominance whereas a genotype of Aa is an example of heterozygous dominance. A genotype of aa is an instance of homozygous recessive. The genotype is a major factor that determines the phenotype of an organism. For example, the genotype determines the color of the petal of a pea plant. ...http://www.conservapedia.com/Genotype
FDA Approves Hologic's HPV Genotype Assay for Panther | GenomeWeb
NEW YORK (GenomeWeb News) - Hologic said after the close of the market on Thursday that the US Food and Drug Administration has approved the Aptima HPV 16 18/45 genotype assay for use on the Panther system.https://www.genomeweb.com/pcrsample-prep/fda-approves-hologics-hpv-genotype-assay-panther
High Throughput Genotyping Project (HTPG) - ICRISAT- Center of Excellence in Genomics & Systems Biology
The shared genotyping facility is expected to increase throughput ten-fold and reduce costs by about 75-80% in comparison to current procedures. Lowering the genotyping cost will enable CGIAR and other public sector breeders to utilize marker-based selection in forward breeding and also change their current breeding procedures to take advantage of low-cost genotyping. It will be then possible to generate several-fold higher numbers of lines and select them with diagnostic markers for key traits before phenotyping, increasing selection intensity for yield and selection accuracy for other traits. This will accelerate genetic gains in CGIAR mandate crops. The genotyping data demand across from all/leading CGIAR Centers can be aggregated, the costs can be brought down in the range of US$ 1-5 per sample (with 10-100 markers). ...http://ceg.icrisat.org/high-throughput-genotyping-project-htpg/
Frequency distribution of apolipoprotein e genotypes in elderly Han Chinese population and relationship with senile dementia -...
RESULTS: We found that the most prevalent genotype was Apo Eε3/3, followed in order by Apo Eε3/4 and Apo Eε2/2. The estimated ApoE allelic frequencies in individuals with SD were 0.095, 0.560, and 0.345 for ε2, ε3, and ε4, respectively. In controls, the corresponding Apo E allelic frequencies were 0.146, 0.699, and 0.155. The percentage of ε4 allele carriers in SD group was significantly higher than that in control group ( ...https://www.minervamedica.it/it/riviste/neurosurgical-sciences/articolo.php?cod=R38Y9999N00A140043
Practical considerations regarding the use of genotype - Semantic Scholar
22 Genome-wide association studies of complex traits are often complicated by relatedness 23 among individuals. Ignoring or inappropriately accounting for relatedness often results in 24 inflated type I error rates. Either genotype or pedigree data can be used to estimate relat25 edness for use in mixed-models when undertaking QTL mapping. We performed simulations 26 to investigate methods for controlling type I error and optimizing power considering both 27 full and partial pedigrees and, similarly, both sparse and dense marker coverage; we also ex28 amined real data sets. 1) When marker density was low, estimating relatedness by genotype 29 data alone failed to control the type I error rate; 2) this was resolved by combining both 30 genotype and pedigree data. 3) When sufficiently dense marker data was used to estimate 31 relatedness, type I error was well controlled and power increased; however, 4) this was only 32 true when the relatedness was estimated using genotype data that excluded genotypes onhttps://www.semanticscholar.org/paper/Practical-considerations-regarding-the-use-of-geno-Cheng-Parker/09386fdb37f130d2054a1a5cca9c1ad3b64410c4
lane 1 represents homozygous CC genotypes, lane 2 and 5 | Open-i
lane 1 represents homozygous CC genotypes, lane 2 and 5 represents heterozygous AC genotypes and lane 3, 4, 6, and 7 represents homozygous AA genotypes of A20Chttps://openi.nlm.nih.gov/detailedresult.php?img=PMC2656464_1475-2840-8-11-2&req=4
Recently with the rapid improvements in high-throughout genotyping techniques, researchers are | Thioredoxin Reductase and its...
Recently with the rapid improvements in high-throughout genotyping techniques, researchers are facing the very challenging task of analyzing large-scale genetic associations, especially at the whole-genome level, without an optimal solution. genotype data, it does not require any computationally rigorous phasing program to account for uncertain haplotype phase. Background Currently, with Artesunate the availability of large-scale genotyping technologies, the genotyping cost of genome-wide association (GWA) studies has been largely reduced and a boom of large-scale GWA studies is underway. Nevertheless, the success of most association studies is based on the linkage disequilibrium (LD) between the functional mutations and markers in a local region of the genome. Varieties of statistical methods that rely on LD pattern have been developed to map functional variants (Spielman et al. 1993; Olson et al. 1994; Rannala and Reeve 2001; Ardlie et al. ...http://livingseas.org/recently-with-the-rapid-improvements-in-high-throughout-genotyping-techniques-researchers-are/
Gene Variants in the HTRA1 and ARMS2 genes and Outcome of Anti-VEGF Treatment in Neovascular AMD | IOVS | ARVO Journals
Mean age of patients was 78±6.7 years with a baseline VA of 51±17 ETDRS letter scores. Mean change in VA was +6.8±12.3, +5.1±13.4 and 3.3±14.9 letters at 3, 6 and 12 months, respectively. Patients received 4.2±1.1 and 6.4±2.3 injections in the first 6 and over 12 months, respectively. The AA genotype at rs11200638 (HTRA1 promoter SNP) predicted a better outcome of +7 and +9 letters after 6 (p= 0.003) and 12 months (p,0.0001), respectively. Similarly, the CC genotype at rs3793917 (LOC387715/ARMS2) was associated with increased VA outcome of +7 letters after 6 (p=0.006) and 12 months (p=0.001), whereas the TT genotype at rs10490924 (LOC387715/ARMS2) predicted a poorer VA response of -7 and -8 letters at 6 (p=0.004) and 12 months (p=0.001).. ...http://iovs.arvojournals.org/article.aspx?articleid=2354510
Genotype - SNPedia
As most commonly used within SNPedia, genotype refers to the pair of SNPs inherited at a given chromosomal position, one inherited from Dad, one inherited from Mom. Example: rs1234(A;C) is how we indicate someone with a (A;C) genotype at snp rs1234. However, this definition of 'genotype' varies a bit from the one intended when it first introduced over 100 years ago [10.1126/science.35.896.340], and even from the most common usage in genetics textbooks. Although genotype can refer to an individual's genetic constitution (as a whole), the most typical usage is to refer to the pair of alleles carried by an individual at a given locus (or gene). Alleles are classically defined by their protein products and mode of inheritance (e.g. dominant, recessive, etc.), but at a molecular level, alleles may also be defined by one or more co-inherited SNPs. See also Magnitude and Repute Notable genotypes ...https://www.snpedia.com/index.php/Genotype
Effects of polymorphisms in apolipoproteins E, A-IV, and H on quantitative traits related to risk for cardiovascular disease. |...
The impact of the common alleles at structural loci coding for apolipoprotein (apos) A-IV, E, and H on 12 quantitative risk factors for cardiovascular disease (apos A-I, A-II, B, C-II, C-III, and E; total cholesterol; triglycerides; high density lipoprotein cholesterol; systolic blood pressure; diastolic blood pressure; and red blood cell sodium-lithium countertransport) was estimated in 453 unrelated individuals (227 men and 226 women) aged 26-63 years from the Rochester Family Heart Study, who were not using medications affecting lipid levels or blood pressure. Each risk factor was adjusted for concomitants (assay date, age, age, squared, height, weight and smoking status) before the genotypic effects on mean levels and variances were estimated. Allele frequencies were the same in men and women and were similar to those observed in other studies of US Caucasians. There were very different gender-specific estimates of the relative contribution of concomitants, measured genetic effects, and ...http://atvb.ahajournals.org/content/11/5/1330
GigaDB Dataset - DOI 10.5524/100199 - Supporting information for 'Gigwa - Genotype Investigator for Genome Wide Analyses'.
Exploring the structure of genomes and analysing their evolution is essential to understand the ecological adaptation of organisms. However, with the large amounts of data being produced by Next Generation Sequencing (NGS), computational challenges arise in terms of storage, search, sharing, analysis, and visualisation. This is particularly true regarding genomic variation studies that are currently lacking scalable and user-friendly data exploration solutions. Here we present Gigwa, a web-based tool which provides an easy and intuitive way to explore large amounts of genotyping data by filtering the latter based not only on variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability perspectives. Gigwa can handle multiple databases and may be deployed in either single or multi-user mode. Finally, it provides a wide range of popular export formats. The Gigwa application is suitable to manage large ...http://ensembl.genomics.org.cn/dataset/100199
The use of genotyping in antimalarial clinical trials: a systematic review of published studies from 1995-2005 | Malaria...
The results of this study show that the use of genotyping for clinical antimalarial efficacy trials increased dramatically from 2001-2005, especially in Africa where the majority of these trials are now performed. There was wide variation in the methods used for all steps in the genotyping process, from the choice of subjects to genotype to the interpretation of mixed results. Trials in Africa had the highest proportion of subjects with recurrent parasitaemia, and thus the largest proportion of outcomes potentially affected by genotyping. Several factors had a significant effect on genotyping outcomes in the multivariate logistic regression analysis. The interpretation of mixed genotyping results as not always a recrudescence, the use of ACT, the location of a trial in Africa, and a follow-up duration of more than 28 days were all associated with a statistically significant increase in the number of recurrent parasitaemia ...https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-5-122
Phytophthora-ID | About
We redesigned Phytophthora-ID from the ground up in version 2.0 so it is now faster and more stable. We have also developed a new tool for multilocus genotyping of P. ramorum and P. infestans. We hope you enjoy the current implementation.. The sequence based identification module of Phytophthora-ID was created by the Grünwald lab in collaboration with Everett Hansen and Frank Martin, with funding from the Pacific Southwest Research Station, USDA-ARS and the US Forest Service.. The genotype identification module of Phytophthora-ID was created by the Grünwald lab in collaboration with Howard Judelson, Bill Fry, Chris Smart, and Jean Ristaino, with funding from USDA-NIFA and USDA-ARS.. If you use Phytophthora-ID for species identification please cite the following references:. ...http://phytophthora-id.org/about.html