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Genetic variants

Tìm thấy 20+ kết quả cho từ khóa "Genetic variants"

Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

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In order to achieve a greater understanding of the gen- etic differences between these two Brazilian white-egg layer and broiler lines, a deep catalog of genetic variants (SNPs and INDELs) were generated by sequencing the genome of 28 chickens (14 per line) at medium sequen- cing coverage.

Genetic variants in nuclear DNA along with environmental factors modify mitochondrial DNA copy number: A population-based exome-wide association study

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However, the environmental factors (such as PM 2.5 exposure level and smoking) were not considered in previous study and these genetic variants only explained a small frac- tion of the total variation. Therefore, more efforts are warranted to evaluate the association between genetic variants and mtDNA copy number in Chinese population..

Genetic variants in the SIRT6 transcriptional regulatory region affect gene activity and carcass quality traits in indigenous Chinese beef cattle (Bos taurus)

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Differential expression of CYB5A in Chinese and European pig breeds due to genetic variations in the promoter region. Wei D-W, Gui L-S, Raza SHA, Zhang S, Khan R, Wang L, et al. NRF1 and ZSCAN10 bind to the promoter region of the SIX1 gene and their effects body measurements in Qinchuan cattle. Fu Y, Sun W, Xu C, Gu S, Li Y, Liu Z, et al. Genetic variants in KDR transcriptional regulatory region affect promoter activity and intramuscular fat deposition in Erhualian pigs.

Deciphering the mode of action and position of genetic variants impacting on egg number in broiler breeders

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Such studies would entail tar- geted re-sequencing and molecular characterization of the candidate variants to facilitate the identification of true causal variants.. Statistically significant SNPs per genetic model were se- lected at the optimal step of the stepwise regression according to the extended Bayesian Information Criterion (eBIC [38])..

Cruxome: A powerful tool for annotating, interpreting and reporting genetic variants

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Third, the “locus searching” tool can be used to calculate frequency of variants in all samples in the personal knowledge base (Fig. users can easily re-analyze cases stored in the knowledge base, and potentially identify novel pathogenic variants.. However, in the current version of Cruxome, only variants from WES and panel data are supported, and file. 3 Interface of Cruxome. Users enter the submodule by clicking the corresponding text in the left panel.

Association of cervical carcinogenesis risk with HPV16 E6 and E7 variants in the Taizhou area, China

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In the present study, we investigated the genetic variants in HPV16 E6 and E7 oncoprotein-encoding genes and their involvement in cervical carcinogenesis in the Taizhou area, Southeast China.. The E6 and E7 variants in the HPV16 sequences were aligned using the ClustalW tool applied by BioEdit Sequence Alignment Editor.

Genome-wide association analysis identified both RNA-seq and DNA variants associated to paratuberculosis in Canadian Holstein cattle ‘in vitro’ experimentally infected macrophages

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The objective of our work was to use the genetic infor- mation from the transcripts and regulatory sequences of the macrophages from JD. cows in the genetic association study. Genetic variants from the rest- ing macrophages (unchallenged controls) and those called to respond to MAP infection were combined with the imputed SNPs to obtain a dense portray of the gen- etics variations of these innate immune sentinel cells.. points were merged with the RNA-seq sample of the un- challenged controls.

Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

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Prediction of superior pure line and hybrid revealed the potential of the QTSs in the improvement of cottonseed traits, and the hybrid could achieve higher or lower genetic values compared with pure lines.. the identified genetic variants and estimated genetic component effects of gene, gene-gene and gene-environment interaction provide cotton geneticist or breeders new knowledge on the genetic mechanism of the traits and the potential molecular breeding design strategy..

Genetic ancestry, admixture and health determinants in Latin America

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In- deed, genomes from modern Latin American popula- tions are evolutionarily novel in the sense that they contain combinations of genetic variants (haplotypes) that never previously existed together on the same gen- etic background.

Combined genetic influence of the nicotinic receptor gene cluster CHRNA5/A3/ B4 on nicotine dependence

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A hallmark of evolutionary selections, long haplotype struc- tures with high frequency in this cluster create a local reg- ulome with multiple genetic variants defining the overall genetic influence of the entire cluster [5]. have iden- tified at least three LD-bin tagging SNPs, including rs16969968, a SNP in the promoter region of CHRNA5 (rs588765), and a SNP located in the CHRNA3 locus (rs6495308), all significantly associated with smoking behavior [10].

Assessing cell-specific effects of genetic variations using tRNA microarrays

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From VarI-COSI 2018: identification and annotation of genetic variants in the context of structure, function, and disease Chicago, IL, USA.

A phenomics-based approach for the detection and interpretation of shared genetic influences on 29 biochemical indices in southern Chinese men

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Genome-wide association study for intracranial aneurysm in the Japanese population identifies three candidate susceptible loci and a functional genetic variant at EDNRA. Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk

Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

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All genetic variants were derived from draft genome sequences of isolates from a multicenter cross-sectional study conducted in the Netherlands during 2016 and 2017. To verify the suitability of the methods used, the genetic differences between the genera Shigella and Escherichia were used as control..

Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle

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Given the economic importance of carcass traits in cattle, an understanding of the genetic variants that contribute to the underlying inter-animal variability is of practical im- portance for any breeding or management strategy in cattle..

A deep auto-encoder model for gene expression prediction

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Gene expression is affected by various factors including genotypes of genetic variants. With an aim of delineating the genetic impact on gene expression, we build a deep auto-encoder model to assess how good genetic variants will contribute to gene expression changes. Results: To demonstrate the usage of this model, we apply MLP-SAE to a real genomic datasets with genotypes and gene expression profiles measured in yeast.

Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples

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Examination of allelic frequency of called variants revealed that a number of called-variants were enriched in the zone of low alternative allele fre- quency (AAF) (percentage of variants with AAF <. in particular, the esti- mated FDRs for QA-FFPE and QGR-FFPE samples are 94.8 and 69.8% with variants with AAF below 1%. FDRs tend to dramatically reduce with an increase in the AAF cutoff, e.g. with AAF 5% or above, both DNA extraction methods had FDR lower than 20%.

Heritability and genome-wide association analyses of fasting plasma glucose in Chinese adult twins

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Here, we performed this twin-based genetic epidemiological study to evaluate the magnitude of the genetic influence on FPG variation and further conducted a GWAS to identify specific genetic variants related to the FPG level in a sample of 382 Chinese twin pairs.. 0.04–0.36) was much lower than half of the MZ twin correlation (r MZ CI suggesting the genetic effect on the FPG level (Additional file 2)..

Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics

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Specifically, if an investigator is interested in identifying genetic variants associated with a trait but has no a priori knowledge of where in the genome such variants are likely to be located, then the relevant metric is the average correlation between imputed genotype calls and true genotypes.

Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing

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The discovery of the mechanisms leading to resist- ance and the underlying causative genetic variants has the potential to reduce this cost via incorporation of functional SNPs into the genomic prediction models.. Previous studies into AGD-infected Atlantic salmon have suggested that the amoebae might elicit an immunosuppressive effect on the innate response of the host, with a concurrent up-regulation of the adaptive Th2-mediated response [16–18].

Polygenic risk prediction models for colorectal cancer: A systematic review

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Genetic risk score, combined lifestyle factors and risk of colorectal cancer. Diabetes mellitus, genetic variants in the insulin-like growth factor pathway and colorectal cancer risk. Plasma C-reactive protein, genetic risk score, and risk of common cancers in the atherosclerosis risk in communities study. Systematic evaluation of cancer- specific genetic risk score for 11 types of cancer in the cancer genome atlas and electronic medical records and genomics cohorts.