snp data
Prediction of treatment response in Rheumatoid Arthritis patients using genome-wide SNP data
... use data from the MAximising Ther- apeutic Utility for Rheumatoid Arthritis (MATURA) consortium (Barton & Pitzalis, 2017) and focus on predicting the change in C ‐ reactive protein score (CRP), in 28 swollen ...
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Population genetic analysis of ascertained SNP data
... an SNP discovery protocol in which loci with high frequency alleles have been chosen preferentially has caused a reduction in power compared with randomly sampled ...the data with respect to common alleles ...
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The Effect of Genomic Inversions on Estimation of Population Genetic Parameters from SNP Data
... the data have levels of heterozygosity and linkage disequilibrium reflecting those observed in humans (Hoggart et ...these data were used as input to a second invertFREGENE run that modeled ...final ...
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Using penalized regression to predict phenotype from SNP data
... (SNP) data using standard procedures outlined in Turner et al. [13]. SNP-level QC removes 63,907 SNPs with low minor allele frequency (< ...have SNP data, the simulated phenotype is ...
6
Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data
... for SNP genotyping using the Illumina SNP50 Beadchip according to the manufac- turer’s ...intensity data using GenomeStudio (Illumina) with the minimum gencall score threshold of ...
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fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
... genetic data are now used in a wide variety of applications in population ...modern data sets imposes severe computational ...a data set and a new hierarchical prior to detect weak population ...
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Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion
... tral Wright–Fisher process made it possible to solve the as- sociated diffusion equations for one population (Myers et al. 2008). Also, a recently introduced spectral expansion makes it possible to exactly integrate the ...
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Association of repeatedly measured intermediate risk factors for complex diseases with high dimensional SNP data
... this data 3 individuals had a negative LDL cholesterol level and were therefore removed from the data, together with 27 individuals who had less than 2 observations for one or more of the 7 intermediate ...
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Statistical Methods of SNP Data Analysis and Applications
... the data analysis concerning the coronary heart disease and myocardial infarction the Lomonosov Moscow State University supercomputer “Chebyshev” was em- ...
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Trio-R: a script for assessing maternity and paternity in trio studies performed on Agilent chromosomal microarrays
... Background: Trio studies, which involve the testing of samples from a proband and both parents, are often used by clinical laboratories to help with the classification of genetic variants, including copy number variants. ...
5
Targeted re-sequencing confirms the importance of chemosensory genes in aphid host race differentiation.
... large SNP genotyping data ...sequencing data and Lo. corniculatus in GoldenGate SNP data), PCAdapt was able to identify unexpected substructure within races, which are nor- mally found ...
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Development of Strategies for SNP Detection in RNA Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data
... generates data on sequence variation in expressed ...RNA-seq SNP data. We evaluated the performance of different SNP-calling methods following alignment to both genome and transcriptome by ...
9
Comparing the efficacy of SNP filtering methods for identifying a single causal SNP in a known association region
... causal SNP resolution may be improved by includ- ing information other than the genotype ...much data freely available on features of indi- vidual genetic variants in online databases such as the En- ...
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Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals
... For this study, we perform several analyses to identify and validate genetic interactions associated with circulating lipid levels. Our motivation for studying the contribution of interactions to lipid levels is ...
20
A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis
... The most significant interactions were then further assessed in relation to quantitative biomarkers of VT risk in MARTHA patients. For this, standard linear re- gression analyses were conducted with the same additive ...
7
Lamina, Claudia (2009): Misclassification in genetic variants and its impact on genetic association studies. Dissertation, LMU München: Medizinische Fakultät
... when assuming a dominant or recessive effect on haplotypes. Sensitivity and specificity are also sufficient to describe the misclassification matrix, if only pure reconstruction error (i.e. no genotype error) applies. It ...
121
SNP-SNP interaction analysis of NF-κB signaling pathway on breast cancer survival.
... the SNP-SNP interaction between these loci can only be speculated on at this point, our ENCODE and eQTL analyses indicated that SNPs at both of these loci may influence gene expression, particularly ...
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Novel approach for deriving genome wide SNP analysis data from archived blood spots
... Illumina SNP chip were typically between ...these SNP chips (Cambridge Genomic Services, personal ...protocol, SNP chip data were re-analysed and specific regions of the genome that ...
7
Comparing the Efficacy of SNP Filtering Methods for Identifying a Single Causal SNP in a Known Association Region
... causal SNP resolution may be improved by includ- ing information other than the genotype ...much data freely available on features of indi- vidual genetic variants in online databases such as the En- ...
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The effect of mislabeled phenotypic status on the identification of mutation carriers from SNP genotypes in dairy cattle
... When data get noisier, it is more difficult for predicting algorithms to classify observations correctly, as shown also by the increased computation time ...the data, predictive models may break down and ...
9