single-nucleotide polymorphism genotype data
Analysis of high density single nucleotide polymorphism data: three novel methods that control for linkage disequilibrium between markers in a linkage analysis
... founders. Genotype data was available for only ~15% of the pedigree founders, and because the total number of individuals with genotype data was large (n = 1991 individuals) the estimated ...
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Comparison of tagging single nucleotide polymorphism methods in association analyses
... for single-nucleotide polymorphism (SNP) selection has empowered genetic epidemiologic ...using data from public projects [1] or a subset of study partici- pants, then genotype only the ...
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Joint analysis of sequence data and single nucleotide polymorphism data using pedigree information for imputation and recombination inference
... one haplotype has already been assigned. Genotypes of unsequenced individuals can then be imputed based on their assigned haplotypes (see Figure 1 for the frame- work and an example). Conflicts may occur when the ...
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Software for tag single nucleotide polymorphism selection
... for single nucleotide polymorphism (SNP) tagging and considers the use of current software made freely available for this ...SNP genotype data from the HapMap is used to judge the ...
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Principal component based population structure adjustment in the North American Rheumatoid Arthritis Consortium data: impact of single nucleotide polymorphism set and analysis method
... a single SNP subset (S3, filtered SNPs omitting MHC and inversion poly- morphism SNPs) for exploration of adjustment methods (see Results for rationale for the choice of Set ...SNP genotype as the count of ...
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Identification of a Haarlem Genotype Specific Single Nucleotide Polymorphism in the mgtC Virulence Gene of Mycobacterium tuberculosis
... the nucleotide at codon 182 of mgtC. All data were unambiguous, and we found that all additional Haarlem strains tested had an A at position 182, whereas all non-Haarlem strains, including strains from ...
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Application of sex specific single nucleotide polymorphism filters in genome wide association data
... (the NARAC and Swedish Epidemiologic Investigation of Rheumatoid Arthritis (EIRA) data sets were filtered separately) [1]. Such global SNP filters are effective in removing SNPs with clustering problems, thus ...
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Association of single nucleotide polymorphism rs6983267 with the risk of prostate cancer
... between single nucleotide polymorphism (SNP) rs6983267 and the risk of prostate ...available data and performed a meta-analysis to determine this ...rs6983267 polymorphism and risk of ...
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Disentangling Linkage Disequilibrium and Linkage From Dense Single-Nucleotide Polymorphism Trio Data
... of data from parent to ...mission data between multiple pairs of overlapping densely spaced markers is combined to reduce var- iance and produce accurate estimates of ...
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Evaluation of single nucleotide polymorphism imputation using random forests
... non-missing data of a reference population is a possible approach to overcome this as described in Algorithm 1 Step ...the data contain only genotypes, this precondition is not ...use genotype ...
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Original Article Nested ARMS-qPCR is a fast and cost-saving method for single nucleotide polymorphism genotyping in clinical service
... ARMS-qPCR for SNP may be implemented as several strategies, including one-step ARMS- qPCR, Taqman ARMS-qPCR, and nested ARMS- qPCR. One-step ARMS-qPCR means SNP is genotyped by amplifying with a pair of primers directly. ...
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Fine-Scale Estimation of Location of Birth from Genome-Wide Single-Nucleotide Polymorphism Data
... the accuracy of pcLOCATE with the approach of Novembre et al. (2008), in which linear models for longitude and latitude were employed with linear and quadratic effects for the first two PCs (Novembre et al. 2008). PCA of ...
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Associating multiple longitudinal traits with high dimensional single nucleotide polymorphism data: application to the Framingham Heart Study
... To decrease computation time, the number of SNP variables was reduced, using univariate analysis. Each of the four intercept variables were separately associated with the SNPs set using the optimal scaling method. Only ...
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The genetics of regulatory variation in the human genome
... of data produced in microarray exper- iments require some significant statistical ...low-quality data from the primary ...the data to adjust for any sources of variability due to the experiment ...
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Gene based Higher Criticism methods for large scale exonic single nucleotide polymorphism data
... each data replicate we calculate one set of marginal T or Z statistics and then combine the 200 sets of test statistics from the 200 replicates to calculate the Pearson correlation coeffi- ...
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A General Overview of Detection Methods for Single Nucleotide Polymorphism
... MAQ, on behalf of mapping and assembly with qualities, is a diversity filtering algorithm based on short sequences alignment and can be used to address very short sequence segments generated by NGS technology. MAQ can ...
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Functional single nucleotide polymorphism-based association studies
... Association studies hold great promise for the elucidation of the genetic basis of diseases. Studies based on functional single nucleotide polymorphisms (SNPs) or on linkage disequilibrium (LD) represent ...
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Polymorphisms in the Haem Oxygenase 1 promoter are not associated with severity of Plasmodium falciparum malaria in Ghanaian children
... L/L genotype. The allele and genotype frequencies are shown in Table ...and genotype fre- quencies of ...the data was analysed comparing genotypes containing at least one “L” allele (S/L, M/L, ...
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A functional single nucleotide polymorphism of SET8 is prognostic for breast cancer
... A single-nucleotide polymorphism (SNP) locus rs16917496 (T > C) within the 3′-untranslated region (3′-UTR) of SET8 was associated with susceptibility in several malignancies including breast ...TT ...
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Analyzing a single nucleotide polymorphism in schizophrenia: a meta-analysis approach
... that single nucleotide polymorphism (SNP) involving variant rs1344706 from the ZNF804A gene in human beings is associated with the risk of schizo- phrenia in several ...
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