Core genome single nucleotide polymorphisms (SNPs) and phylogeny
Single Nucleotide Polymorphisms: A Window into the Informatics of the Living Genome
... human genome function as one integrated whole system, orchestrating the expression of thou- sands of genes underlying the biological characteristics of the cell, individual and the ...in single ...
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Imputation of Single-Nucleotide Polymorphisms in Inbred Mice Using Local Phylogeny
... ABSTRACT We present full-genome genotype imputations for 100 classical laboratory mouse strains, using a novel method. Using genotypes at 549,683 SNP loci obtained with the Mouse Diversity Array, we partitioned ...
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Single Nucleotide Polymorphisms in the Mycobacterium bovis Genome Resolve Phylogenetic Relationships
... DISCUSSION Genomewide SNPs of M. bovis differentiate between isolates. In a 2009 study by Garcia Pelayo et al. (9), 782 SNPs were identified across the entire genomes of M. bovis and M. bovis BCG. We de- rived ...
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Detection of Single Nucleotide Polymorphisms
... the genome through cloning of size- selected restriction fragments from a pooled DNA sample, the same loci were sequenced multiple times when a large number of clones from each library was sequenced (Altshuler et ...
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Mathematical Modeling the Biology of Single Nucleotide Polymorphisms (SNPs) in Whole Genome Adaptation
... human genome sequence ...human genome, only about 0.1% consist of bi-allelic single nucleotide polymorphisms (SNPs) distri- buted throughout the genome ...of polymorphisms ...
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Picking single nucleotide polymorphisms in forests
... genetic polymorphisms predisposing for a complex disease, genome-wide association studies have become more promising with the advances in technolog- ical ...k single-nucleotide ...
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Increasing Power of Genome-Wide Association Studies by Collecting Additional Single-Nucleotide Polymorphisms
... ABSTRACT Genome-wide association studies (GWASs) have been effectively identifying the genomic regions associ- ated with a disease ...the single-nucleotide polymorphisms (SNPs), called tag ...
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Genome-wide identification and analysis of miRNA-related single nucleotide polymorphisms (SNPs) in rice
... Conclusions Based on the identified several millions of high-quality SNPs in rice, a genome-wide scan of SNPs in pre- miRNAs was performed. We find that compared with deeply conserved miRNAs, young miRNAs tend to ...
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A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
... the genome (sorted by GC content) was within 10% of the expected value for all ...a single analytic tool (SsahaSNP, an implementation of the NQS; ...available genome sequence (finished and draft with ...
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Linkage Disequilibrium Grouping of Single Nucleotide Polymorphisms (SNPs) Reflecting Haplotype Phylogeny for Efficient Selection of Tag SNPs
... Selection of one SNP from each of the complete LD subgroups constitutes a tag SNP set. For ex- ample, in the Japanese, there were seven LD groups. Among them, the topmost LD group consists of 10 SNPs, and it separates ...
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Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower
... W erner et al. 2005; G underson et al. 2006; S yvanen 2001, 2005). SNP abundance in sunflower and other plant genomes: The genic loci we sampled supply an estimate of the number of common SNPs in the sunflower ...
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Network analysis of single nucleotide polymorphisms in asthma
... Family studies using linkage methodologies conducted to date have not been very successful in identifying the genetic determinants of this complex disease. 10 The revolution in genotyping technology with high-throughput ...
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Single nucleotide polymorphisms and disease gene mapping
... Although much is known about patterns of LD within the MHC, the important outstanding question for human genet- ics is whether the same pattern of LD exists elsewhere in the genome. The large, dense set of SNPs ...
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Ultraconserved Elements in the Human Genome: Association and Transmission Analyses of Highly Constrained Single-Nucleotide Polymorphisms
... human genome likely harbor important biological functions as they are dosage sensitive and are able to direct tissue-specific ...distributed genome-wide among ultraconserved and nearly ultraconserved ...
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Effect of population stratification on the identification of significant single nucleotide polymorphisms in genome wide association studies
... We used the stratification score of Epstein et al. to adjust our analyses for confounding due to population stratification [7]. The authors focus on adjusting association tests using a limited number of ancestry- ...
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Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing
... tionary path that passes through the root (Fig. 6C), the outgroup will be contained by itself at a node, indicating the precise location of the root for the B. anthracis phylogeny. On the other hand, when ...
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The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome
... A 4 G and A 4 C/G 4 T, the true neighborhood patterns for A 4 T and C 4 G might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the ...
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Role of single nucleotide polymorphisms (SNPs) in common migraine
... GWAS: Genome-wide association study; HMG: Hydroxy methyl glutarate; KCCN3: Potassium calcium-activated channel subfamily N member 3; LRP1: Lipoprotein receptor 1; MA: Migraine with aura; MEF2D: Myocyte enhancer ...
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Identification of functional single nucleotide polymorphisms in the branchpoint site
... human genome contains millions of single nucleotide polymorphisms (SNPs); many of these SNPs are intronic and have unknown functional ...a genome-wide branchpoint site SNP ...
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Single nucleotide polymorphisms (SNPs) in occupational exposure assessment
... 84 3.5 Discussion In this second SNP genetic association with quantitative biomarker level study in exposure assessment, we provide useful information and analysis of the impact of individual genetic variability on a ...
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