Genome alignment and single-nucleotide polymorphism calling
Genome-Wide Single-Nucleotide Polymorphism Map for Candida albicans
... LOH in selected strains of C. albicans. To address concerns that various genetic manipulations such as transformation or growth on selective media might increase the rate of LOH, we examined loci that had been targets of ...
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Whole genome sequencing of a single Bos taurusanimal for single nucleotide polymorphism discovery
... Conclusions By sequencing a single diploid genome to a depth of 7.4-fold, we were able to generate more than 2 million SNPs, thereby almost doubling the existing SNP resource in cattle. We eval- uated the ...
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Assessment of Linkage Disequilibrium in Potato Genome With Single Nucleotide Polymorphism Markers
... potato genome. Analysis of these fragments indicates relatively high nucleotide variation in potato as compared to other plant ...biallelic nucleotide substitutions with equal frequency of ...
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Application of sex specific single nucleotide polymorphism filters in genome wide association data
... autosomal single-nucleotide polymorphisms flagged by sex quality control filters were missed by filters of call rate at 95% and Hardy-Weinberg equilibrium at 10 -6 ...two single-nucleotide ...
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Software for tag single nucleotide polymorphism selection
... human genome in 270 subjects sampled from four different ethnic groups, are now available for haplotype discovery, and thus may be con- sidered for the use of tag SNP ...
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Fine-Scale Estimation of Location of Birth from Genome-Wide Single-Nucleotide Polymorphism Data
... Figure 3A shows a box plot of the distance between the predicted and true location of parental birthplace strati fi ed by region of birth of the parents (for individuals with both parents[r] ...
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Rapid High Resolution Single Nucleotide Polymorphism–Comparative Genome Hybridization Mapping in Caenorhabditis elegans
... Accepted for publication October 24, 2008 ABSTRACT We have developed a significantly improved and simplified method for high-resolution mapping of phenotypic traits in Caenorhabditis elegans using a combination of ...
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Single nucleotide polymorphism-based genome-wide linkage analysis in Japanese atopic dermatitis families
... approach, genome-wide linkage analysis, and across the entire genome polymorphic DNA markers positioned at specific intervals along each chromosome are screened for linkage to the disease of ...4 ...
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Comparison of genome wide single nucleotide polymorphism linkage analyses in Caucasian and Hispanic NARAC families
... showed genome-wide significant evidence for linkage in Caucasians for chromosomes 2q and 6p, but no significant evidence for any linkages in the Hispanics, including little evidence for linkage to chromosome 6p in ...
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Transmission and evolution of "Mycobacterium tuberculosis" studied by whole genome sequencing and single nucleotide polymorphism-typing
... whole genome sequencing to delineate micro- and macroevolutionary events in a transmission cluster and on the global diversity ...a single genotype causing a TB outbreak in Bern, Switzerland, over two ...
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High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays
... Introduction Single nucleotide polymorphisms (SNPs) are the most common genetic variants in the human genome, and it is believed that more than 10 million common SNPs with minor-allele frequency N1% ...
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Towards pan-genome read alignment to improve variation calling
... variation calling on com- plex regions with larger indels and/or densely located simpler variants, where significant improvements are still ...ular single-reference based indexing approach with a highly ...
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Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads
... We then examined the corresponding WES tumor data for evidence of the mosaic call made in the WGS data. We considered a mosaic variant call to be ‘‘validated’’ if (1) the corresponding WES tumor sample had at least 50 ...
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A single nucleotide polymorphism in the Epstein-Barr virus genome is strongly associated with a high risk of nasopharyngeal carcinoma
... whole genome sequence of EBV to define haplotypes, instead of a single SNP, for genotyp- ing the virus detected in healthy subjects or patients with different disorders and different ...
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Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections
... the genome. However, the choice of a reference genome can significantly influence the number of identified SNPs and the accuracy of the reconstructed phylogenetic relationships ...
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Genome-Wide Single-Nucleotide Polymorphism Array Analysis Improves Prognostication of Acute Lymphoblastic Leukemia/Lymphoma
... It is not uncommon to have inadequate or normal cyto- genetic results in ALL, 2,5,6 which limits the value of karyo- typic analysis in prognostication of ALL. In this study, SNP arrays identi fied chromosome aberrations ...
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A General Overview of Detection Methods for Single Nucleotide Polymorphism
... reference genome sequence ...two-sequence alignment is based on the similarity between the two ...sequence alignment, while smith-waterman algorithm which has made some improvements on the former is ...
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Functional single nucleotide polymorphism-based association studies
... Conserved sequences Computational efforts have consistently found that approxi- mately 5 per cent of the human genome shows conservation with other species. 112,141 – 148 Although some regions may be conserved due ...
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Mapping of monogenic and quantitative trait loci using a whole genome scan approach and single nucleotide polymorphism platforms
... The recessive defect, hypotrichosis is an autosomal recessive form of hairlessness that affects Hereford cattle. A whole-genome association analysis was conducted using BovineSNP50 BeadChip to map the ...
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Genome wide single nucleotide polymorphism linkage analyses of quantitative rheumatoid arthritis phenotypes in Caucasian NARAC families
... We applied nonparametric quantitative trait linkage analysis to two rheumatoid arthritis quantitative phenotypes, IgM rheumatoid factor (RF) and anti-cyclic citrullinated peptide autoantibody titer measurements, using ...
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