variant detection
Automated Anonymization as Spelling Variant Detection
... The issue of privacy has always been a concern when clinical texts are used for research pur- poses. Personal health information (PHI) (such as name and identification number) needs to be removed so that patients cannot ...
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Systematic comparative analysis of single nucleotide variant detection methods from single cell RNA sequencing data
... One possible limitation of our study is that only two aligners, STAR and GSNAP, were compared, as our study mainly focused on the comparison of different variant cal- lers. STAR showed higher sensitivities than ...
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Comparison of somatic variant detection algorithms using Ion Torrent targeted deep sequencing data
... be variant to sequencing noise and filtered with a panel of normal samples to reduce miscalled germline ...as variant detection but with more stringent threshold ...
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Cpipe: a shared variant detection pipeline designed for diagnostic settings
... Prioritisation, categorisation and filtering of variants One of the most significant challenges in bringing high throughput sequencing into routine clinical care is that of scaling the difficult and highly manual job of ...
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Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
... Crowdsourced benchmarking of somatic SV calling The SV component of the Challenge consisted of the same three synthetic tumor-normal datasets used in the SNV component [10]. Briefly, the datasets were derived from ...
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Terminology Extraction with Term Variant Detection
... Since the first TermSuite release (Rocheteau and Daille, 2011), several enhancements about TET have been made. We developed UIMA To- kens Regex, a tool to define term and variant pat- terns using word annotations ...
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Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine
... transcript detection from RNA-seq is commonly used [2–4], use of RNA-seq for SNV or Indel mutation detection in clinical settings is still rare, which is contributed by several ...reasons. Detection ...
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“Omics” data integration and functional analyses link Enoyl-CoA hydratase, short chain 1 to drug refractory dilated cardiomyopathy
... and variant detection is a versatile approach to tease out genes that are causal from those that are effect modi- ...pathogenic variant in DBT, a differentially expressed gene provides added ...
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It Is Not All about Single Nucleotide Polymorphisms: Comparison of Mobile Genetic Elements and Deletions in Listeria monocytogenes Genomes Links Cases of Hospital Acquired Listeriosis to the Environmental Source
... Assembly and phylogenetic analysis. De novo assembly was per- formed on sequencing reads using the Torrent suite assembler plugin version 3.4.2.0, which uses MIRA (version 3.9.9) to assemble contigs. The contigs were ...
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Assessing biases of information contained in pedigrees for the classification of BRCA-genetic variants: a study arising from the ENIGMA analytical working group
... pathogenic variant than in wt families, which is one of the factors that explains why pathogenic variant detection probabilities were different between the most recent and the intake pedigree in ...
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Rapid Differentiation of Mixed Influenza A/H1N1 Virus Infections with Seasonal and Pandemic Variants by Multitemperature Single Stranded Conformational Polymorphism Analysis
... minor variant enrichment ...genetic variant detection procedure based on the MSSCP separation, RT-PCR products of the hemagglutinin gene region from seasonal and pandemic variants were mixed at ...
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Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease
... Overall, we have identified pathogenic variants for 404/722 individuals with IRD in the NIHR-BioResource Rare Diseases study, which is a pathogenic variant detection rate of 56%. Factors that influence this ...
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Detection of rare variant effects in association studies: extreme values, iterative regression, and a hybrid approach
... power. In the iterative regression strategy, common sin- gle-nucleotide polymorphisms (SNPs) and rare variant combinations are tested first. Then a best variant is selected. The regression is repeated ...
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Efficient Mapping and Cloning of Mutations in Zebrafish by Low-Coverage Whole-Genome Sequencing
... mutation detection in zebrafish is the high level of inter- and intrastrain variation (Stickney et ...homozygous variant is a causative mutation or a low- frequency single-nucleotide polymorphism ...
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Molecular Epidemiology of Norovirus Gastroenteritis Investigated Using Samples Collected from Children in Tunisia during a Four Year Period: Detection of the Norovirus Variant GGII 4 Hunter as Early as January 2003
... Received 25 September 2008/Returned for modification 15 November 2008/Accepted 12 December 2008 Human noroviruses (NoVs) cause epidemic and endemic acute gastroenteritis in children and adults. To study the prevalence ...
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Exploiting T. monococcum as a model for detection of traits, genes and variant alleles and for identifying phenotype:genotype relationships
... functional genomic platform and will be used for novel allele mining by the TILLING technique. The gene RAR1, coding for one of the important signalling components in plant defence responses, has been selected as the ...
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Genetic variants of Anaplasma phagocytophilum from 14 equine granulocytic anaplasmosis cases
... gene variant “b” from this study has previously been detected in horses with EGA in Europe [15,19,38], but horses suffering from EGA from Italy (Sardinia) contained different variants, which were not detected in ...
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Identification of rare DNA sequence variants in high-risk autism families and their prevalence in a large case/control population
... calculation except those that failed sample quality con- trol (QC). Prior to calculating principal components, the SNPs were filtered according to the following criteria: autosomes only, call rate > 0.95, minor allele ...
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Original Article Detection of IDH1 and TERT promoter mutations with droplet digital PCR in diffuse gliomas
... A total of 80 patients who underwent intracra- nial tumor surgery were enrolled in this study. The clinical features of these patients are shown in Table 1. For these patients, 63.75% (51/80) were male, the median age at ...
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Object Detection and Motion Based Tracking Using LSK and Variant Mask Template Matching
... object detection and motion based tracking of moving ...object detection, second object tracking, third occlusion detection and object ...object detection is done through manually selection of ...
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