high-throughput DNA sequencing
High throughput DNA sequencing to detect differences in the subgingival plaque microbiome in elderly subjects with and without dementia
... of high throughput DNA sequencing and bioinformatics tools provide a broadly available and increasingly cost ef- fective method to identify bacterial populations found in polymicrobial ...
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CODEX2: full spectrum copy number variation detection by high throughput DNA sequencing
... heterogeneity and normal cell contamination, copy num- bers may not be integers and are assumed to be continu- ous and fractional to represent attenuated mean estimates of the genome mixtures. We categorize a CNA event ...
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Spectrum of mutations in monogenic diabetes genes identified from high-throughput DNA sequencing of 6888 individuals
... exome sequencing study found a modest but statistically significant enrichment of rare deleterious vari- ants in monogenic diabetes genes in individuals with T2D compared to controls ...
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Coupling Unbiased Mutagenesis to High-throughput DNA Sequencing Uncovers Functional Domains in the Ndc80 Kinetochore Protein of Saccharomyces cerevisiae
... ABSTRACT During mitosis, kinetochores physically link chromosomes to the dynamic ends of spindle microtubules. This linkage depends on the Ndc80 complex, a conserved and essential microtubule-binding component of the ...
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From cheek swabs to consensus sequences : an A to Z protocol for high throughput DNA sequencing of complete human mitochondrial genomes
... the DNA-bead mixture on a SPRIPlate and then discard- ing the derived buffer as per the manufacturer’s ...short DNA fragments and any buffer components from previous ...size-selected sequencing ...
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B cell repertoires in HLA sensitized kidney transplant candidates undergoing desensitization therapy
... a high-throughput DNA sequencing assay to measure circulating B cell reper- toires in highly HLA-sensitized kidney transplant candi- dates undergoing desensitization therapy to lower HLA ...
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Identification of RUNX2 variants associated with cleidocranial dysplasia
... Background: Cleidocranial dysplasia (CCD) is a rare autosomal dominant disorder mainly characterized by hypoplastic or absent clavicles, delayed closure of the fontanelles, multiple dental abnormalities, and short ...
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Application of resequencing to rice genomics, functional genomics and evolutionary analysis
... for high-throughput measurements of gene expression levels (Jiao et ...next-generation high-throughput DNA sequencing technologies, RNA-seq has shown ad- vantages over ...
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Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing
... In our research, the intergenic regions contained the largest number of RNA editing sites, which is different from humans, where intronic editing sites are the most common. A possible explanation for the difference is ...
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Non-invasive diagnosis of early-stage lung cancer using high-throughput targeted DNA methylation sequencing of circulating tumor DNA (ctDNA)
... by DNA methyltransferases and DNA demethylases, which plays a critical role in the maintenance of heterochromatin structure and regulation of gene expression during development ...abnormal DNA ...
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Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization
... The quality of the raw reads was assessed by Fast QC v0.10.1. Raw reads were trimmed and quality-filtered with a FASTX-Toolkit v 0.013 to give 90-bp length reads with 90% of bases having a minimum Phred score of 20. To ...
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Abnormal plasma DNA profiles in early ovarian cancer using a non-invasive prenatal testing platform: implications for cancer screening
... deep sequencing [10, ...tumor DNA using an existing low coverage sequen- cing platform. Thus, high throughput whole genome plasma sequencing, with or without the addition of other ...
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Protocol: a versatile, inexpensive, high-throughput plant genomic DNA extraction method suitable for genotyping-by-sequencing
... freeze-drier and apply an effective vacuum as soon as possible. This avoids a pre-freezing stage and the poten- tial for tissue to thaw and cell components to rupture in the initial freeze-drying process, which we have ...
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Spontaneous Mutation Discovery via High-Throughput Sequencing of Pedigrees
... to DNA quantity-sensitive applications such as gene expression profiling 65 ...human sequencing is the Heliscope sequencer, sold by ...Heliscope sequencing error profile, and incorporating a naïve ...
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Analysis options for high throughput sequencing in miRNA expression profiling
... library DNA) seed analysis pipeline C (r = ...library DNA (r = ...and high-throughput sequencing data are highly correlated when the appropriate analysis method (seed analysis pipeline ...
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Empirical assessment of sequencing errors for high throughput pyrosequencing data
... the sequencing error characteristics of GS FLX data through the analysis of the sequence ...control DNA fragments over three runs of the GS FLX Titanium ...
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Assessing Illumina technology for the high throughput sequencing of bacteriophage genomes
... the sequencing of phage isolates have previously been discussed in detail (Klumpp, Fouts & Sozhamannan, ...Previously sequencing of phage genomes had been problematic due to cloning phage DNA for ...
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Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches
... Plasma samples for unbiased HTS were centrifuged at 10,000 ⫻ g for 10 min. The supernatant was treated with 40 U of Turbo DNase (Ambion, Rotkreuz, Switzerland) prior to RNA and DNA extraction and library ...
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High-throughput sequencing of cytosine methylation in plant DNA
... Despite the progress being made in analysis of high- throughput sequencing data and specifically that pertain- ing to the methylome, there exist some clear areas for improvement. The question of ...
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Validation of high throughput sequencing and microbial forensics applications
... Inc.) sequencing preparation method requires approximately 100 ng to 1 μg [77], Haloplex (Agilent, Santa Clara, CA, USA) 225 ng [78], Nextera XT (Illumina) 1 ng [79], and polymerase chain reaction (PCR)-based ...
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