next-generation sequencing next-generation sequencing ngs Search Results


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  • 99
    Thermo Fisher next generation sequencing ngs platform
    Characteristics of sample reads by platform. (A) Average number of reads produced, (B) percent of reads mapped to the reference sample, (C) the number of contigs within the assembly, (D) total number of basepairs assembled; dashed red line represent the bps in the reference, and (E) the N50 of the assembly. Boxes depict the interquartile (IQR) range and whiskers indicate 1.5 IQR; the horizontal black line represents the mean. The <t>IonTorrent</t> platform is abbreviated as IonT. Points represent observed values; points were also offset from one another (‘jittered’) to reduce overlap. See Table 1 for sample sizes per <t>NGS</t> platform.
    Next Generation Sequencing Ngs Platform, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher next generation sequencing ngs
    Characteristics of sample reads by platform. (A) Average number of reads produced, (B) percent of reads mapped to the reference sample, (C) the number of contigs within the assembly, (D) total number of basepairs assembled; dashed red line represent the bps in the reference, and (E) the N50 of the assembly. Boxes depict the interquartile (IQR) range and whiskers indicate 1.5 IQR; the horizontal black line represents the mean. The <t>IonTorrent</t> platform is abbreviated as IonT. Points represent observed values; points were also offset from one another (‘jittered’) to reduce overlap. See Table 1 for sample sizes per <t>NGS</t> platform.
    Next Generation Sequencing Ngs, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 166 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc next generation sequencing ngs platforms
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Next Generation Sequencing Ngs Platforms, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 179 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher benchtop next generation sequencing ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Benchtop Next Generation Sequencing Ngs, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc next generation sequencing ngs platform
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Next Generation Sequencing Ngs Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 96/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc miseq next generation sequencing ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Miseq Next Generation Sequencing Ngs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 61 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Welgene Biotech next generation sequencing ngs analysis
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Next Generation Sequencing Ngs Analysis, supplied by Welgene Biotech, used in various techniques. Bioz Stars score: 88/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    82
    Roche next generation sequencing platforms ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Next Generation Sequencing Platforms Ngs, supplied by Roche, used in various techniques. Bioz Stars score: 82/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Diagenode bioruptor next generation sequencing ngs ultrasonicator
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Bioruptor Next Generation Sequencing Ngs Ultrasonicator, supplied by Diagenode, used in various techniques. Bioz Stars score: 97/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher pgm next generation sequencing ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Pgm Next Generation Sequencing Ngs, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    83
    PerkinElmer zephyr next generation sequencing ngs workstation
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Zephyr Next Generation Sequencing Ngs Workstation, supplied by PerkinElmer, used in various techniques. Bioz Stars score: 83/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Guardant Health standard next generation sequencing ngs techniques
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Standard Next Generation Sequencing Ngs Techniques, supplied by Guardant Health, used in various techniques. Bioz Stars score: 83/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Welgene Biotech rna next generation sequencing ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Rna Next Generation Sequencing Ngs, supplied by Welgene Biotech, used in various techniques. Bioz Stars score: 80/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Solexa next generation sequencing ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Next Generation Sequencing Ngs, supplied by Solexa, used in various techniques. Bioz Stars score: 87/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Becton Dickinson next generation sequencing ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Next Generation Sequencing Ngs, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    GeneDx Inc next generation sequencing ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Next Generation Sequencing Ngs, supplied by GeneDx Inc, used in various techniques. Bioz Stars score: 91/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Epigenomics next generation sequencing ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Next Generation Sequencing Ngs, supplied by Epigenomics, used in various techniques. Bioz Stars score: 97/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Biotechnology Information next generation sequencing ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Next Generation Sequencing Ngs, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 87/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Ambry Genetics next generation sequencing ngs
    Specific validation of biomarker <t>miRNAs</t> and their discrimination power. (A) We used qPCR to validate the expression profiles through <t>NGS</t> in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P
    Next Generation Sequencing Ngs, supplied by Ambry Genetics, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Personal Genome Diagnostics Inc next generation sequencing ngs
    Study design. The study design coupled pre-analytical FFPE DNA characterization across three methods (spectrophotometry, fluorescence dye-based quantification, and QFI-PCR) with variant calling results from targeted <t>NGS</t> and confirmation assays to assess the impact of template quality and set thresholds for minimum ‘functional’ DNA inputs. dsDNA, double-stranded DNA; HS, high sensitivity.
    Next Generation Sequencing Ngs, supplied by Personal Genome Diagnostics Inc, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Foundation Medicine Inc next generation sequencing ngs
    Characterization of RET fusions in CRC patients A. Frequency of RET fusions in unselected metastatic CRC patients as detected by <t>NGS.</t> B. Genetic and clinicopathologic characteristics of 6 patients harboring RET fusion kinase. nd = no data and WT = wild type. C. Fusion of CCDC6 exon 11 (green) containing the coiled-coil domain to RET exon 11 (red) containing the tyrosine kinase domain to generate CCDC6-RET fusion kinase. D. Fusion of NCOAT exon 9 (orange) containing the coiled-coil domain to RET exon 12 (red) containing the tyrosine domain to generate NCOAT-RET fusion kinase.
    Next Generation Sequencing Ngs, supplied by Foundation Medicine Inc, used in various techniques. Bioz Stars score: 87/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Kapa Biosystems next generation sequencing ngs
    Characterization of RET fusions in CRC patients A. Frequency of RET fusions in unselected metastatic CRC patients as detected by <t>NGS.</t> B. Genetic and clinicopathologic characteristics of 6 patients harboring RET fusion kinase. nd = no data and WT = wild type. C. Fusion of CCDC6 exon 11 (green) containing the coiled-coil domain to RET exon 11 (red) containing the tyrosine kinase domain to generate CCDC6-RET fusion kinase. D. Fusion of NCOAT exon 9 (orange) containing the coiled-coil domain to RET exon 12 (red) containing the tyrosine domain to generate NCOAT-RET fusion kinase.
    Next Generation Sequencing Ngs, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 88/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Agilent technologies next generation sequencing ngs
    Characterization of RET fusions in CRC patients A. Frequency of RET fusions in unselected metastatic CRC patients as detected by <t>NGS.</t> B. Genetic and clinicopathologic characteristics of 6 patients harboring RET fusion kinase. nd = no data and WT = wild type. C. Fusion of CCDC6 exon 11 (green) containing the coiled-coil domain to RET exon 11 (red) containing the tyrosine kinase domain to generate CCDC6-RET fusion kinase. D. Fusion of NCOAT exon 9 (orange) containing the coiled-coil domain to RET exon 12 (red) containing the tyrosine domain to generate NCOAT-RET fusion kinase.
    Next Generation Sequencing Ngs, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Genewiz next generation sequencing ngs
    Characterization of RET fusions in CRC patients A. Frequency of RET fusions in unselected metastatic CRC patients as detected by <t>NGS.</t> B. Genetic and clinicopathologic characteristics of 6 patients harboring RET fusion kinase. nd = no data and WT = wild type. C. Fusion of CCDC6 exon 11 (green) containing the coiled-coil domain to RET exon 11 (red) containing the tyrosine kinase domain to generate CCDC6-RET fusion kinase. D. Fusion of NCOAT exon 9 (orange) containing the coiled-coil domain to RET exon 12 (red) containing the tyrosine domain to generate NCOAT-RET fusion kinase.
    Next Generation Sequencing Ngs, supplied by Genewiz, used in various techniques. Bioz Stars score: 89/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Macrogen next generation sequencing ngs sequencing
    Characterization of RET fusions in CRC patients A. Frequency of RET fusions in unselected metastatic CRC patients as detected by <t>NGS.</t> B. Genetic and clinicopathologic characteristics of 6 patients harboring RET fusion kinase. nd = no data and WT = wild type. C. Fusion of CCDC6 exon 11 (green) containing the coiled-coil domain to RET exon 11 (red) containing the tyrosine kinase domain to generate CCDC6-RET fusion kinase. D. Fusion of NCOAT exon 9 (orange) containing the coiled-coil domain to RET exon 12 (red) containing the tyrosine domain to generate NCOAT-RET fusion kinase.
    Next Generation Sequencing Ngs Sequencing, supplied by Macrogen, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Oxford Gene Technology next generation sequencing ngs
    Characterization of RET fusions in CRC patients A. Frequency of RET fusions in unselected metastatic CRC patients as detected by <t>NGS.</t> B. Genetic and clinicopathologic characteristics of 6 patients harboring RET fusion kinase. nd = no data and WT = wild type. C. Fusion of CCDC6 exon 11 (green) containing the coiled-coil domain to RET exon 11 (red) containing the tyrosine kinase domain to generate CCDC6-RET fusion kinase. D. Fusion of NCOAT exon 9 (orange) containing the coiled-coil domain to RET exon 12 (red) containing the tyrosine domain to generate NCOAT-RET fusion kinase.
    Next Generation Sequencing Ngs, supplied by Oxford Gene Technology, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ArcherDX next generation sequencing ngs
    Characterization of RET fusions in CRC patients A. Frequency of RET fusions in unselected metastatic CRC patients as detected by <t>NGS.</t> B. Genetic and clinicopathologic characteristics of 6 patients harboring RET fusion kinase. nd = no data and WT = wild type. C. Fusion of CCDC6 exon 11 (green) containing the coiled-coil domain to RET exon 11 (red) containing the tyrosine kinase domain to generate CCDC6-RET fusion kinase. D. Fusion of NCOAT exon 9 (orange) containing the coiled-coil domain to RET exon 12 (red) containing the tyrosine domain to generate NCOAT-RET fusion kinase.
    Next Generation Sequencing Ngs, supplied by ArcherDX, used in various techniques. Bioz Stars score: 89/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Nugen next generation sequencing ngs
    Characterization of RET fusions in CRC patients A. Frequency of RET fusions in unselected metastatic CRC patients as detected by <t>NGS.</t> B. Genetic and clinicopathologic characteristics of 6 patients harboring RET fusion kinase. nd = no data and WT = wild type. C. Fusion of CCDC6 exon 11 (green) containing the coiled-coil domain to RET exon 11 (red) containing the tyrosine kinase domain to generate CCDC6-RET fusion kinase. D. Fusion of NCOAT exon 9 (orange) containing the coiled-coil domain to RET exon 12 (red) containing the tyrosine domain to generate NCOAT-RET fusion kinase.
    Next Generation Sequencing Ngs, supplied by Nugen, used in various techniques. Bioz Stars score: 87/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc next generation sequencer ngs
    The advancement of <t>next‐generation</t> sequencing ( <t>NGS</t> ) technology. (a and b) The decreasing pattern of NGS ‐based costs (per Mb). (c) The number of published genome papers from 2002 to 2014. (d) The genome size distribution of plants that have been sequenced. (e) The advancement of the Pacific Bioscience (PacBio) read length. (f) Accumulated NGS sequences in the Sequence Read Archive ( SRA ) for each plant species. (g) Pie chart of the NGS platforms of which sequences have been deposited in SRA .
    Next Generation Sequencer Ngs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    CLC Bio next generation sequencing ngs
    The advancement of <t>next‐generation</t> sequencing ( <t>NGS</t> ) technology. (a and b) The decreasing pattern of NGS ‐based costs (per Mb). (c) The number of published genome papers from 2002 to 2014. (d) The genome size distribution of plants that have been sequenced. (e) The advancement of the Pacific Bioscience (PacBio) read length. (f) Accumulated NGS sequences in the Sequence Read Archive ( SRA ) for each plant species. (g) Pie chart of the NGS platforms of which sequences have been deposited in SRA .
    Next Generation Sequencing Ngs, supplied by CLC Bio, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Medical Scientific and Chemicals Inc next generation sequencing ngs based method
    The advancement of <t>next‐generation</t> sequencing ( <t>NGS</t> ) technology. (a and b) The decreasing pattern of NGS ‐based costs (per Mb). (c) The number of published genome papers from 2002 to 2014. (d) The genome size distribution of plants that have been sequenced. (e) The advancement of the Pacific Bioscience (PacBio) read length. (f) Accumulated NGS sequences in the Sequence Read Archive ( SRA ) for each plant species. (g) Pie chart of the NGS platforms of which sequences have been deposited in SRA .
    Next Generation Sequencing Ngs Based Method, supplied by Medical Scientific and Chemicals Inc, used in various techniques. Bioz Stars score: 80/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Characteristics of sample reads by platform. (A) Average number of reads produced, (B) percent of reads mapped to the reference sample, (C) the number of contigs within the assembly, (D) total number of basepairs assembled; dashed red line represent the bps in the reference, and (E) the N50 of the assembly. Boxes depict the interquartile (IQR) range and whiskers indicate 1.5 IQR; the horizontal black line represents the mean. The IonTorrent platform is abbreviated as IonT. Points represent observed values; points were also offset from one another (‘jittered’) to reduce overlap. See Table 1 for sample sizes per NGS platform.

    Journal: PeerJ

    Article Title: An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella

    doi: 10.7717/peerj.620

    Figure Lengend Snippet: Characteristics of sample reads by platform. (A) Average number of reads produced, (B) percent of reads mapped to the reference sample, (C) the number of contigs within the assembly, (D) total number of basepairs assembled; dashed red line represent the bps in the reference, and (E) the N50 of the assembly. Boxes depict the interquartile (IQR) range and whiskers indicate 1.5 IQR; the horizontal black line represents the mean. The IonTorrent platform is abbreviated as IonT. Points represent observed values; points were also offset from one another (‘jittered’) to reduce overlap. See Table 1 for sample sizes per NGS platform.

    Article Snippet: Given the impact that conclusions derived from such analyses may have, we have evaluated the robustness of clustering individuals based on WGS data to three key factors: (1) next-generation sequencing (NGS) platform (HiSeq, MiSeq, IonTorrent, 454, and SOLiD), (2) algorithms used to construct a SNP (single nucleotide polymorphism) matrix (reference-based and reference-free), and (3) phylogenetic inference method (FastTreeMP, GARLI, and RAxML).

    Techniques: Produced, Next-Generation Sequencing

    Specific validation of biomarker miRNAs and their discrimination power. (A) We used qPCR to validate the expression profiles through NGS in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P

    Journal: Frontiers in Psychiatry

    Article Title: Blood-Bourne MicroRNA Biomarker Evaluation in Attention-Deficit/Hyperactivity Disorder of Han Chinese Individuals: An Exploratory Study

    doi: 10.3389/fpsyt.2018.00227

    Figure Lengend Snippet: Specific validation of biomarker miRNAs and their discrimination power. (A) We used qPCR to validate the expression profiles through NGS in all RNA samples from the Training Set. The Y-axis denotes the ΔCt values with U44 as the internal control. For each miRNA, * and * * denote P

    Article Snippet: We identified 20 candidate miRNAs with the next-generation sequencing (NGS) technique (Illumina).

    Techniques: Biomarker Assay, Real-time Polymerase Chain Reaction, Expressing, Next-Generation Sequencing

    Error rate distribution. Analysis of the NGS library preparation, Illumina MiSeq amplification and sequencing using 15,000 reads of P. aeruginosa DSM 50071 T . Substitution (blue), unknown base (red), and deletion (green) rates are shown.

    Journal: Frontiers in Microbiology

    Article Title: Pseudomonas-Specific NGS Assay Provides Insight Into Abundance and Dynamics of Pseudomonas Species Including P. aeruginosa in a Cooling Tower

    doi: 10.3389/fmicb.2018.01958

    Figure Lengend Snippet: Error rate distribution. Analysis of the NGS library preparation, Illumina MiSeq amplification and sequencing using 15,000 reads of P. aeruginosa DSM 50071 T . Substitution (blue), unknown base (red), and deletion (green) rates are shown.

    Article Snippet: In the present study, an Illumina-based next-generation sequencing (NGS) approach using Pseudomonas -specific primers targeting the 16S rRNA gene was evaluated and applied to a set of freshwater samples from different environments including a cooling tower sampled monthly during 2 years.

    Techniques: Next-Generation Sequencing, Amplification, Sequencing

    Study design. The study design coupled pre-analytical FFPE DNA characterization across three methods (spectrophotometry, fluorescence dye-based quantification, and QFI-PCR) with variant calling results from targeted NGS and confirmation assays to assess the impact of template quality and set thresholds for minimum ‘functional’ DNA inputs. dsDNA, double-stranded DNA; HS, high sensitivity.

    Journal: Genome Medicine

    Article Title: Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies

    doi: 10.1186/gm481

    Figure Lengend Snippet: Study design. The study design coupled pre-analytical FFPE DNA characterization across three methods (spectrophotometry, fluorescence dye-based quantification, and QFI-PCR) with variant calling results from targeted NGS and confirmation assays to assess the impact of template quality and set thresholds for minimum ‘functional’ DNA inputs. dsDNA, double-stranded DNA; HS, high sensitivity.

    Article Snippet: Abbreviations Bp: Base pair; CI: Confidence interval; Cq: Quantification cycle; CV: Coefficient of variation; FFPE: Formalin-fixed paraffin-embedding/embedded; HS: High sensitivity; Nex-StoCT: Next-generation Sequencing Standardization of Clinical Testing; NGS: Next-generation sequencing; PCR: Polymerase chain reaction; PGM: Personal Genome Machine; QFI: Quantitative functional index; qPCR: quantitative polymerase chain reaction; SNP: Single-nucleotide polymorphism.

    Techniques: Formalin-fixed Paraffin-Embedded, Spectrophotometry, Fluorescence, Polymerase Chain Reaction, Variant Assay, Next-Generation Sequencing, Functional Assay

    Effect of amplifiable FFPE DNA copy number on the detection of mutational load by targeted NGS. The amplifiable DNA copy number (Cp#) for two clinical FFPE samples was calculated to be 370 and 289 copies based on the QFI (9% for both samples) and a well-characterized mutation frequency of 30.0 ± 3.4% for BRAF V600E or 38.4 ± 4.6% for PIK3CA H1047R, respectively. BRAF and PIK3CA loci were enriched using PCR [ 14 ] and sequenced on the MiSeq. The graph shows a dilution series of the DNA, from 24 to 3,030 amplifiable DNA copies and each point (blue, BRAF ; red, PIK3CA ) represents the fraction of reads with the target mutation.

    Journal: Genome Medicine

    Article Title: Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies

    doi: 10.1186/gm481

    Figure Lengend Snippet: Effect of amplifiable FFPE DNA copy number on the detection of mutational load by targeted NGS. The amplifiable DNA copy number (Cp#) for two clinical FFPE samples was calculated to be 370 and 289 copies based on the QFI (9% for both samples) and a well-characterized mutation frequency of 30.0 ± 3.4% for BRAF V600E or 38.4 ± 4.6% for PIK3CA H1047R, respectively. BRAF and PIK3CA loci were enriched using PCR [ 14 ] and sequenced on the MiSeq. The graph shows a dilution series of the DNA, from 24 to 3,030 amplifiable DNA copies and each point (blue, BRAF ; red, PIK3CA ) represents the fraction of reads with the target mutation.

    Article Snippet: Abbreviations Bp: Base pair; CI: Confidence interval; Cq: Quantification cycle; CV: Coefficient of variation; FFPE: Formalin-fixed paraffin-embedding/embedded; HS: High sensitivity; Nex-StoCT: Next-generation Sequencing Standardization of Clinical Testing; NGS: Next-generation sequencing; PCR: Polymerase chain reaction; PGM: Personal Genome Machine; QFI: Quantitative functional index; qPCR: quantitative polymerase chain reaction; SNP: Single-nucleotide polymorphism.

    Techniques: Formalin-fixed Paraffin-Embedded, Next-Generation Sequencing, Mutagenesis, Polymerase Chain Reaction

    Effect of FFPE DNA copy number on NGS variant calling using a commercial targeted enrichment cancer panel. A) Correlation between QFI and number of variants detected on the PGM following enrichment using the AmpliSeq Cancer Panel. (B) Samples with the lowest QFI produced a significantly larger number of variants from AmpliSeq NGS compared to those with > 6% QFI ( P -value 0.006).

    Journal: Genome Medicine

    Article Title: Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies

    doi: 10.1186/gm481

    Figure Lengend Snippet: Effect of FFPE DNA copy number on NGS variant calling using a commercial targeted enrichment cancer panel. A) Correlation between QFI and number of variants detected on the PGM following enrichment using the AmpliSeq Cancer Panel. (B) Samples with the lowest QFI produced a significantly larger number of variants from AmpliSeq NGS compared to those with > 6% QFI ( P -value 0.006).

    Article Snippet: Abbreviations Bp: Base pair; CI: Confidence interval; Cq: Quantification cycle; CV: Coefficient of variation; FFPE: Formalin-fixed paraffin-embedding/embedded; HS: High sensitivity; Nex-StoCT: Next-generation Sequencing Standardization of Clinical Testing; NGS: Next-generation sequencing; PCR: Polymerase chain reaction; PGM: Personal Genome Machine; QFI: Quantitative functional index; qPCR: quantitative polymerase chain reaction; SNP: Single-nucleotide polymorphism.

    Techniques: Formalin-fixed Paraffin-Embedded, Next-Generation Sequencing, Variant Assay, Produced

    Characterization of RET fusions in CRC patients A. Frequency of RET fusions in unselected metastatic CRC patients as detected by NGS. B. Genetic and clinicopathologic characteristics of 6 patients harboring RET fusion kinase. nd = no data and WT = wild type. C. Fusion of CCDC6 exon 11 (green) containing the coiled-coil domain to RET exon 11 (red) containing the tyrosine kinase domain to generate CCDC6-RET fusion kinase. D. Fusion of NCOAT exon 9 (orange) containing the coiled-coil domain to RET exon 12 (red) containing the tyrosine domain to generate NCOAT-RET fusion kinase.

    Journal: Oncotarget

    Article Title: Identification and characterization of RET fusions in advanced colorectal cancer

    doi:

    Figure Lengend Snippet: Characterization of RET fusions in CRC patients A. Frequency of RET fusions in unselected metastatic CRC patients as detected by NGS. B. Genetic and clinicopathologic characteristics of 6 patients harboring RET fusion kinase. nd = no data and WT = wild type. C. Fusion of CCDC6 exon 11 (green) containing the coiled-coil domain to RET exon 11 (red) containing the tyrosine kinase domain to generate CCDC6-RET fusion kinase. D. Fusion of NCOAT exon 9 (orange) containing the coiled-coil domain to RET exon 12 (red) containing the tyrosine domain to generate NCOAT-RET fusion kinase.

    Article Snippet: Next generation sequencing Next-generation sequencing (NGS) assay covering 3,769 exons of 236 cancer-related genes and 47 introns of 19 genes frequently rearranged in cancer ( ) was performed by Foundation Medicine, Inc., a CLIA-certified and CAP-accredited laboratory, based on a modified published protocol.

    Techniques: Next-Generation Sequencing

    The advancement of next‐generation sequencing ( NGS ) technology. (a and b) The decreasing pattern of NGS ‐based costs (per Mb). (c) The number of published genome papers from 2002 to 2014. (d) The genome size distribution of plants that have been sequenced. (e) The advancement of the Pacific Bioscience (PacBio) read length. (f) Accumulated NGS sequences in the Sequence Read Archive ( SRA ) for each plant species. (g) Pie chart of the NGS platforms of which sequences have been deposited in SRA .

    Journal: Plant Biotechnology Journal

    Article Title: Translational genomics for plant breeding with the genome sequence explosion

    doi: 10.1111/pbi.12449

    Figure Lengend Snippet: The advancement of next‐generation sequencing ( NGS ) technology. (a and b) The decreasing pattern of NGS ‐based costs (per Mb). (c) The number of published genome papers from 2002 to 2014. (d) The genome size distribution of plants that have been sequenced. (e) The advancement of the Pacific Bioscience (PacBio) read length. (f) Accumulated NGS sequences in the Sequence Read Archive ( SRA ) for each plant species. (g) Pie chart of the NGS platforms of which sequences have been deposited in SRA .

    Article Snippet: Leading manufacturers of the next‐generation sequencer (NGS), such as Illumina and Pacific Biosciences (PacBio), have continuously launched new sequencing chemistries and platforms that decrease sequencing cost and increase read length and reliability.

    Techniques: Next-Generation Sequencing, Sequencing