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Illumina Inc ngs platform
(A) Number of MDS variants (horizontal axis) in genes listed on the vertical axis. Colors indicate dynamics of the variants. Variants are also listed within the Supplementary Table 2 , the data were obtained by <t>NGS</t> utilizing the <t>TruSight</t> kit (see M M). (B) Mutation heatmap (row: genes, column: patients), unmutated genes are not listed.
Ngs Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 67 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Somatic mutation dynamics in MDS patients treated with azacitidine indicate clonal selection in patients-responders"

Article Title: Somatic mutation dynamics in MDS patients treated with azacitidine indicate clonal selection in patients-responders

Journal: Oncotarget

doi: 10.18632/oncotarget.22957

(A) Number of MDS variants (horizontal axis) in genes listed on the vertical axis. Colors indicate dynamics of the variants. Variants are also listed within the Supplementary Table 2 , the data were obtained by NGS utilizing the TruSight kit (see M M). (B) Mutation heatmap (row: genes, column: patients), unmutated genes are not listed.
Figure Legend Snippet: (A) Number of MDS variants (horizontal axis) in genes listed on the vertical axis. Colors indicate dynamics of the variants. Variants are also listed within the Supplementary Table 2 , the data were obtained by NGS utilizing the TruSight kit (see M M). (B) Mutation heatmap (row: genes, column: patients), unmutated genes are not listed.

Techniques Used: Next-Generation Sequencing, Mutagenesis

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Next-Generation Sequencing:

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Article Title: Don't just dump your data and run
Article Snippet: .. It contains DNA‐ and RNA‐sequencing (DNA‐seq and RNA‐seq) reads of every kind, from bisulfite‐seq to strand‐specific RNA‐seq to single‐cell DNA‐seq, and it accepts reads from every type of NGS platform, be it Illumina, Ion Torrent, or PacBio sequencing. ..

Article Title: Somatic mutation dynamics in MDS patients treated with azacitidine indicate clonal selection in patients-responders
Article Snippet: .. The NGS platform was the TruSight Myeloid Sequencing Panel (Illumina, San Diego, USA) that is a set of 568 amplicons and 108 kilobases designed to detect somatic variants of 54 genes previously associated with myeloid malignancies. .. 92% of our MDS cohort bore at least one somatic mutation with mostly 3 mutations per patient (range 1-8).

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Sequencing:

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Article Title: Somatic mutation dynamics in MDS patients treated with azacitidine indicate clonal selection in patients-responders
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Polymerase Chain Reaction:

Article Title: HLA-G Haplotypes Are Differentially Associated with Asthmatic Features
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Bisulfite Sequencing:

Article Title: Don't just dump your data and run
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    Illumina Inc ngs platforms
    <t>HIV-1</t> diversity in cervical samples and blood at very early and early infection. Average nucleotide p-distance (s/nt) and the number of unique sequences were analyzed following <t>NGS.</t> Average distance and number of unique sequences of cervical (red symbols and boxplot) and plasma (blue symbols and boxplot) samples were grouped into very early (0–3 months) and early infection (3–7 months) ( A-D ). Analysis of significance was done using a two-tailed Mann-Whitney test. Each symbol represents an individual subject.
    Ngs Platforms, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 73 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ngs platforms/product/Illumina Inc
    Average 93 stars, based on 73 article reviews
    Price from $9.99 to $1999.99
    ngs platforms - by Bioz Stars, 2020-07
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    Illumina Inc ngs illumina hiseq 2000 platform
    HIV-1 mutant library and <t>NGS</t> sample preparation. (A) Genomic region for each HIV-1 mutation library. (B) The two-step PCR amplicon approach for NGS sample preparation. Virion cDNA from each mutant viral population cell passage is used as template for a HIV-1 specific staggered PCR step that uses primers specific to the HIV-1 mutagenized region containing overhangs with a complex 10 ‘N’ nucleotide tag with two keto “K” or amino “M” nucleotide positions that identify the specific fragment and population, respectively. PCR products from step one are pooled, the amplicon molecule concentration is accurately measured, and then decreased for error correction. The pooled sample is then used as template for a second PCR using a single primer set containing the remainder of the <t>Illumina</t> adapter region for NGS.
    Ngs Illumina Hiseq 2000 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc illumina ngs platform
    HIV-1 mutant library and <t>NGS</t> sample preparation. (A) Genomic region for each HIV-1 mutation library. (B) The two-step PCR amplicon approach for NGS sample preparation. Virion cDNA from each mutant viral population cell passage is used as template for a HIV-1 specific staggered PCR step that uses primers specific to the HIV-1 mutagenized region containing overhangs with a complex 10 ‘N’ nucleotide tag with two keto “K” or amino “M” nucleotide positions that identify the specific fragment and population, respectively. PCR products from step one are pooled, the amplicon molecule concentration is accurately measured, and then decreased for error correction. The pooled sample is then used as template for a second PCR using a single primer set containing the remainder of the <t>Illumina</t> adapter region for NGS.
    Illumina Ngs Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 121 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 91 stars, based on 121 article reviews
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    Image Search Results


    HIV-1 diversity in cervical samples and blood at very early and early infection. Average nucleotide p-distance (s/nt) and the number of unique sequences were analyzed following NGS. Average distance and number of unique sequences of cervical (red symbols and boxplot) and plasma (blue symbols and boxplot) samples were grouped into very early (0–3 months) and early infection (3–7 months) ( A-D ). Analysis of significance was done using a two-tailed Mann-Whitney test. Each symbol represents an individual subject.

    Journal: PLoS Pathogens

    Article Title: Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection

    doi: 10.1371/journal.ppat.1006754

    Figure Lengend Snippet: HIV-1 diversity in cervical samples and blood at very early and early infection. Average nucleotide p-distance (s/nt) and the number of unique sequences were analyzed following NGS. Average distance and number of unique sequences of cervical (red symbols and boxplot) and plasma (blue symbols and boxplot) samples were grouped into very early (0–3 months) and early infection (3–7 months) ( A-D ). Analysis of significance was done using a two-tailed Mann-Whitney test. Each symbol represents an individual subject.

    Article Snippet: In this study, we compared the results of deep sequencing the HIV V3 env region from chronically infected patient samples using four different NGS platforms: Illumina MiSeq, IonTorrent PGM, Roche 454, and PacBio RS.

    Techniques: Infection, Next-Generation Sequencing, Two Tailed Test, MANN-WHITNEY

    Higher HIV-1 diversity in the female genital tract than in blood within 7 months of infection. The HIV-1 C2-V3-C3 env region present in cervical (red symbols and red boxplot) and plasma (blue symbols and blue boxplot) samples were PCR amplified and analysed by NGS. The average p-distance (s/nt) of HIV sequences within C2-V3-C3 region were calculated using MEGA 6 with sequences below 200bp excluded from analysis ( A ). The number of unique sequences within each sample were identified using online Galaxy software to collapse all sequence reads for each sample ( B ). Frequency of clones in cervical ( C ) and plasma samples ( D ) were determined from the number of unique clones. Average distance ( E ) and the number of unique sequences ( F ) in cervical and plasma samples grouped by subtype of infection. Analysis of significance was done using a two-tailed Mann-Whitney test. Each symbol represents an individual subject.

    Journal: PLoS Pathogens

    Article Title: Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection

    doi: 10.1371/journal.ppat.1006754

    Figure Lengend Snippet: Higher HIV-1 diversity in the female genital tract than in blood within 7 months of infection. The HIV-1 C2-V3-C3 env region present in cervical (red symbols and red boxplot) and plasma (blue symbols and blue boxplot) samples were PCR amplified and analysed by NGS. The average p-distance (s/nt) of HIV sequences within C2-V3-C3 region were calculated using MEGA 6 with sequences below 200bp excluded from analysis ( A ). The number of unique sequences within each sample were identified using online Galaxy software to collapse all sequence reads for each sample ( B ). Frequency of clones in cervical ( C ) and plasma samples ( D ) were determined from the number of unique clones. Average distance ( E ) and the number of unique sequences ( F ) in cervical and plasma samples grouped by subtype of infection. Analysis of significance was done using a two-tailed Mann-Whitney test. Each symbol represents an individual subject.

    Article Snippet: In this study, we compared the results of deep sequencing the HIV V3 env region from chronically infected patient samples using four different NGS platforms: Illumina MiSeq, IonTorrent PGM, Roche 454, and PacBio RS.

    Techniques: Infection, Polymerase Chain Reaction, Amplification, Next-Generation Sequencing, Software, Sequencing, Clone Assay, Two Tailed Test, MANN-WHITNEY

    Logistics and feasibility of the study. a logistic workflow of the study, b inclusion criteria and number of patients with successful results, c anatomical distribution of biopsied lesions with breakdown by recruiting centre, d global distribution of patients by recruiting centre, e turnaround time for each patient with breakdown by recruiting centre, f median global turnaround time by recruiting centre, and g median delivery turnaround time by recruiting centre. In a , the Illumina sequencing and Affymetrix OncoScan SNP arrays were done as batch processes. 19 patients were sequenced by Illumina targeted NGS and 18 patients were genotyped using the Affymetrix SNP arrays. However, these are not fully overlapping subsets and only 14 (54%) patients had the full set of all three data types. In a and b , the Ion Torrent sequencing results were obtained in real-time and in ( e ), the darker shades indicate delivery turnaround time (TAT) whilst the lighter shades indicate global turnaround time. The colour codes for the recruiting centres in c to g are indicated in ( d )

    Journal: NPJ Breast Cancer

    Article Title: The AURORA pilot study for molecular screening of patients with advanced breast cancer–a study of the breast international group

    doi: 10.1038/s41523-017-0026-6

    Figure Lengend Snippet: Logistics and feasibility of the study. a logistic workflow of the study, b inclusion criteria and number of patients with successful results, c anatomical distribution of biopsied lesions with breakdown by recruiting centre, d global distribution of patients by recruiting centre, e turnaround time for each patient with breakdown by recruiting centre, f median global turnaround time by recruiting centre, and g median delivery turnaround time by recruiting centre. In a , the Illumina sequencing and Affymetrix OncoScan SNP arrays were done as batch processes. 19 patients were sequenced by Illumina targeted NGS and 18 patients were genotyped using the Affymetrix SNP arrays. However, these are not fully overlapping subsets and only 14 (54%) patients had the full set of all three data types. In a and b , the Ion Torrent sequencing results were obtained in real-time and in ( e ), the darker shades indicate delivery turnaround time (TAT) whilst the lighter shades indicate global turnaround time. The colour codes for the recruiting centres in c to g are indicated in ( d )

    Article Snippet: Both distributions were bimodal with 6 (35%) and 5 (29%) patients showing low values of α < 0.5 and α < 0.6 for the Ion Torrent and Illumina NGS platforms, respectively.

    Techniques: Sequencing, Next-Generation Sequencing

    Genome-wide copy number profiles inferred from SNP arrays and targeted NGS data. Genome-wide Log 2 ratio profiles of patient IJB0021 obtained using a SNP array b Ion Torrent and c Illumina targeted NGS data. The solid vertical lines represent chromosome boundaries whilst the dashed horizontal lines indicate canonical copy numbers inferred from the cancer cell fraction and ploidy of the sample, both estimated from the SNP array. The solid horizontal lines represent the segmented Log 2 ratios. Correlation of segmented Log 2 ratios between d the SNP array and the Ion Torrent platform, e the SNP arrays and the Illumina platform, and f the two NGS platforms for the same case patient. In a – c , the loci are sorted according to their coordinate on the human genome reference hg19/GRCh37. For ease of representation, they are plotted by indices

    Journal: NPJ Breast Cancer

    Article Title: The AURORA pilot study for molecular screening of patients with advanced breast cancer–a study of the breast international group

    doi: 10.1038/s41523-017-0026-6

    Figure Lengend Snippet: Genome-wide copy number profiles inferred from SNP arrays and targeted NGS data. Genome-wide Log 2 ratio profiles of patient IJB0021 obtained using a SNP array b Ion Torrent and c Illumina targeted NGS data. The solid vertical lines represent chromosome boundaries whilst the dashed horizontal lines indicate canonical copy numbers inferred from the cancer cell fraction and ploidy of the sample, both estimated from the SNP array. The solid horizontal lines represent the segmented Log 2 ratios. Correlation of segmented Log 2 ratios between d the SNP array and the Ion Torrent platform, e the SNP arrays and the Illumina platform, and f the two NGS platforms for the same case patient. In a – c , the loci are sorted according to their coordinate on the human genome reference hg19/GRCh37. For ease of representation, they are plotted by indices

    Article Snippet: Both distributions were bimodal with 6 (35%) and 5 (29%) patients showing low values of α < 0.5 and α < 0.6 for the Ion Torrent and Illumina NGS platforms, respectively.

    Techniques: Genome Wide, Next-Generation Sequencing

    Orthogonal cross-testing of substitution calls using Illumina NGS. a distribution of % concordance for single nucleotide substitutions indexed from the Ion Torrent and Illumina NGS platforms using different mutation callers, b % error rate of the different mutation callers over three substitution clusters compared to the Ion Torrent sequencing, c correlation of VAF for substitutions indexed from the Ion Torrent and Illumina NGS using a majority rule of any two of three mutation callers, d comparison of sequencing coverage between the Ion Torrent and Illumina NGS for substitutions in cluster 1 , e empirical cumulative distribution of theoretical residual coverage from the Illumina sequencing for substitutions in cluster 1 and cluster 2 false negatives, f comparison of sequencing coverage from the Ion Torrent NGS for substitutions in cluster 2 false positives, and g comparison of sequencing coverage from the Illumina NGS for substitutions in cluster 2 false negatives. In a , the different mutation callers and any combination thereof are colour coded and indicated at the bottom. The leftmost panel gives the number of substitutions called. In b – g , the cluster numbers are relative to ( c ). Substitutions in clusters 1 and 3 are exclusive to one of the sequencing platforms and have 0% VAF in the alternate data. Substitutions in cluster 2 are those found by either or both NGS platforms and have non-zero VAF in both sequencing data. False negatives in cluster 2 are substitutions indexed by Ion Torrent NGS only whilst false positives are substitutions indexed by Illumina NGS only using a given mutation caller or any combination thereof. The size of each dots is proportional to the difference in coverage between the two sequencing platforms. In e , the residual coverage is obtained by subtracting the theoretical coverage required to achieve 99% power for indexing a substitution given one mutated copy out of n total copies from the observed value of sequencing depth. Only two substitutions in cluster 1 failed the criteria of positive residual for detection and are non-callable loci

    Journal: NPJ Breast Cancer

    Article Title: The AURORA pilot study for molecular screening of patients with advanced breast cancer–a study of the breast international group

    doi: 10.1038/s41523-017-0026-6

    Figure Lengend Snippet: Orthogonal cross-testing of substitution calls using Illumina NGS. a distribution of % concordance for single nucleotide substitutions indexed from the Ion Torrent and Illumina NGS platforms using different mutation callers, b % error rate of the different mutation callers over three substitution clusters compared to the Ion Torrent sequencing, c correlation of VAF for substitutions indexed from the Ion Torrent and Illumina NGS using a majority rule of any two of three mutation callers, d comparison of sequencing coverage between the Ion Torrent and Illumina NGS for substitutions in cluster 1 , e empirical cumulative distribution of theoretical residual coverage from the Illumina sequencing for substitutions in cluster 1 and cluster 2 false negatives, f comparison of sequencing coverage from the Ion Torrent NGS for substitutions in cluster 2 false positives, and g comparison of sequencing coverage from the Illumina NGS for substitutions in cluster 2 false negatives. In a , the different mutation callers and any combination thereof are colour coded and indicated at the bottom. The leftmost panel gives the number of substitutions called. In b – g , the cluster numbers are relative to ( c ). Substitutions in clusters 1 and 3 are exclusive to one of the sequencing platforms and have 0% VAF in the alternate data. Substitutions in cluster 2 are those found by either or both NGS platforms and have non-zero VAF in both sequencing data. False negatives in cluster 2 are substitutions indexed by Ion Torrent NGS only whilst false positives are substitutions indexed by Illumina NGS only using a given mutation caller or any combination thereof. The size of each dots is proportional to the difference in coverage between the two sequencing platforms. In e , the residual coverage is obtained by subtracting the theoretical coverage required to achieve 99% power for indexing a substitution given one mutated copy out of n total copies from the observed value of sequencing depth. Only two substitutions in cluster 1 failed the criteria of positive residual for detection and are non-callable loci

    Article Snippet: Both distributions were bimodal with 6 (35%) and 5 (29%) patients showing low values of α < 0.5 and α < 0.6 for the Ion Torrent and Illumina NGS platforms, respectively.

    Techniques: Next-Generation Sequencing, Mutagenesis, Sequencing

    HIV-1 mutant library and NGS sample preparation. (A) Genomic region for each HIV-1 mutation library. (B) The two-step PCR amplicon approach for NGS sample preparation. Virion cDNA from each mutant viral population cell passage is used as template for a HIV-1 specific staggered PCR step that uses primers specific to the HIV-1 mutagenized region containing overhangs with a complex 10 ‘N’ nucleotide tag with two keto “K” or amino “M” nucleotide positions that identify the specific fragment and population, respectively. PCR products from step one are pooled, the amplicon molecule concentration is accurately measured, and then decreased for error correction. The pooled sample is then used as template for a second PCR using a single primer set containing the remainder of the Illumina adapter region for NGS.

    Journal: Retrovirology

    Article Title: High-throughput profiling of point mutations across the HIV-1 genome

    doi: 10.1186/s12977-014-0124-6

    Figure Lengend Snippet: HIV-1 mutant library and NGS sample preparation. (A) Genomic region for each HIV-1 mutation library. (B) The two-step PCR amplicon approach for NGS sample preparation. Virion cDNA from each mutant viral population cell passage is used as template for a HIV-1 specific staggered PCR step that uses primers specific to the HIV-1 mutagenized region containing overhangs with a complex 10 ‘N’ nucleotide tag with two keto “K” or amino “M” nucleotide positions that identify the specific fragment and population, respectively. PCR products from step one are pooled, the amplicon molecule concentration is accurately measured, and then decreased for error correction. The pooled sample is then used as template for a second PCR using a single primer set containing the remainder of the Illumina adapter region for NGS.

    Article Snippet: Next-generation sequencing of virus mutants We conceptually designed a two-step PCR strategy to prepare isolated viral RNA (cDNA) after each selection round that is specific for the NGS Illumina HiSeq 2000 platform.

    Techniques: Mutagenesis, Next-Generation Sequencing, Sample Prep, Polymerase Chain Reaction, Amplification, Concentration Assay

    HIV-1 mutant library and NGS sample preparation. (A) Genomic region for each HIV-1 mutation library. (B) The two-step PCR amplicon approach for NGS sample preparation. Virion cDNA from each mutant viral population cell passage is used as template for a HIV-1 specific staggered PCR step that uses primers specific to the HIV-1 mutagenized region containing overhangs with a complex 10 ‘N’ nucleotide tag with two keto “K” or amino “M” nucleotide positions that identify the specific fragment and population, respectively. PCR products from step one are pooled, the amplicon molecule concentration is accurately measured, and then decreased for error correction. The pooled sample is then used as template for a second PCR using a single primer set containing the remainder of the Illumina adapter region for NGS.

    Journal: Retrovirology

    Article Title: High-throughput profiling of point mutations across the HIV-1 genome

    doi: 10.1186/s12977-014-0124-6

    Figure Lengend Snippet: HIV-1 mutant library and NGS sample preparation. (A) Genomic region for each HIV-1 mutation library. (B) The two-step PCR amplicon approach for NGS sample preparation. Virion cDNA from each mutant viral population cell passage is used as template for a HIV-1 specific staggered PCR step that uses primers specific to the HIV-1 mutagenized region containing overhangs with a complex 10 ‘N’ nucleotide tag with two keto “K” or amino “M” nucleotide positions that identify the specific fragment and population, respectively. PCR products from step one are pooled, the amplicon molecule concentration is accurately measured, and then decreased for error correction. The pooled sample is then used as template for a second PCR using a single primer set containing the remainder of the Illumina adapter region for NGS.

    Article Snippet: Our fragment based design of seven distinct libraries was used to maximize sequencing of only targeted mutational fragments on the finite Illumina NGS platform and not waste resources sequencing WT genomic regions not targeted for error-prone PCR.

    Techniques: Mutagenesis, Next-Generation Sequencing, Sample Prep, Polymerase Chain Reaction, Amplification, Concentration Assay