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Illumina Inc truseq amplicon
Truseq Amplicon, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/truseq amplicon/product/Illumina Inc
Average 88 stars, based on 5 article reviews
Price from $9.99 to $1999.99
truseq amplicon - by Bioz Stars, 2020-09
88/100 stars

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Polymerase Chain Reaction:

Article Title: Amplification of overlapping DNA amplicons in a single-tube multiplex PCR for targeted next-generation sequencing of BRCA1 and BRCA2
Article Snippet: .. TruSeq Amplicon requires only one reaction pool per sample, but it utilizes hybrid capture followed by PCR [ ]. .. Overall, this report provides a practical and economical single-tube multiplex PCR for targeted next generation sequencing.

Article Title: Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes
Article Snippet: .. Techniques such as consensus PCR, Ion Ampliseq (Life Technologies) [ ], TruSeq Amplicon (Illumina), and Haloplex (Agilent) [ ] apply highly multiplexed PCR for target enrichment. .. Targeted enrichment should preferentially amplify the target virus over host or environmental DNA/RNA, in contrast to random amplification commonly used prior to whole genome sequencing.

Genotyping Assay:

Article Title: Next-Generation Sequencing for Cancer Diagnostics: a Practical Perspective
Article Snippet: .. The ‘TruSeq Amplicon’ approach is derived from the method used for the Illumina ‘Golden Gate Genotyping’ assay. .. Instead of using MIP, two independent left and right flanking oligonucleotides are hybridised to a genomic DNA template enabling polymerase extension and ligation.

Amplification:

Article Title: Detecting circulating tumor material and digital pathology imaging during pancreatic cancer progression
Article Snippet: .. A variety of commercial platforms are now available for detection of amplified CTC DNA such as TruSeq Amplicon (Illumina) and Ion Torrent AmpliSeq™ (Life Technologies). .. Levels of RNA expression can also be measured by RT-PCR or directly imaged by in situ RNA hybridization using platforms such as ViewRNA™ CTC Platform (Affymetrix).

Article Title: Single-cell genomic profiling of acute myeloid leukemia for clinical use: A pilot study
Article Snippet: .. The TruSeq Amplicon (BaseSpace Workflow; version 1.1.0.0; Illumina, Inc.) was used to generate the BAM and VCF files. ..

Article Title: Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer
Article Snippet: .. The technology used for the Ion Ampliseq™ (Life Technologies) and Truseq® Amplicon (Illumina) hotspot panels is based on this library preparation approach and enrichment. .. In the Illumina kits, there is also a prior targeted capture of the regions of interest by means of oligonucleotide probes.

Article Title: Amplification of overlapping DNA amplicons in a single-tube multiplex PCR for targeted next-generation sequencing of BRCA1 and BRCA2
Article Snippet: .. Hybridization-extension-ligation amplicon enrichment methods include Haloplex (Agilent) and TruSeq Amplicon (Illumina). .. One long, looped oligo (HaloPlex) or two-tagged oligos (TruSeq) are hybridized to the flanking sequences of the targeted region of interest followed by extension and ligation to fill the gaps between the hybridization sites.

Article Title: Next-Generation Sequencing for Cancer Diagnostics: a Practical Perspective
Article Snippet: .. The ‘TruSeq Amplicon’ approach is derived from the method used for the Illumina ‘Golden Gate Genotyping’ assay. .. Instead of using MIP, two independent left and right flanking oligonucleotides are hybridised to a genomic DNA template enabling polymerase extension and ligation.

Article Title: Amplification of overlapping DNA amplicons in a single-tube multiplex PCR for targeted next-generation sequencing of BRCA1 and BRCA2
Article Snippet: .. TruSeq Amplicon requires only one reaction pool per sample, but it utilizes hybrid capture followed by PCR [ ]. .. Overall, this report provides a practical and economical single-tube multiplex PCR for targeted next generation sequencing.

Article Title: Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes
Article Snippet: .. Techniques such as consensus PCR, Ion Ampliseq (Life Technologies) [ ], TruSeq Amplicon (Illumina), and Haloplex (Agilent) [ ] apply highly multiplexed PCR for target enrichment. .. Targeted enrichment should preferentially amplify the target virus over host or environmental DNA/RNA, in contrast to random amplification commonly used prior to whole genome sequencing.

Article Title: Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine
Article Snippet: .. For tumor organoid specimens where the amount of 200ng could not be reached a targeted cancer gene panel of 50 genes was run using TruSeq Amplicon (Illumina). .. We applied CLONET ( ) to study whole exome sequencing tumor and matched germline data to first assess tumor ploidy and purity ( ).

Derivative Assay:

Article Title: Next-Generation Sequencing for Cancer Diagnostics: a Practical Perspective
Article Snippet: .. The ‘TruSeq Amplicon’ approach is derived from the method used for the Illumina ‘Golden Gate Genotyping’ assay. .. Instead of using MIP, two independent left and right flanking oligonucleotides are hybridised to a genomic DNA template enabling polymerase extension and ligation.

Hybridization:

Article Title: Amplification of overlapping DNA amplicons in a single-tube multiplex PCR for targeted next-generation sequencing of BRCA1 and BRCA2
Article Snippet: .. Hybridization-extension-ligation amplicon enrichment methods include Haloplex (Agilent) and TruSeq Amplicon (Illumina). .. One long, looped oligo (HaloPlex) or two-tagged oligos (TruSeq) are hybridized to the flanking sequences of the targeted region of interest followed by extension and ligation to fill the gaps between the hybridization sites.

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  • 93
    Illumina Inc truseq amplicon cancer panels
    Intragenic copy number detection and comparison to commercial panels. ( A ) Control genomic DNA samples were acquired from kConFab for sensitivity testing. Three of these samples included known exon duplications in BRCA1 , TP53 and MSH2 , which were assessed by the DeCON tool. Exons are numbered along the x-axis, and those of normal copy number are presented as blue dots. Amplifications are shown in red. The TP53 and AURKB genes are on opposing DNA strands hence the presence of the latter and its exons in this Figure. A similar genetic-overlap is observed for MSH2 to the left of the panel. ( B ) A commercially available pool of synthetic oligos against a normal genomic background was also obtained. Mutations were provided at variant allele frequencies (VAF) of 5–15% and 15–35%, or at germline frequencies. Presented are the number of detected and missed variants in our PV1 and PV2 panels relative to what was expected in AcroMetrix. This was compared to three other panels [AmpliSeq Cancer Hotspot Panel v2 (CHPv2), Illumina <t>TruSeq</t> <t>Amplicon</t> – Cancer Panel (TSCAP) and TruSight Tumor Panel 26 (TSTP)], the data for which were provided by the AcroMetrix manufacturer. Percent values on the right indicate the proportion of AcroMetrix variants actually targeted by the panels.
    Truseq Amplicon Cancer Panels, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq amplicon cancer panels/product/Illumina Inc
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    truseq amplicon cancer panels - by Bioz Stars, 2020-09
    93/100 stars
      Buy from Supplier

    93
    Illumina Inc truseq amplicon cancer panel tscap
    Intragenic copy number detection and comparison to commercial panels. ( A ) Control genomic DNA samples were acquired from kConFab for sensitivity testing. Three of these samples included known exon duplications in BRCA1 , TP53 and MSH2 , which were assessed by the DeCON tool. Exons are numbered along the x-axis, and those of normal copy number are presented as blue dots. Amplifications are shown in red. The TP53 and AURKB genes are on opposing DNA strands hence the presence of the latter and its exons in this Figure. A similar genetic-overlap is observed for MSH2 to the left of the panel. ( B ) A commercially available pool of synthetic oligos against a normal genomic background was also obtained. Mutations were provided at variant allele frequencies (VAF) of 5–15% and 15–35%, or at germline frequencies. Presented are the number of detected and missed variants in our PV1 and PV2 panels relative to what was expected in AcroMetrix. This was compared to three other panels [AmpliSeq Cancer Hotspot Panel v2 (CHPv2), Illumina <t>TruSeq</t> <t>Amplicon</t> – Cancer Panel (TSCAP) and TruSight Tumor Panel 26 (TSTP)], the data for which were provided by the AcroMetrix manufacturer. Percent values on the right indicate the proportion of AcroMetrix variants actually targeted by the panels.
    Truseq Amplicon Cancer Panel Tscap, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq amplicon cancer panel tscap/product/Illumina Inc
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    truseq amplicon cancer panel tscap - by Bioz Stars, 2020-09
    93/100 stars
      Buy from Supplier

    91
    Illumina Inc amplicon assay
    Targeted validation of promoter mutations a , Targeted sequencing validation of selected promoter mutations in 47 patients from the ExomePlus cohort with Illumina TruSeq Custom <t>Amplicon</t> panel (TSCA)-targeted sequencing technology. b , Validation rate of promoter mutations calculated as validated mutations over all sequenced and powered mutations. c , Median detection sensitivity at mutated sites for significantly mutated promoters. Each point indicates a single mutated position. d , PCR-MiSeq for the FOXA1 promoter locus for 126 patients with sufficient coverage for mutation calling from the original ExomePlus cohort. Three out of four mutations validated in experiment (green and red bars). PCR-MiSeq for 140 patients included but not covered in original ExomePlus experiment and 64 additional tumours yielded three novel mutations in each set (light and dark blue bars). No germline mutations at this site were detected in normal samples.
    Amplicon Assay, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon assay/product/Illumina Inc
    Average 91 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    amplicon assay - by Bioz Stars, 2020-09
    91/100 stars
      Buy from Supplier

    84
    Illumina Inc self designed amplicon panel
    Enteric BAC with loss of ARID1A. HE ( a ) and anti-ARID1A ( b ) staining of a case of BAC (enteric type) with loss of ARID1A expression in tumour tissue (black scale bar equals 250 μm). c Truncating ARID1A mutation with an allele frequency of 88% (c.6160G > T, p.Glu2054*, estimated tumour content 80%). d Relative coverage for all exons of ARID1A showing a deletion for sample AE-8. These results were derived through calculation of the relative coverage deviation of each <t>amplicon</t> from the coverage of five correlated amplicons of the same sample. In a normal diploid state with two copies, no deviation in coverage would be detected (= 0)
    Self Designed Amplicon Panel, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/self designed amplicon panel/product/Illumina Inc
    Average 84 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    self designed amplicon panel - by Bioz Stars, 2020-09
    84/100 stars
      Buy from Supplier

    Image Search Results


    Intragenic copy number detection and comparison to commercial panels. ( A ) Control genomic DNA samples were acquired from kConFab for sensitivity testing. Three of these samples included known exon duplications in BRCA1 , TP53 and MSH2 , which were assessed by the DeCON tool. Exons are numbered along the x-axis, and those of normal copy number are presented as blue dots. Amplifications are shown in red. The TP53 and AURKB genes are on opposing DNA strands hence the presence of the latter and its exons in this Figure. A similar genetic-overlap is observed for MSH2 to the left of the panel. ( B ) A commercially available pool of synthetic oligos against a normal genomic background was also obtained. Mutations were provided at variant allele frequencies (VAF) of 5–15% and 15–35%, or at germline frequencies. Presented are the number of detected and missed variants in our PV1 and PV2 panels relative to what was expected in AcroMetrix. This was compared to three other panels [AmpliSeq Cancer Hotspot Panel v2 (CHPv2), Illumina TruSeq Amplicon – Cancer Panel (TSCAP) and TruSight Tumor Panel 26 (TSTP)], the data for which were provided by the AcroMetrix manufacturer. Percent values on the right indicate the proportion of AcroMetrix variants actually targeted by the panels.

    Journal: Scientific Reports

    Article Title: Development and validation of a targeted gene sequencing panel for application to disparate cancers

    doi: 10.1038/s41598-019-52000-3

    Figure Lengend Snippet: Intragenic copy number detection and comparison to commercial panels. ( A ) Control genomic DNA samples were acquired from kConFab for sensitivity testing. Three of these samples included known exon duplications in BRCA1 , TP53 and MSH2 , which were assessed by the DeCON tool. Exons are numbered along the x-axis, and those of normal copy number are presented as blue dots. Amplifications are shown in red. The TP53 and AURKB genes are on opposing DNA strands hence the presence of the latter and its exons in this Figure. A similar genetic-overlap is observed for MSH2 to the left of the panel. ( B ) A commercially available pool of synthetic oligos against a normal genomic background was also obtained. Mutations were provided at variant allele frequencies (VAF) of 5–15% and 15–35%, or at germline frequencies. Presented are the number of detected and missed variants in our PV1 and PV2 panels relative to what was expected in AcroMetrix. This was compared to three other panels [AmpliSeq Cancer Hotspot Panel v2 (CHPv2), Illumina TruSeq Amplicon – Cancer Panel (TSCAP) and TruSight Tumor Panel 26 (TSTP)], the data for which were provided by the AcroMetrix manufacturer. Percent values on the right indicate the proportion of AcroMetrix variants actually targeted by the panels.

    Article Snippet: Firstly, genes were selected from the following commercially available panels: TruSight Tumour 26 and TruSeq Amplicon Cancer Panels (Illumina), SureSeq Solid Tumour panel (Oxford Gene Technology), Foundation One Panel (Foundation Medicine), OncoCarta Panels Versions 1–3 (OncoCarta) and Haloplex Cancer Research Panel (Agilent).

    Techniques: Variant Assay, Amplification

    Intragenic copy number detection and comparison to commercial panels. ( A ) Control genomic DNA samples were acquired from kConFab for sensitivity testing. Three of these samples included known exon duplications in BRCA1 , TP53 and MSH2 , which were assessed by the DeCON tool. Exons are numbered along the x-axis, and those of normal copy number are presented as blue dots. Amplifications are shown in red. The TP53 and AURKB genes are on opposing DNA strands hence the presence of the latter and its exons in this Figure. A similar genetic-overlap is observed for MSH2 to the left of the panel. ( B ) A commercially available pool of synthetic oligos against a normal genomic background was also obtained. Mutations were provided at variant allele frequencies (VAF) of 5–15% and 15–35%, or at germline frequencies. Presented are the number of detected and missed variants in our PV1 and PV2 panels relative to what was expected in AcroMetrix. This was compared to three other panels [AmpliSeq Cancer Hotspot Panel v2 (CHPv2), Illumina TruSeq Amplicon – Cancer Panel (TSCAP) and TruSight Tumor Panel 26 (TSTP)], the data for which were provided by the AcroMetrix manufacturer. Percent values on the right indicate the proportion of AcroMetrix variants actually targeted by the panels.

    Journal: Scientific Reports

    Article Title: Development and validation of a targeted gene sequencing panel for application to disparate cancers

    doi: 10.1038/s41598-019-52000-3

    Figure Lengend Snippet: Intragenic copy number detection and comparison to commercial panels. ( A ) Control genomic DNA samples were acquired from kConFab for sensitivity testing. Three of these samples included known exon duplications in BRCA1 , TP53 and MSH2 , which were assessed by the DeCON tool. Exons are numbered along the x-axis, and those of normal copy number are presented as blue dots. Amplifications are shown in red. The TP53 and AURKB genes are on opposing DNA strands hence the presence of the latter and its exons in this Figure. A similar genetic-overlap is observed for MSH2 to the left of the panel. ( B ) A commercially available pool of synthetic oligos against a normal genomic background was also obtained. Mutations were provided at variant allele frequencies (VAF) of 5–15% and 15–35%, or at germline frequencies. Presented are the number of detected and missed variants in our PV1 and PV2 panels relative to what was expected in AcroMetrix. This was compared to three other panels [AmpliSeq Cancer Hotspot Panel v2 (CHPv2), Illumina TruSeq Amplicon – Cancer Panel (TSCAP) and TruSight Tumor Panel 26 (TSTP)], the data for which were provided by the AcroMetrix manufacturer. Percent values on the right indicate the proportion of AcroMetrix variants actually targeted by the panels.

    Article Snippet: In comparison to the three other commercial sequencing panels presented in Fig. , our panel had greater breadth, targeting 100% of the AcroMetrix oligo pool, and greater sensitivity, detecting proportionally more expected variants, with AmpliSeq Cancer Hotspot Panel v2 (CHPv2), Illumina’s TruSeq Amplicon – Cancer Panel (TSCAP) and TruSight Tumor Panel 26 (TSTP) detecting 98.8%, 97.1% and 97.4% of their respective targets.

    Techniques: Variant Assay, Amplification

    Targeted validation of promoter mutations a , Targeted sequencing validation of selected promoter mutations in 47 patients from the ExomePlus cohort with Illumina TruSeq Custom Amplicon panel (TSCA)-targeted sequencing technology. b , Validation rate of promoter mutations calculated as validated mutations over all sequenced and powered mutations. c , Median detection sensitivity at mutated sites for significantly mutated promoters. Each point indicates a single mutated position. d , PCR-MiSeq for the FOXA1 promoter locus for 126 patients with sufficient coverage for mutation calling from the original ExomePlus cohort. Three out of four mutations validated in experiment (green and red bars). PCR-MiSeq for 140 patients included but not covered in original ExomePlus experiment and 64 additional tumours yielded three novel mutations in each set (light and dark blue bars). No germline mutations at this site were detected in normal samples.

    Journal: Nature

    Article Title: Recurrent and functional regulatory mutations in breast cancer

    doi: 10.1038/nature22992

    Figure Lengend Snippet: Targeted validation of promoter mutations a , Targeted sequencing validation of selected promoter mutations in 47 patients from the ExomePlus cohort with Illumina TruSeq Custom Amplicon panel (TSCA)-targeted sequencing technology. b , Validation rate of promoter mutations calculated as validated mutations over all sequenced and powered mutations. c , Median detection sensitivity at mutated sites for significantly mutated promoters. Each point indicates a single mutated position. d , PCR-MiSeq for the FOXA1 promoter locus for 126 patients with sufficient coverage for mutation calling from the original ExomePlus cohort. Three out of four mutations validated in experiment (green and red bars). PCR-MiSeq for 140 patients included but not covered in original ExomePlus experiment and 64 additional tumours yielded three novel mutations in each set (light and dark blue bars). No germline mutations at this site were detected in normal samples.

    Article Snippet: We designed a targeted amplicon assay (Illumina TruSeq Custom Amplicon) to validate several recurrently mutated promoter mutations in 47 patients from our initial cohort and 46 additional breast cancer cell lines (median coverage across samples and genes was approximately 3,900×).

    Techniques: Sequencing, Amplification, Polymerase Chain Reaction, Mutagenesis

    Enteric BAC with loss of ARID1A. HE ( a ) and anti-ARID1A ( b ) staining of a case of BAC (enteric type) with loss of ARID1A expression in tumour tissue (black scale bar equals 250 μm). c Truncating ARID1A mutation with an allele frequency of 88% (c.6160G > T, p.Glu2054*, estimated tumour content 80%). d Relative coverage for all exons of ARID1A showing a deletion for sample AE-8. These results were derived through calculation of the relative coverage deviation of each amplicon from the coverage of five correlated amplicons of the same sample. In a normal diploid state with two copies, no deviation in coverage would be detected (= 0)

    Journal: Virchows Archiv

    Article Title: Comparative genomic profiling of glandular bladder tumours

    doi: 10.1007/s00428-020-02787-8

    Figure Lengend Snippet: Enteric BAC with loss of ARID1A. HE ( a ) and anti-ARID1A ( b ) staining of a case of BAC (enteric type) with loss of ARID1A expression in tumour tissue (black scale bar equals 250 μm). c Truncating ARID1A mutation with an allele frequency of 88% (c.6160G > T, p.Glu2054*, estimated tumour content 80%). d Relative coverage for all exons of ARID1A showing a deletion for sample AE-8. These results were derived through calculation of the relative coverage deviation of each amplicon from the coverage of five correlated amplicons of the same sample. In a normal diploid state with two copies, no deviation in coverage would be detected (= 0)

    Article Snippet: Targeted next-generation sequencing For NGS, a self-designed amplicon panel (TruSeq Custom Amplicon v1.5, Illumina, San Diego, CA, USA) was used covering all coding exons of 20 genes known to be frequently mutated in either BLCA or CORAD (APC , ARID1A , BRAF , CDKN1A , CDKN2A , CTNNB1 , FBXW7 , FGFR3 , HRAS , KDM6A , KRAS , MSH6 , NRAS , PIK3CA , PTEN , RB1 , SMAD4 , STAG2 , TP53 , TSC1 ).

    Techniques: BAC Assay, Staining, Expressing, Mutagenesis, Derivative Assay, Amplification