truseq custom amplicon  (Illumina Inc)

 
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    Name:
    TruSeq Custom Amplicon Filter Plate
    Description:
    The TruSight Myeloid Sequencing Panel uses expert defined content and proven next generation sequencing NGS technology to identify somatic variants in myeloid malignancies The panel content was designed by a consortium of recognized experts in blood cancer disorders and targets genes frequently mutated in Acute myeloid leukemia AML Myelodysplastic syndrome MDS Myeloproliferative neoplasms MPN Chronic myelogenous leukemia CML Chronic myelomonocytic leukemia CMML Juvenile myelomonocytic leukemia JMML The TruSight Myeloid Sequencing Panel covers 15 full genes exons only and 39 additional genes where oncogenic hotspots are covered providing a comprehensive assessment of the key genes known to be involved in myeloid malignancies in a single test The result is an accurate cost effective solution that enables researchers to profile liquid tumors View the gene list TruSight Myeloid libraries are ideally suited to run on a desktop sequencer and perform alignment and variant calling with the MiSeq Reporter or Local Run Manager Amplicon workflow with Somatic Variant Caller Filtering and annotation can then be performed using BaseSpace Variant Interpreter See All Illumina Cancer Research Panels
    Catalog Number:
    fc-130-1006
    Price:
    None
    Category:
    Clinical Research Products
    Buy from Supplier


    Structured Review

    Illumina Inc truseq custom amplicon
    TruSeq Custom Amplicon Filter Plate
    The TruSight Myeloid Sequencing Panel uses expert defined content and proven next generation sequencing NGS technology to identify somatic variants in myeloid malignancies The panel content was designed by a consortium of recognized experts in blood cancer disorders and targets genes frequently mutated in Acute myeloid leukemia AML Myelodysplastic syndrome MDS Myeloproliferative neoplasms MPN Chronic myelogenous leukemia CML Chronic myelomonocytic leukemia CMML Juvenile myelomonocytic leukemia JMML The TruSight Myeloid Sequencing Panel covers 15 full genes exons only and 39 additional genes where oncogenic hotspots are covered providing a comprehensive assessment of the key genes known to be involved in myeloid malignancies in a single test The result is an accurate cost effective solution that enables researchers to profile liquid tumors View the gene list TruSight Myeloid libraries are ideally suited to run on a desktop sequencer and perform alignment and variant calling with the MiSeq Reporter or Local Run Manager Amplicon workflow with Somatic Variant Caller Filtering and annotation can then be performed using BaseSpace Variant Interpreter See All Illumina Cancer Research Panels
    https://www.bioz.com/result/truseq custom amplicon/product/Illumina Inc
    Average 98 stars, based on 46 article reviews
    Price from $9.99 to $1999.99
    truseq custom amplicon - by Bioz Stars, 2020-07
    98/100 stars

    Images

    1) Product Images from "Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments"

    Article Title: Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments

    Journal: Genome Biology

    doi: 10.1186/s13059-014-0420-4

    Adaptation of Illumina TruSeq Custom Amplicon Kit to allow for single molecule tagging. (A) Schematic of method showing amplification of target DNA using custom probes and flanking primers. The P5-SMT primer is the same as the standard P5 index primer, but contains a degenerate 12 N-mer sequence in place of the index. The incorporation of an Ampure Bead size selection step after two rounds of PCR removes unused P5-SMT, and the P5 primer is added to facilitate downstream amplification. Figure schematic is adapted from Illumina promotional material. (B) Stacked barplot showing number of paired-end reads, split into unique reads (dark grey) and SMT-identified duplicate reads (light-grey) in 24 samples (18 germline, 6 tumor). (C) For each of 18 germline samples, we show the number of SMTs by duplicate cluster size (the number of times that an SMT was observed at a given target within a sample). Higher overall duplicate rates within a sample were associated with larger duplicate clusters. Except for the sample with the highest duplicate rate, duplicate cluster sizes were generally less than 10. The length of the SMT (8- versus 12-mer) did not affect the distribution. SMT, single molecule tag.
    Figure Legend Snippet: Adaptation of Illumina TruSeq Custom Amplicon Kit to allow for single molecule tagging. (A) Schematic of method showing amplification of target DNA using custom probes and flanking primers. The P5-SMT primer is the same as the standard P5 index primer, but contains a degenerate 12 N-mer sequence in place of the index. The incorporation of an Ampure Bead size selection step after two rounds of PCR removes unused P5-SMT, and the P5 primer is added to facilitate downstream amplification. Figure schematic is adapted from Illumina promotional material. (B) Stacked barplot showing number of paired-end reads, split into unique reads (dark grey) and SMT-identified duplicate reads (light-grey) in 24 samples (18 germline, 6 tumor). (C) For each of 18 germline samples, we show the number of SMTs by duplicate cluster size (the number of times that an SMT was observed at a given target within a sample). Higher overall duplicate rates within a sample were associated with larger duplicate clusters. Except for the sample with the highest duplicate rate, duplicate cluster sizes were generally less than 10. The length of the SMT (8- versus 12-mer) did not affect the distribution. SMT, single molecule tag.

    Techniques Used: Amplification, Sequencing, Selection, Polymerase Chain Reaction

    Related Articles

    Sequencing:

    Article Title: Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
    Article Snippet: .. Exome sequencing studies at moderate (approximately 100X) depth rely on read position to identify potential PCR duplicates [ ], but amplicon-based (molecular inversion probes [ ], RainDrop Digital PCR (RainDance Technologies, Billerica, MA, USA), TruSeq Custom Amplicon (Illumina, San Diego, CA, USA)) methods commonly used for targeted sequencing have reads with the same start and stop positions. ..

    Article Title: Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer
    Article Snippet: .. Growth of a pure population of fibroblasts was confirmed by a PCR-based targeted sequencing assay using the TruSeq Custom Amplicon platform (Illumina). ..

    Article Title: An Integrated Genomic Strategy Delineates Candidate Mediator Genes Regulating Grain Size and Weight in Rice
    Article Snippet: .. The targeted resequencing of coding and non-coding intronic and regulatory sequence components of 55 MED genes in 384 diverse low and high grain weight rice accessions (association panel) using the Illumina TruSeq Custom Amplicon strategy mined 3971 high-quality SNPs with an average frequency of 72.2 SNPs/gene ( , , ). ..

    Article Title: Prognostic signature and clonality pattern of recurrently mutated genes in inactive chronic lymphocytic leukemia
    Article Snippet: .. Targeted sequencing We designed a TruSeq Custom Amplicon panel (Illumina, Inc. San Diego, CA, USA) containing 13 genes and covering 28.099 bases ( ). .. For some genes known mutation hotspots were targeted; and for those with a widespread localization of the lesions, the entire coding sequence was analyzed.

    Article Title: Genetic and Clinical Analysis of ABCA4-Associated Disease in African American Patients
    Article Snippet: .. Sequencing and Data Analysis All 50 exons and exon–intron boundaries of the ABCA4 gene were amplified using Illumina TruSeq Custom Amplicon protocol (Illumina, San Diego, CA), followed by sequencing on Illumina MiSeq platform. .. The next-generation sequencing reads were analyzed and compared to the ABCA4 reference sequence NG_009073.1, using the variant discovery software NextGENe (SoftGenetics LLC, State College, PA).

    Article Title: Invariant patterns of clonal succession determine specific clinical features of myelodysplastic syndromes
    Article Snippet: .. Targeted sequencing Targeted sequencing was performed using a TruSeq Custom Amplicon (Illumina) or a custom cRNA bait library (SureSelect; Agilent Technology) as previously described , , . ..

    Article Title: Elucidating the genetic architecture of Adams–Oliver syndrome in a large European cohort, et al. Elucidating the genetic architecture of Adams–Oliver syndrome in a large European cohort
    Article Snippet: .. The majority of the samples were sequenced by targeted next‐generation resequencing (n = 140) using either the HaloPlex Target Enrichment System (Agilent Technologies, Santa Clara, CA) as described previously (Meester et al., ), or a TruSeq Custom Amplicon Panel (Illumina, San Diego, CA) followed by sequencing on a MiSeq system (Illumina, San Diego, CA) with 150 bp paired‐end reads. .. Sequence data obtained from the TruSeq Custom Amplicon Panel were analyzed using Illumina's VariantStudio Data Analysis Software v3.0.

    Polymerase Chain Reaction:

    Article Title: Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
    Article Snippet: .. Exome sequencing studies at moderate (approximately 100X) depth rely on read position to identify potential PCR duplicates [ ], but amplicon-based (molecular inversion probes [ ], RainDrop Digital PCR (RainDance Technologies, Billerica, MA, USA), TruSeq Custom Amplicon (Illumina, San Diego, CA, USA)) methods commonly used for targeted sequencing have reads with the same start and stop positions. ..

    Article Title: Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer
    Article Snippet: .. Growth of a pure population of fibroblasts was confirmed by a PCR-based targeted sequencing assay using the TruSeq Custom Amplicon platform (Illumina). ..

    Amplification:

    Article Title: Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
    Article Snippet: .. Exome sequencing studies at moderate (approximately 100X) depth rely on read position to identify potential PCR duplicates [ ], but amplicon-based (molecular inversion probes [ ], RainDrop Digital PCR (RainDance Technologies, Billerica, MA, USA), TruSeq Custom Amplicon (Illumina, San Diego, CA, USA)) methods commonly used for targeted sequencing have reads with the same start and stop positions. ..

    Article Title: Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer
    Article Snippet: .. Growth of a pure population of fibroblasts was confirmed by a PCR-based targeted sequencing assay using the TruSeq Custom Amplicon platform (Illumina). ..

    Article Title: An Integrated Genomic Strategy Delineates Candidate Mediator Genes Regulating Grain Size and Weight in Rice
    Article Snippet: .. The targeted resequencing of coding and non-coding intronic and regulatory sequence components of 55 MED genes in 384 diverse low and high grain weight rice accessions (association panel) using the Illumina TruSeq Custom Amplicon strategy mined 3971 high-quality SNPs with an average frequency of 72.2 SNPs/gene ( , , ). ..

    Article Title: Molecular methods for somatic mutation testing in lung adenocarcinoma: EGFR and beyond
    Article Snippet: .. The Illumina Truseq Custom Amplicon Cancer Panel recommends 250 ng of input DNA, however results can be obtained with as little as 150 ng. ..

    Article Title: Prognostic signature and clonality pattern of recurrently mutated genes in inactive chronic lymphocytic leukemia
    Article Snippet: .. Targeted sequencing We designed a TruSeq Custom Amplicon panel (Illumina, Inc. San Diego, CA, USA) containing 13 genes and covering 28.099 bases ( ). .. For some genes known mutation hotspots were targeted; and for those with a widespread localization of the lesions, the entire coding sequence was analyzed.

    Article Title: Genetic and Clinical Analysis of ABCA4-Associated Disease in African American Patients
    Article Snippet: .. Sequencing and Data Analysis All 50 exons and exon–intron boundaries of the ABCA4 gene were amplified using Illumina TruSeq Custom Amplicon protocol (Illumina, San Diego, CA), followed by sequencing on Illumina MiSeq platform. .. The next-generation sequencing reads were analyzed and compared to the ABCA4 reference sequence NG_009073.1, using the variant discovery software NextGENe (SoftGenetics LLC, State College, PA).

    Article Title: Invariant patterns of clonal succession determine specific clinical features of myelodysplastic syndromes
    Article Snippet: .. Targeted sequencing Targeted sequencing was performed using a TruSeq Custom Amplicon (Illumina) or a custom cRNA bait library (SureSelect; Agilent Technology) as previously described , , . ..

    Article Title: Elucidating the genetic architecture of Adams–Oliver syndrome in a large European cohort, et al. Elucidating the genetic architecture of Adams–Oliver syndrome in a large European cohort
    Article Snippet: .. The majority of the samples were sequenced by targeted next‐generation resequencing (n = 140) using either the HaloPlex Target Enrichment System (Agilent Technologies, Santa Clara, CA) as described previously (Meester et al., ), or a TruSeq Custom Amplicon Panel (Illumina, San Diego, CA) followed by sequencing on a MiSeq system (Illumina, San Diego, CA) with 150 bp paired‐end reads. .. Sequence data obtained from the TruSeq Custom Amplicon Panel were analyzed using Illumina's VariantStudio Data Analysis Software v3.0.

    Digital PCR:

    Article Title: Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
    Article Snippet: .. Exome sequencing studies at moderate (approximately 100X) depth rely on read position to identify potential PCR duplicates [ ], but amplicon-based (molecular inversion probes [ ], RainDrop Digital PCR (RainDance Technologies, Billerica, MA, USA), TruSeq Custom Amplicon (Illumina, San Diego, CA, USA)) methods commonly used for targeted sequencing have reads with the same start and stop positions. ..

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  • 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, 2020-07
    91/100 stars
      Buy from Supplier

    97
    Illumina Inc truseq custom amplicon tsca
    <t>TruSeq</t> Custom <t>Amplicon</t> assay workflow diagram.
    Truseq Custom Amplicon Tsca, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 97/100, based on 94 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq custom amplicon tsca/product/Illumina Inc
    Average 97 stars, based on 94 article reviews
    Price from $9.99 to $1999.99
    truseq custom amplicon tsca - by Bioz Stars, 2020-07
    97/100 stars
      Buy from Supplier

    Image Search Results


    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

    TruSeq Custom Amplicon assay workflow diagram.

    Journal: The Journal of Molecular Diagnostics : JMD

    Article Title: Validation and Implementation of a Custom Next-Generation Sequencing Clinical Assay for Hematologic Malignancies

    doi: 10.1016/j.jmoldx.2016.02.003

    Figure Lengend Snippet: TruSeq Custom Amplicon assay workflow diagram.

    Article Snippet: The assay relies on an Illumina Truseq Custom Amplicon (TSCA) (San Diego, CA) kit and identifies single nucleotide variants (SNVs) and insertions/deletions (indels) in genes that are recurrently mutated in myeloid disorders and sequence variants in certain genes that are commonly mutated in lymphoid leukemias, such as NOTCH1 , NOTCH2, STAT3 , and MYD88 ., , , Genes covered by the assay encode a diverse collection of transcription factors, epigenetic regulators, cohesin family members, splicing factors, cell surface receptors, and downstream signaling components.

    Techniques: Amplification

    Adaptation of Illumina TruSeq Custom Amplicon Kit to allow for single molecule tagging. (A) Schematic of method showing amplification of target DNA using custom probes and flanking primers. The P5-SMT primer is the same as the standard P5 index primer, but contains a degenerate 12 N-mer sequence in place of the index. The incorporation of an Ampure Bead size selection step after two rounds of PCR removes unused P5-SMT, and the P5 primer is added to facilitate downstream amplification. Figure schematic is adapted from Illumina promotional material. (B) Stacked barplot showing number of paired-end reads, split into unique reads (dark grey) and SMT-identified duplicate reads (light-grey) in 24 samples (18 germline, 6 tumor). (C) For each of 18 germline samples, we show the number of SMTs by duplicate cluster size (the number of times that an SMT was observed at a given target within a sample). Higher overall duplicate rates within a sample were associated with larger duplicate clusters. Except for the sample with the highest duplicate rate, duplicate cluster sizes were generally less than 10. The length of the SMT (8- versus 12-mer) did not affect the distribution. SMT, single molecule tag.

    Journal: Genome Biology

    Article Title: Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments

    doi: 10.1186/s13059-014-0420-4

    Figure Lengend Snippet: Adaptation of Illumina TruSeq Custom Amplicon Kit to allow for single molecule tagging. (A) Schematic of method showing amplification of target DNA using custom probes and flanking primers. The P5-SMT primer is the same as the standard P5 index primer, but contains a degenerate 12 N-mer sequence in place of the index. The incorporation of an Ampure Bead size selection step after two rounds of PCR removes unused P5-SMT, and the P5 primer is added to facilitate downstream amplification. Figure schematic is adapted from Illumina promotional material. (B) Stacked barplot showing number of paired-end reads, split into unique reads (dark grey) and SMT-identified duplicate reads (light-grey) in 24 samples (18 germline, 6 tumor). (C) For each of 18 germline samples, we show the number of SMTs by duplicate cluster size (the number of times that an SMT was observed at a given target within a sample). Higher overall duplicate rates within a sample were associated with larger duplicate clusters. Except for the sample with the highest duplicate rate, duplicate cluster sizes were generally less than 10. The length of the SMT (8- versus 12-mer) did not affect the distribution. SMT, single molecule tag.

    Article Snippet: Adapting Illumina TruSeq to use single molecule tagging The Illumina TruSeq Custom Amplicon Kit is a multiplex system for targeted sequencing that allows for approximately 1,500 amplicons to be sequenced at the same time.

    Techniques: Amplification, Sequencing, Selection, Polymerase Chain Reaction