amplicon based sequencing  (Thermo Fisher)


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    Structured Review

    Thermo Fisher amplicon based sequencing
    Distribution of newly identified gene mutations in nodal T-cell lymphomas. The results of Sanger sequencing and/or <t>amplicon-based</t> deep sequencing for some newly identified gene mutations in whole tumor, PD1+ cells and CD20+ cells are shown. The numeric values indicate allele frequencies of mutations defined by deep sequencing. The AITL samples are indicated in black letters. The PTCL-NOS/nodal PTCL with TFH phenotype sample is indicated in blue letters. NA, not analyzed by deep sequencing. The filled and dashed red arrows indicate mutations and no mutations, respectively.
    Amplicon Based Sequencing, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon based sequencing/product/Thermo Fisher
    Average 88 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    amplicon based sequencing - by Bioz Stars, 2020-07
    88/100 stars

    Images

    1) Product Images from "Identification of cell-type-specific mutations in nodal T-cell lymphomas"

    Article Title: Identification of cell-type-specific mutations in nodal T-cell lymphomas

    Journal: Blood Cancer Journal

    doi: 10.1038/bcj.2016.122

    Distribution of newly identified gene mutations in nodal T-cell lymphomas. The results of Sanger sequencing and/or amplicon-based deep sequencing for some newly identified gene mutations in whole tumor, PD1+ cells and CD20+ cells are shown. The numeric values indicate allele frequencies of mutations defined by deep sequencing. The AITL samples are indicated in black letters. The PTCL-NOS/nodal PTCL with TFH phenotype sample is indicated in blue letters. NA, not analyzed by deep sequencing. The filled and dashed red arrows indicate mutations and no mutations, respectively.
    Figure Legend Snippet: Distribution of newly identified gene mutations in nodal T-cell lymphomas. The results of Sanger sequencing and/or amplicon-based deep sequencing for some newly identified gene mutations in whole tumor, PD1+ cells and CD20+ cells are shown. The numeric values indicate allele frequencies of mutations defined by deep sequencing. The AITL samples are indicated in black letters. The PTCL-NOS/nodal PTCL with TFH phenotype sample is indicated in blue letters. NA, not analyzed by deep sequencing. The filled and dashed red arrows indicate mutations and no mutations, respectively.

    Techniques Used: Sequencing, Amplification

    B-cell-specific mutations in nodal T-cell lymphomas. The results of Sanger sequencing and/or amplicon-based deep sequencing for some newly identified gene mutations in whole tumor, PD1+ cells and CD20+ cells are shown. The numeric values indicate allele frequencies of mutations defined by deep sequencing. The AITL samples are indicated in black letters. The PTCL-NOS/nodal PTCL with TFH phenotype sample is indicated in blue letters. NA, not analyzed by deep sequencing. The filled and dashed red arrows indicate mutations and no mutations, respectively. NOTCH1 is marked by red letters because this is repetitive.
    Figure Legend Snippet: B-cell-specific mutations in nodal T-cell lymphomas. The results of Sanger sequencing and/or amplicon-based deep sequencing for some newly identified gene mutations in whole tumor, PD1+ cells and CD20+ cells are shown. The numeric values indicate allele frequencies of mutations defined by deep sequencing. The AITL samples are indicated in black letters. The PTCL-NOS/nodal PTCL with TFH phenotype sample is indicated in blue letters. NA, not analyzed by deep sequencing. The filled and dashed red arrows indicate mutations and no mutations, respectively. NOTCH1 is marked by red letters because this is repetitive.

    Techniques Used: Sequencing, Amplification

    RHOA mutations are specific to PD1+ cells. ( a ) An example of the immunostaining pattern for PD1 and CD20 in AITL. Left, PD1+ cells; right, CD20+ cells. ( b ) Sequences of G17V RHOA mutations in whole tumor, PD1+ cells and CD20+ cells. The numeric values indicate allele frequencies of mutations defined by amplicon-based deep sequencing. The AITL samples are indicated in black letters. The nodal PTCL with TFH phenotype sample is indicated in red letters *: RHOA c.A51T:p.G17V, silent mutation. The filled and dashed red arrows indicate mutations and no mutations, respectively.
    Figure Legend Snippet: RHOA mutations are specific to PD1+ cells. ( a ) An example of the immunostaining pattern for PD1 and CD20 in AITL. Left, PD1+ cells; right, CD20+ cells. ( b ) Sequences of G17V RHOA mutations in whole tumor, PD1+ cells and CD20+ cells. The numeric values indicate allele frequencies of mutations defined by amplicon-based deep sequencing. The AITL samples are indicated in black letters. The nodal PTCL with TFH phenotype sample is indicated in red letters *: RHOA c.A51T:p.G17V, silent mutation. The filled and dashed red arrows indicate mutations and no mutations, respectively.

    Techniques Used: Immunostaining, Amplification, Sequencing, Mutagenesis

    2) Product Images from "Identification of novel SNPs in differentially expressed genes and its association with horn cancer of Bos indicus bullocks by next-generation sequencing"

    Article Title: Identification of novel SNPs in differentially expressed genes and its association with horn cancer of Bos indicus bullocks by next-generation sequencing

    Journal: 3 Biotech

    doi: 10.1007/s13205-015-0351-0

    Summary of amplicon sequencing runs for each sample of HC and HN using Ion Torrent PGM sequencing system
    Figure Legend Snippet: Summary of amplicon sequencing runs for each sample of HC and HN using Ion Torrent PGM sequencing system

    Techniques Used: Amplification, Sequencing

    Related Articles

    Sequencing:

    Article Title: Identification of cell-type-specific mutations in nodal T-cell lymphomas
    Article Snippet: .. Amplicon-based sequencing The libraries were prepared using the Ion Plus Fragment Library Kit according to the protocol for preparing short amplicon libraries (Life Technologies). .. Briefly, PCR amplicons were ligated to the barcode adapters and P1 adapters and then amplified.

    Article Title: Somatic Point Mutation Calling in Low Cellularity Tumors
    Article Snippet: .. On the SOLiD v4 platform qSNP called 85% of the 454 previously verified somatic mutations as well as 25 novel mutations that were verified using amplicon-based sequencing on the Ion Torrent platform ( , ). ..

    Article Title: Somatic Point Mutation Calling in Low Cellularity Tumors
    Article Snippet: .. All somatic qSNP calls made in the 100% cell line sample were selected for verification by amplicon-based sequencing on the Ion Torrent PGM. .. The remaining mutation calls were assessed for evidence on an alternate sequencing platform - HiSeq 2000 for calls made on the SOLiD v4 platform and vice versa.

    Article Title: Live-Cell Mesothelioma Biobank to Explore Mechanisms of Tumor Progression
    Article Snippet: .. For targeted amplicon-based sequencing, we developed a custom-designed Ion AmpliSeq MPM Panel (Thermo Fisher Scientific), covering the coding regions of 30 genes that were reported to be commonly mutated in MPM. .. 10 ng of either FFPE tumor or primary cell DNA were used as an input for library preparation, following the Ion AmpliSeq DNA Library Preparation user guide (Thermo Fisher Scientific).

    Article Title: Identification of novel SNPs in differentially expressed genes and its association with horn cancer of Bos indicus bullocks by next-generation sequencing
    Article Snippet: .. Results To validate the SNPs identified in our previous study as well as to investigate the suitability of amplicon-based sequencing in identifying mutations in marginally small number of samples using Ion Torrent PGM, we successfully amplified the 91 SNPs located in 69 genes out of 100 targeted SNPs across the 75 genes in 52 samples of each HC and HN (91 % coverage of targeted SNPs). .. Equal amounts of DNA from 69 PCR products were pooled and subjected to Ion Torrent PGM sequencing system using 316 chip and 300 bp chemistry.

    Article Title: High frequency of inactivating tetraspanin CD37 mutations in diffuse large B-cell lymphoma at immune-privileged sites
    Article Snippet: .. CD37 mutation analysis of the discovery cohort was performed by amplicon-based sequencing with Ion Torrent and Sanger sequencing. .. For the validation cohort, single-molecule molecular inversion probe mutation analysis and sequencing with Ion Torrent included the CD37 gene and hotspot loci of CARD11 , CD79A , CD79B , and MYD88 .

    Mutagenesis:

    Article Title: High frequency of inactivating tetraspanin CD37 mutations in diffuse large B-cell lymphoma at immune-privileged sites
    Article Snippet: .. CD37 mutation analysis of the discovery cohort was performed by amplicon-based sequencing with Ion Torrent and Sanger sequencing. .. For the validation cohort, single-molecule molecular inversion probe mutation analysis and sequencing with Ion Torrent included the CD37 gene and hotspot loci of CARD11 , CD79A , CD79B , and MYD88 .

    Amplification:

    Article Title: Identification of cell-type-specific mutations in nodal T-cell lymphomas
    Article Snippet: .. Amplicon-based sequencing The libraries were prepared using the Ion Plus Fragment Library Kit according to the protocol for preparing short amplicon libraries (Life Technologies). .. Briefly, PCR amplicons were ligated to the barcode adapters and P1 adapters and then amplified.

    Article Title: Somatic Point Mutation Calling in Low Cellularity Tumors
    Article Snippet: .. On the SOLiD v4 platform qSNP called 85% of the 454 previously verified somatic mutations as well as 25 novel mutations that were verified using amplicon-based sequencing on the Ion Torrent platform ( , ). ..

    Article Title: Somatic Point Mutation Calling in Low Cellularity Tumors
    Article Snippet: .. All somatic qSNP calls made in the 100% cell line sample were selected for verification by amplicon-based sequencing on the Ion Torrent PGM. .. The remaining mutation calls were assessed for evidence on an alternate sequencing platform - HiSeq 2000 for calls made on the SOLiD v4 platform and vice versa.

    Article Title: Live-Cell Mesothelioma Biobank to Explore Mechanisms of Tumor Progression
    Article Snippet: .. For targeted amplicon-based sequencing, we developed a custom-designed Ion AmpliSeq MPM Panel (Thermo Fisher Scientific), covering the coding regions of 30 genes that were reported to be commonly mutated in MPM. .. 10 ng of either FFPE tumor or primary cell DNA were used as an input for library preparation, following the Ion AmpliSeq DNA Library Preparation user guide (Thermo Fisher Scientific).

    Article Title: Identification of novel SNPs in differentially expressed genes and its association with horn cancer of Bos indicus bullocks by next-generation sequencing
    Article Snippet: .. Results To validate the SNPs identified in our previous study as well as to investigate the suitability of amplicon-based sequencing in identifying mutations in marginally small number of samples using Ion Torrent PGM, we successfully amplified the 91 SNPs located in 69 genes out of 100 targeted SNPs across the 75 genes in 52 samples of each HC and HN (91 % coverage of targeted SNPs). .. Equal amounts of DNA from 69 PCR products were pooled and subjected to Ion Torrent PGM sequencing system using 316 chip and 300 bp chemistry.

    Article Title: High frequency of inactivating tetraspanin CD37 mutations in diffuse large B-cell lymphoma at immune-privileged sites
    Article Snippet: .. CD37 mutation analysis of the discovery cohort was performed by amplicon-based sequencing with Ion Torrent and Sanger sequencing. .. For the validation cohort, single-molecule molecular inversion probe mutation analysis and sequencing with Ion Torrent included the CD37 gene and hotspot loci of CARD11 , CD79A , CD79B , and MYD88 .

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