direct cancer hotspot panel  (New England Biolabs)


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    Name:
    NEBNext Direct Cancer HotSpot Panel
    Description:
    NEBNext Direct Cancer HotSpot Panel 24 rxns
    Catalog Number:
    e7000l
    Price:
    3259
    Size:
    24 rxns
    Category:
    PCR Product Detection Kits
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    Structured Review

    New England Biolabs direct cancer hotspot panel
    NEBNext Direct Cancer HotSpot Panel
    NEBNext Direct Cancer HotSpot Panel 24 rxns
    https://www.bioz.com/result/direct cancer hotspot panel/product/New England Biolabs
    Average 95 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    direct cancer hotspot panel - by Bioz Stars, 2020-10
    95/100 stars

    Images

    1) Product Images from "Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling"

    Article Title: Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling

    Journal: Cancers

    doi: 10.3390/cancers12061588

    Accuracy rates of three NGS assays assessed with the Seraseq ctDNA Reference Material. ( A – D ) To assess the variant calling accuracy of the tested assays, we set 0.5%, 0.2%, and 0.1% thresholds for the limit of detection (LOD). Variants known to be present in the Seraseq ctDNA Reference Material v2 and called with a VAFs above the LOD were considered as true positives. Variants with VAFs higher than the LOD but not reported by SeraCare were considered as false positives. Shown are accuracy rates results for five different reference materials with various VAFs for ( A ) the Oncomine Lung cfDNA Assay (Oncomine) ( B ) a pre-filtered set of variants located in hotspot regions from the Oncomine Lung cfDNA Assay (Oncomine) ( C ) the AVENIO Targeted Kit (AVENIO), ( D ) the QIAseq Actionable Panel (QIAseq) ( E ) Accuracy of the AVENIO Targeted kit assessed with the Seraseq ctDNA Complete reference material.
    Figure Legend Snippet: Accuracy rates of three NGS assays assessed with the Seraseq ctDNA Reference Material. ( A – D ) To assess the variant calling accuracy of the tested assays, we set 0.5%, 0.2%, and 0.1% thresholds for the limit of detection (LOD). Variants known to be present in the Seraseq ctDNA Reference Material v2 and called with a VAFs above the LOD were considered as true positives. Variants with VAFs higher than the LOD but not reported by SeraCare were considered as false positives. Shown are accuracy rates results for five different reference materials with various VAFs for ( A ) the Oncomine Lung cfDNA Assay (Oncomine) ( B ) a pre-filtered set of variants located in hotspot regions from the Oncomine Lung cfDNA Assay (Oncomine) ( C ) the AVENIO Targeted Kit (AVENIO), ( D ) the QIAseq Actionable Panel (QIAseq) ( E ) Accuracy of the AVENIO Targeted kit assessed with the Seraseq ctDNA Complete reference material.

    Techniques Used: Next-Generation Sequencing, Variant Assay

    Detection rates of five commercially available mutation analysis kits. Shown are the detection rates of mutations (SNVs and indels) in the Seraseq ctDNA Reference Material v2 at various variant allele frequencies (VAF) for ( A ) the Oncomine Lung cfDNA Assay (Oncomine), ( B ) the AVENIO Targeted Kit (AVENIO Targeted), ( C ) the QIAseq Human Actionable Solid Tumor Panel (QIAseq), ( D ) the GeneRead QIAact Lung UMI Panel (QIAact), and ( E ) the NebNext Direct Cancer Hotspot Panel (NEB). ( F ) Shown are the detection rates of mutations in the Seraseq ctDNA Complete reference Material for the AVENIO Targeted kit. The numbers in brackets reflect the number of mutations covered by the panel.
    Figure Legend Snippet: Detection rates of five commercially available mutation analysis kits. Shown are the detection rates of mutations (SNVs and indels) in the Seraseq ctDNA Reference Material v2 at various variant allele frequencies (VAF) for ( A ) the Oncomine Lung cfDNA Assay (Oncomine), ( B ) the AVENIO Targeted Kit (AVENIO Targeted), ( C ) the QIAseq Human Actionable Solid Tumor Panel (QIAseq), ( D ) the GeneRead QIAact Lung UMI Panel (QIAact), and ( E ) the NebNext Direct Cancer Hotspot Panel (NEB). ( F ) Shown are the detection rates of mutations in the Seraseq ctDNA Complete reference Material for the AVENIO Targeted kit. The numbers in brackets reflect the number of mutations covered by the panel.

    Techniques Used: Mutagenesis, Variant Assay

    Related Articles

    Mutagenesis:

    Article Title: Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling
    Article Snippet: .. Sensitivity Assessment of Five Commercially Available Mutation Assays Using the Seraseq® ctDNA Reference Materials Next, we assessed the performance of five commercially available mutation assays, i.e., the AVENIO Targeted Kit (Roche, herein referred to AVENIO Targeted; sequenced on an Illumina NextSeq), the QIAseq Human Actionable Solid Tumor (QIAGEN, herein referred to QIAseq; sequenced on an Illumina NextSeq), the NebNext Direct Cancer Hotspot Panel (New England Biolabs, herein referred to NEB; sequenced on an Illumina NextSeq), the GeneRead QIAact Lung UMI Panel (QIAGEN, herein referred to QIAact; sequenced on a QIAGEN GeneReader) and the Oncomine Lung cfDNA Assay (Thermo Fisher, herein referred to Oncomine; sequenced on the Thermo Fisher IonTorrent) at a single center (MUG) ( B left leg, ). ..

    Sonication:

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: .. Genomic DNA was fragmented to 150–200 bp by sonication using a Covaris S2 (7 min, 0.5% duty, intensity = 0.1, 50 cycles/burst; Covaris, Inc., Woburn, MA, USA) for three library preparation kits: the Archer® Reveal ctDNA™ 28, NEBNext Direct® Cancer HotSpot Panel, and Nugen Ovation® Custom Cancer Panel. .. In the Qiagen HCCP and HASTP, genomic DNA was fragmented in the fragmentation buffer included in the kits.

    Next-Generation Sequencing:

    Article Title: Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors
    Article Snippet: .. Next-generation sequencingNext-generation sequencing (NGS) was performed on the Illumina MiSeq System (Illumina, Inc., CA) using the NEBNext Direct Cancer HotSpot Panel (New England BioLabs, Inc., MA). .. Isolated genomic DNA from CRCs and PBTs was quantified using the Quantifluor ONE dsDNA kit (Promega Corporation, WI) by following the manufacturer’s protocol.

    Article Title: Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors
    Article Snippet: .. Targeted next-generation sequencing Targeted next-generation sequencing was performed on three pairs of CRCs and corresponding PBTs (cases 2, 4 and 6) and in one unpaired CRC line (case 3) using the MiSeq platform and the NEBNext Direct Cancer Hotspot Panel. ..

    Sequencing:

    Article Title: Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors
    Article Snippet: .. Next-generation sequencingNext-generation sequencing (NGS) was performed on the Illumina MiSeq System (Illumina, Inc., CA) using the NEBNext Direct Cancer HotSpot Panel (New England BioLabs, Inc., MA). .. Isolated genomic DNA from CRCs and PBTs was quantified using the Quantifluor ONE dsDNA kit (Promega Corporation, WI) by following the manufacturer’s protocol.

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    New England Biolabs direct cancer hotspot panel
    Accuracy rates of three NGS assays assessed with the Seraseq ctDNA Reference Material. ( A – D ) To assess the variant calling accuracy of the tested assays, we set 0.5%, 0.2%, and 0.1% thresholds for the limit of detection (LOD). Variants known to be present in the Seraseq ctDNA Reference Material v2 and called with a VAFs above the LOD were considered as true positives. Variants with VAFs higher than the LOD but not reported by SeraCare were considered as false positives. Shown are accuracy rates results for five different reference materials with various VAFs for ( A ) the Oncomine Lung cfDNA Assay (Oncomine) ( B ) a pre-filtered set of variants located in <t>hotspot</t> regions from the Oncomine Lung cfDNA Assay (Oncomine) ( C ) the AVENIO Targeted Kit (AVENIO), ( D ) the QIAseq Actionable Panel (QIAseq) ( E ) Accuracy of the AVENIO Targeted kit assessed with the Seraseq ctDNA Complete reference material.
    Direct Cancer Hotspot Panel, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/direct cancer hotspot panel/product/New England Biolabs
    Average 95 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    direct cancer hotspot panel - by Bioz Stars, 2020-10
    95/100 stars
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    Accuracy rates of three NGS assays assessed with the Seraseq ctDNA Reference Material. ( A – D ) To assess the variant calling accuracy of the tested assays, we set 0.5%, 0.2%, and 0.1% thresholds for the limit of detection (LOD). Variants known to be present in the Seraseq ctDNA Reference Material v2 and called with a VAFs above the LOD were considered as true positives. Variants with VAFs higher than the LOD but not reported by SeraCare were considered as false positives. Shown are accuracy rates results for five different reference materials with various VAFs for ( A ) the Oncomine Lung cfDNA Assay (Oncomine) ( B ) a pre-filtered set of variants located in hotspot regions from the Oncomine Lung cfDNA Assay (Oncomine) ( C ) the AVENIO Targeted Kit (AVENIO), ( D ) the QIAseq Actionable Panel (QIAseq) ( E ) Accuracy of the AVENIO Targeted kit assessed with the Seraseq ctDNA Complete reference material.

    Journal: Cancers

    Article Title: Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling

    doi: 10.3390/cancers12061588

    Figure Lengend Snippet: Accuracy rates of three NGS assays assessed with the Seraseq ctDNA Reference Material. ( A – D ) To assess the variant calling accuracy of the tested assays, we set 0.5%, 0.2%, and 0.1% thresholds for the limit of detection (LOD). Variants known to be present in the Seraseq ctDNA Reference Material v2 and called with a VAFs above the LOD were considered as true positives. Variants with VAFs higher than the LOD but not reported by SeraCare were considered as false positives. Shown are accuracy rates results for five different reference materials with various VAFs for ( A ) the Oncomine Lung cfDNA Assay (Oncomine) ( B ) a pre-filtered set of variants located in hotspot regions from the Oncomine Lung cfDNA Assay (Oncomine) ( C ) the AVENIO Targeted Kit (AVENIO), ( D ) the QIAseq Actionable Panel (QIAseq) ( E ) Accuracy of the AVENIO Targeted kit assessed with the Seraseq ctDNA Complete reference material.

    Article Snippet: Sensitivity Assessment of Five Commercially Available Mutation Assays Using the Seraseq® ctDNA Reference Materials Next, we assessed the performance of five commercially available mutation assays, i.e., the AVENIO Targeted Kit (Roche, herein referred to AVENIO Targeted; sequenced on an Illumina NextSeq), the QIAseq Human Actionable Solid Tumor (QIAGEN, herein referred to QIAseq; sequenced on an Illumina NextSeq), the NebNext Direct Cancer Hotspot Panel (New England Biolabs, herein referred to NEB; sequenced on an Illumina NextSeq), the GeneRead QIAact Lung UMI Panel (QIAGEN, herein referred to QIAact; sequenced on a QIAGEN GeneReader) and the Oncomine Lung cfDNA Assay (Thermo Fisher, herein referred to Oncomine; sequenced on the Thermo Fisher IonTorrent) at a single center (MUG) ( B left leg, ).

    Techniques: Next-Generation Sequencing, Variant Assay

    Detection rates of five commercially available mutation analysis kits. Shown are the detection rates of mutations (SNVs and indels) in the Seraseq ctDNA Reference Material v2 at various variant allele frequencies (VAF) for ( A ) the Oncomine Lung cfDNA Assay (Oncomine), ( B ) the AVENIO Targeted Kit (AVENIO Targeted), ( C ) the QIAseq Human Actionable Solid Tumor Panel (QIAseq), ( D ) the GeneRead QIAact Lung UMI Panel (QIAact), and ( E ) the NebNext Direct Cancer Hotspot Panel (NEB). ( F ) Shown are the detection rates of mutations in the Seraseq ctDNA Complete reference Material for the AVENIO Targeted kit. The numbers in brackets reflect the number of mutations covered by the panel.

    Journal: Cancers

    Article Title: Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling

    doi: 10.3390/cancers12061588

    Figure Lengend Snippet: Detection rates of five commercially available mutation analysis kits. Shown are the detection rates of mutations (SNVs and indels) in the Seraseq ctDNA Reference Material v2 at various variant allele frequencies (VAF) for ( A ) the Oncomine Lung cfDNA Assay (Oncomine), ( B ) the AVENIO Targeted Kit (AVENIO Targeted), ( C ) the QIAseq Human Actionable Solid Tumor Panel (QIAseq), ( D ) the GeneRead QIAact Lung UMI Panel (QIAact), and ( E ) the NebNext Direct Cancer Hotspot Panel (NEB). ( F ) Shown are the detection rates of mutations in the Seraseq ctDNA Complete reference Material for the AVENIO Targeted kit. The numbers in brackets reflect the number of mutations covered by the panel.

    Article Snippet: Sensitivity Assessment of Five Commercially Available Mutation Assays Using the Seraseq® ctDNA Reference Materials Next, we assessed the performance of five commercially available mutation assays, i.e., the AVENIO Targeted Kit (Roche, herein referred to AVENIO Targeted; sequenced on an Illumina NextSeq), the QIAseq Human Actionable Solid Tumor (QIAGEN, herein referred to QIAseq; sequenced on an Illumina NextSeq), the NebNext Direct Cancer Hotspot Panel (New England Biolabs, herein referred to NEB; sequenced on an Illumina NextSeq), the GeneRead QIAact Lung UMI Panel (QIAGEN, herein referred to QIAact; sequenced on a QIAGEN GeneReader) and the Oncomine Lung cfDNA Assay (Thermo Fisher, herein referred to Oncomine; sequenced on the Thermo Fisher IonTorrent) at a single center (MUG) ( B left leg, ).

    Techniques: Mutagenesis, Variant Assay