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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    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 4 article reviews
    Price from $9.99 to $1999.99
    direct cancer hotspot panel - by Bioz Stars, 2020-02
    95/100 stars

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    Related Articles

    Amplification:

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: .. For example, the enrichment method of the NEBNext Direct Cancer Hotspot Panel involves a combination of hybrid section-based capture and PCR amplification in which a hybridized bait sequence is used as a primer to enrich targets that are distinct from the others. .. Adaptor ligation and subsequent PCR amplification using combinations of primers targeting specific genomic regions and a universal adaptor sequence are used in the ArcherDx and Qiagen kits.

    Article Title: A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment
    Article Snippet: BST–DSN reaction with ssDNA (synthetic oligonucleotides): Single stranded oligonucleotides (107–2313 bp long) were used with TdT and followed by BST–DSN reaction to produce amplified B-dUTP -labeled probes. .. The probe sets tested were a set of 33 target-specific 120 bp long oligonucleotides previously used in our laboratory for hybridization capture and target enrichment prior to sequencing (Panel A, ‘ultramers’ from IDT, 120 bp/probe); the NEBNext™ Direct hotspot cancer panel (Panel B, 190 targets covering 50 genes probes, 107–2313 bp/probe) and the xGen Pan Cancer panel (Panel C, 7816 ultramer probes covering 127 genes, 120 bp/probe).

    Selection:

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: Target enrichment is a critical component of targeted deep next-generation sequencing for the cost-effective and sensitive detection of mutations, which is predominantly performed by either hybrid selection or PCR. .. In this study, we evaluated and compared the performances of five commercial library kits from four vendors: the Archer® Reveal ctDNA™ 28 Kit, NEBNext Direct® Cancer HotSpot Panel, Nugen Ovation® Custom Target Enrichment System, Qiagen Human Comprehensive Cancer Panel(HCCP), and Qiagen Human Actionable Solid Tumor Panel(HASTP).

    Ligation:

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: For example, the enrichment method of the NEBNext Direct Cancer Hotspot Panel involves a combination of hybrid section-based capture and PCR amplification in which a hybridized bait sequence is used as a primer to enrich targets that are distinct from the others. .. Adaptor ligation and subsequent PCR amplification using combinations of primers targeting specific genomic regions and a universal adaptor sequence are used in the ArcherDx and Qiagen kits.

    Isolation:

    Article Title: Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors
    Article Snippet: Isolated genomic DNA from CRCs and PBTs was quantified using the Quantifluor ONE dsDNA kit (Promega Corporation, WI) by following the manufacturer’s protocol. .. Each sheared DNA sample was enriched for DNA fragments with the NEBNext Direct Cancer HotSpot Panel, which targets 190 cancer hotspot regions in 50 genes.

    Next-Generation Sequencing:

    Article Title: Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors
    Article Snippet: Paragraph title: Next-generation sequencing ... Each sheared DNA sample was enriched for DNA fragments with the NEBNext Direct Cancer HotSpot Panel, which targets 190 cancer hotspot regions in 50 genes.

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: Target enrichment is a critical component of targeted deep next-generation sequencing for the cost-effective and sensitive detection of mutations, which is predominantly performed by either hybrid selection or PCR. .. In this study, we evaluated and compared the performances of five commercial library kits from four vendors: the Archer® Reveal ctDNA™ 28 Kit, NEBNext Direct® Cancer HotSpot Panel, Nugen Ovation® Custom Target Enrichment System, Qiagen Human Comprehensive Cancer Panel(HCCP), and Qiagen Human Actionable Solid Tumor Panel(HASTP).

    Article Title: Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer
    Article Snippet: Paragraph title: Technical comparison of NGS library preparation kits ... In April 2016, New England Biolabs released the NEBNext Direct Cancer HotSpot Panel kit, which relies on the hybridization-based capture method.

    Article Title: Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors
    Article Snippet: .. Next-generation sequencing Next-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. ..

    Polymerase Chain Reaction:

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: Currently, several commercial library construction kits based on PCR enrichment are available for UMIs, but there have been no systematic studies to compare their performances. .. In this study, we evaluated and compared the performances of five commercial library kits from four vendors: the Archer® Reveal ctDNA™ 28 Kit, NEBNext Direct® Cancer HotSpot Panel, Nugen Ovation® Custom Target Enrichment System, Qiagen Human Comprehensive Cancer Panel(HCCP), and Qiagen Human Actionable Solid Tumor Panel(HASTP).

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: .. For example, the enrichment method of the NEBNext Direct Cancer Hotspot Panel involves a combination of hybrid section-based capture and PCR amplification in which a hybridized bait sequence is used as a primer to enrich targets that are distinct from the others. .. Adaptor ligation and subsequent PCR amplification using combinations of primers targeting specific genomic regions and a universal adaptor sequence are used in the ArcherDx and Qiagen kits.

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: .. To accurately compare the kits, target regions in each kit were made by adding 100 bp from the end positions of the target-specific PCR primers, except for in the NEBnext direct® Cancer HotSpot Panel. .. Because the manufacturer policy did not reveal the genomic positions of the target-specific PCR primers, we used the target regions of the NEB kit indicated on their website.

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: The performances of these commercial kits using a PCR-based target enrichment method incorporated with the UMI sequence have not been systematically compared yet. .. In this study, we examined five kits: the Archer® Reveal ctDNA™ 28 Kit, NEBNext Direct® Cancer HotSpot Panel, Nugen Ovation® Custom Target Enrichment System, Qiagen Human Comprehensive Cancer Panel, and Qiagen Human Actionable Solid Tumor Panel.

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: Library preparation A total of five library preparation kits were tested: the Archer® Reveal ctDNA™ 28 Kit (ArcherDX Inc., Boulder, CO, USA), NEBNext Direct® Cancer HotSpot Panel (New England Biolabs, Inc., Ipswich, MA, USA), Nugen Ovation® Custom Target Enrichment System (NuGEN Technologies, Inc., San Carlos, CA, USA), Qiagen Human Comprehensive Cancer Panel, and Qiagen Human Actionable Solid Tumor Panel. .. Also, UMI sequences were included in that Nugen kit to distinguish PCR-duplicated fragments like the Ovation® Cancer Panel 2.0 Target Enrichment System.

    Article Title: Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer
    Article Snippet: For whole genome sequencing, the Accel-NGS® 2S PCR-Free DNA Library Kit is recommended. .. In April 2016, New England Biolabs released the NEBNext Direct Cancer HotSpot Panel kit, which relies on the hybridization-based capture method.

    Construct:

    Article Title: Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors
    Article Snippet: Each sheared DNA sample was enriched for DNA fragments with the NEBNext Direct Cancer HotSpot Panel, which targets 190 cancer hotspot regions in 50 genes. .. Each enriched DNA fragment was constructed into individual indexed libraries by following the manufacturer’s protocol.

    Produced:

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: Sequencing metrics were produced by Picard v1.93. .. To accurately compare the kits, target regions in each kit were made by adding 100 bp from the end positions of the target-specific PCR primers, except for in the NEBnext direct® Cancer HotSpot Panel.

    Concentration Assay:

    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. .. One sample (PBT of case 6) had a low library concentration and did not produce as many reads (14,480 reads) compared to the other samples.

    Generated:

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: After distinct short oligonucleotides with random sequences tagging each template molecule were proposed as unique molecular identifiers (UMIs, also known as molecular barcodes), [ – ] accurately distinguishing PCR duplicates from copies of unique fragments generated by a pair of PCR primer became possible. .. For example, the enrichment method of the NEBNext Direct Cancer Hotspot Panel involves a combination of hybrid section-based capture and PCR amplification in which a hybridized bait sequence is used as a primer to enrich targets that are distinct from the others.

    Article Title: A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment
    Article Snippet: Moreover, BST–DSN products 20–80 bp size were generated irrespective of DNA input amount under the conditions applied, while the full range of products was 15–150 bp. .. The probe sets tested were a set of 33 target-specific 120 bp long oligonucleotides previously used in our laboratory for hybridization capture and target enrichment prior to sequencing (Panel A, ‘ultramers’ from IDT, 120 bp/probe); the NEBNext™ Direct hotspot cancer panel (Panel B, 190 targets covering 50 genes probes, 107–2313 bp/probe) and the xGen Pan Cancer panel (Panel C, 7816 ultramer probes covering 127 genes, 120 bp/probe).

    Article Title: A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment
    Article Snippet: NEBNext Direct™ Cancer hotspot panel (Panel B) and xGen Pan Cancer™ panel (Panel C) were purchased from NEB and IDT, respectively. .. The products generated from TdT reaction were then employed in a 10 μl final volume of BST–DSN reaction master mix containing Biotin-11-dUTP (B-dUTP) and anchored-oligo-dT ( ).

    Formalin-fixed Paraffin-Embedded:

    Article Title: Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer
    Article Snippet: Their newly released NEBNext Ultra II DNA Library Prep Kitis an improved version of the original NEBNext Ultra Kit and is amenable to library construction from as little as 500 pg of input FFPE DNA. .. In April 2016, New England Biolabs released the NEBNext Direct Cancer HotSpot Panel kit, which relies on the hybridization-based capture method.

    In Silico:

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: To accurately compare the kits, target regions in each kit were made by adding 100 bp from the end positions of the target-specific PCR primers, except for in the NEBnext direct® Cancer HotSpot Panel. .. For the in silico down-sampling of the fastq files carried out by GATK v2.2 [ ], we defined the raw read depth as the total number of bases divided by the total size (bp) of the target regions.

    Chromatin Immunoprecipitation:

    Article Title: A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment
    Article Snippet: NEBNext Direct™ Cancer hotspot panel (Panel B) and xGen Pan Cancer™ panel (Panel C) were purchased from NEB and IDT, respectively. .. Nucleotide removal kit (Qiagen) was used to purify the TBD products and the size of TBD products was analyzed on an Agilent DNA Chip 1000 analyzer (Agilent).

    Sequencing:

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: .. For example, the enrichment method of the NEBNext Direct Cancer Hotspot Panel involves a combination of hybrid section-based capture and PCR amplification in which a hybridized bait sequence is used as a primer to enrich targets that are distinct from the others. .. Adaptor ligation and subsequent PCR amplification using combinations of primers targeting specific genomic regions and a universal adaptor sequence are used in the ArcherDx and Qiagen kits.

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: Paragraph title: Sequencing data process ... To accurately compare the kits, target regions in each kit were made by adding 100 bp from the end positions of the target-specific PCR primers, except for in the NEBnext direct® Cancer HotSpot Panel.

    Article Title: A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment
    Article Snippet: .. The probe sets tested were a set of 33 target-specific 120 bp long oligonucleotides previously used in our laboratory for hybridization capture and target enrichment prior to sequencing (Panel A, ‘ultramers’ from IDT, 120 bp/probe); the NEBNext™ Direct hotspot cancer panel (Panel B, 190 targets covering 50 genes probes, 107–2313 bp/probe) and the xGen Pan Cancer panel (Panel C, 7816 ultramer probes covering 127 genes, 120 bp/probe). .. Results showed that 2800, 4500 and 3300 ng of TBD probes were generated from an initial 10, 2.7 and 112 ng of Panels A–C, respectively.

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: The performances of these commercial kits using a PCR-based target enrichment method incorporated with the UMI sequence have not been systematically compared yet. .. In this study, we examined five kits: the Archer® Reveal ctDNA™ 28 Kit, NEBNext Direct® Cancer HotSpot Panel, Nugen Ovation® Custom Target Enrichment System, Qiagen Human Comprehensive Cancer Panel, and Qiagen Human Actionable Solid Tumor Panel.

    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.

    Variant Assay:

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: The features of each kit including variant calling and the method of UMI tagging and enrichment of each kit are summarized (Additional files , and ). .. In this study, we examined five kits: the Archer® Reveal ctDNA™ 28 Kit, NEBNext Direct® Cancer HotSpot Panel, Nugen Ovation® Custom Target Enrichment System, Qiagen Human Comprehensive Cancer Panel, and Qiagen Human Actionable Solid Tumor Panel.

    Article Title: Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier
    Article Snippet: Thus, we thought that the Nugen custom kit should be sufficient to detect low allele frequency variants even though the low AF variant detection capability was not claimed on the specification sheet. .. 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.

    Labeling:

    Article Title: A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment
    Article Snippet: BST–DSN reaction with ssDNA (synthetic oligonucleotides): Single stranded oligonucleotides (107–2313 bp long) were used with TdT and followed by BST–DSN reaction to produce amplified B-dUTP -labeled probes. .. The probe sets tested were a set of 33 target-specific 120 bp long oligonucleotides previously used in our laboratory for hybridization capture and target enrichment prior to sequencing (Panel A, ‘ultramers’ from IDT, 120 bp/probe); the NEBNext™ Direct hotspot cancer panel (Panel B, 190 targets covering 50 genes probes, 107–2313 bp/probe) and the xGen Pan Cancer panel (Panel C, 7816 ultramer probes covering 127 genes, 120 bp/probe).

    Hybridization:

    Article Title: A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment
    Article Snippet: .. The probe sets tested were a set of 33 target-specific 120 bp long oligonucleotides previously used in our laboratory for hybridization capture and target enrichment prior to sequencing (Panel A, ‘ultramers’ from IDT, 120 bp/probe); the NEBNext™ Direct hotspot cancer panel (Panel B, 190 targets covering 50 genes probes, 107–2313 bp/probe) and the xGen Pan Cancer panel (Panel C, 7816 ultramer probes covering 127 genes, 120 bp/probe). .. Results showed that 2800, 4500 and 3300 ng of TBD probes were generated from an initial 10, 2.7 and 112 ng of Panels A–C, respectively.

    Article Title: Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer
    Article Snippet: .. In April 2016, New England Biolabs released the NEBNext Direct Cancer HotSpot Panel kit, which relies on the hybridization-based capture method. .. This kit enables DNA enrichment from 190 targets in 50 cancer-related genes starting with as few as 10 ng of DNA and is suitable for use with cfDNA and FFPE samples.

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  • 95
    New England Biolabs direct cancer hotspot panel
    Direct Cancer Hotspot Panel, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 2 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 2 article reviews
    Price from $9.99 to $1999.99
    direct cancer hotspot panel - by Bioz Stars, 2020-02
    95/100 stars
      Buy from Supplier

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