Product Class: Kit

NEBNext Direct® Genotyping Solution

As of December 15, 2025,  new requests for NEBNext Direct Genotyping Solution Panels will no longer be accepted. For any questions regarding re-ordering of reagents, please contact the customized solutions team. 

Product Introduction

Catalog #E9530

The NEBNext Direct Genotyping Solution delivers cost-effective, high-throughput, sequence-based target genotyping for a wide variety of applications in plant, animal, and human.

  • Ideal solution for genotyping hundreds to thousands of markers
  • Reduce costs and streamline workflow through pre-capture pooling of up to 96 samples
  • Maximize sequencer efficiency through dual barcode sample indexing plus Unique Molecular Identifier
  • Unparalleled target coverage uniformity through unique capture-based enrichment
  • Eliminate marker dropouts with finely tuned bait design
  • Increase sample throughput using 1-day, automatable workflow

 

Bioz Badge Exists : True
Catalog # Size Concentration
E9500S 96 reactions

Product Information

Description

The NEBNext Direct Genotyping Solution combines highly multiplexed, capture-based enrichment with maximum efficiency next-generation sequencing to deliver cost-effective, high-throughput, genotyping for a wide variety of applications. Applicable for marker ranges spanning 100-5,000 markers, pre-capture multiplexing of up to 96 samples combined with dual indexed sequencing allows over 3.8 million genotypes in a single Illumina® sequencing run.

 

Figure 1: NEBNext Direct Genotyping Solution workflow 





Figure 2: Passing filter reads across 96 pooled samples



Passing filter reads across 96 tomato DNA samples that were enriched using a genotyping panel consisting of 2,309 publicly available SolCAP markers and the NEBNext Direct Genotyping Solution. 25 ng of purified tomato DNA was used for each sample. Samples were index-tagged and pooled prior to hybridization and libraries were sequenced on an Illumina® MiSeq® with 20 cycles of Read 1 to sequence the 12 base UMI and 8 base sample index, and 75 cycles of Read 2 to sequence the targets.


Figure 3: NEBNext Direct Genotyping Solution demonstrates similar coverage across 96 pooled samples



Mean SNP coverage of 2,309 SolCAP markers across 96 samples. 25 ng of purified tomato DNA was used for each sample. Samples were index-tagged and pooled prior to hybridization and Libraries were sequenced on an Illumina MiSeq with 20 cycles of Read 1 to sequence the 12 base UMI and 8 base sample index, and 75 cycles of Read 2 to sequence the targets.


Figure 4: Specificity of enrichment of NEBNext Direct Genotyping Solution across 96 pooled samples



The percent of passing filter reads mapping to targeted regions demonstrates high specificity across 96 multiplexed samples using the NEBNext Direct Genotyping Solution. 25 ng of purified tomato DNA was used as input for each sample. Samples were index-tagged and pooled prior to hybridization and Libraries were sequenced on an Illumina MiSeq with 20 cycles of Read 1 to sequence the 12 base UMI and 8 base sample index, and 75 cycles of Read 2 to sequence the targets.


Figure 5: Mean Coverage across 2309 markers within a single sample


Histogram of coverage across each of the 2,309 SolCAP markers demonstrates evenness of enrichment across targets and coverage levels sufficient for genotyping calls. These data represent enrichment of a single tomato sample pooled with 95 others prior to hybridization. 25 ng of purified tomato DNA was used for each sample. Samples were index-tagged and pooled prior to hybridization and libraries were sequenced on an Illumina MiSeq with 20 cycles of Read 1 to sequence the 12 base UMI and 8 base sample index, and 75 cycles of Read 2 to sequence the targets.


Reagents Supplied for E9500

The following reagents are supplied with this product:

  Store at (°C) Concentration
NEBNext Direct® GS Fragmentation Buffer -20  
NEBNext Direct® GS Fragmentation Enzyme Mix -20  
NEBNext Direct® GS Indexed 5′ Adaptor Plate -20  
NEBNext Direct® GS 5' Adaptor Ligation Master Mix -20  
NEBNext Direct® GS Stop Solution 4  
NEBNext Direct® GS Sample Purification Beads RT  

This product is related to the following categories:
Automation for NEBNext® NGS Library Prep,

Properties & Usage

Application Features

  • The most efficient targeted genotyping-by-sequencing solution available
    • Pre-capture multiplexing of up to 96 samples per enrichment
    • Flexibility from 100’s to 1,000’s of markers per sample
    • Dual indexing plus Unique Molecular Identifier (UMI)
    • Optimized bait design captures both DNA strands
  • Unique and rapid, capture-based enrichment for optimal sequencing performance
    • Highly specific enrichment, > 90% of reads mapping to targets
    • Coverage uniformity - sequence less and avoid over- and under-representation
    • Similar performance from DNA across CTAB and column-based extraction procedures
  • Fast and streamlined, automation-friendly workflow, with minimal handling steps and hands-on time'
    • Pooled capture eliminates redundancy
    • Single-day workflow
    • Automation friendly

FAQs & Troubleshooting

FAQs

  1. How many times can the -20°C reagents supplied in the NEBNext Direct® Genotyping Solution be frozen and thawed? 
  2. How many times can the 4°C reagents be brought to room temperature?
  3. My NEBNext Direct Genolytyping Solution 4°C box accidentally froze, can I still use it?
  4. I accidentally stored the Sample Purification Beads and Bead Wash 1 (BW1) at 4°C. Can I still use them?
  5. What is the shelf life of the NEBNext Direct Genotyping Solution?
  6. What method do you recommend for extracting genomic DNA and FFPE DNA before use with the NEBNext Direct Genotyping Solution?
  7. What is the recommended method for quantitating my input DNA?
  8. If my input amount is low, should I dilute the adaptors?
  9. What type and how much starting material do I need to use when preparing libraries using the NEBNext Direct Genotyping Solution?
  10. Which magnets (2 ml and 200 µl sizes) do you recommend?
  11. I used Bead Wash 1 (BW1) when I should have used Bead Wash 2 (BW2) during the Post-reaction Wash. Can I do another wash with Bead Wash 2 (BW2) to save my sample?
  12. Does incomplete removal of Bead Wash 1 prior to adding Bead Wash 2 inhibit the next step?
  13. Can I use any Q5® High-Fidelity DNA Polymerase formulation with this kit?
  14. If I have adaptor dimer in my finished library, can I perform another bead cleanup to remove it?
  15. How many/ few samples can I pool together for my sequencing run?
  16. Are blocking oligos required for this kit?
  17. Is the NEBNext Direct Genotyping Solution available in bulk or customized format?

Quality, Safety & Legal

Quality Assurance Statement

Quality Control tests are performed on each new lot of NEB product to meet the specifications designated for it. Specifications and individual lot data from the tests that are performed for this particular product can be found and downloaded on the Product Specification Sheet, Certificate of Analysis, data card or product manual. Further information regarding NEB product quality can be found here.

Legal and Disclaimers

Products and content are covered by one or more patents, trademarks and/or copyrights owned or controlled by New England Biolabs, Inc (NEB). The use of trademark symbols does not necessarily indicate that the name is trademarked in the country where it is being read; it indicates where the content was originally developed. The use of this product may require the buyer to obtain additional third-party intellectual property rights for certain applications. For more information, please email busdev@neb.com.

This product is intended for research purposes only. This product is not intended to be used for therapeutic or diagnostic purposes in humans or animals.

New England Biolabs (NEB) is committed to practicing ethical science – we believe it is our job as researchers to ask the important questions that when answered will help preserve our quality of life and the world that we live in. However, this research should always be done in safe and ethical manner. Learn more.

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