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.
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
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:
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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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