A complete targeted resequencing solution for a wide range of applications, with fast integrated workflow and options for custom and fixed enrichment panels.
Assay time
Hands-on time
Input quantity
Illumina DNA Prep with Enrichment, previously known as Nextera Flex for Enrichment, is the fastest and most flexible targeted sequencing solution for DNA in the Illumina library prep portfolio.
Find fast, optimized sequencing library preparation solutions for use in a wide range of applications.
Illumina DNA Prep with Enrichment
Fast, integrated DNA-based library preparation and enrichment workflow combining on-bead tagmentation with a single hybridization protocol for targeted sequencing applications.
Fast, integrated library preparation workflow for a wide range of applications, including sequencing of whole human genomes, amplicons, plasmids, and microbial genomes.
High-performing, fast, and integrated PCR-free library preparation workflow for sensitive applications such as human whole-genome sequencing or tumor–normal sequencing.
| Assay time | ~6.5 hr |
|---|---|
| Automation capability | Liquid handling robot(s) |
| Automation details | Explore available automation methods |
| Content specifications |
Custom: 0.5 - 15 Mb genomic content of interest, with Illumina Custom Enrichment Panels and Illumina Custom Enrichment Panel v2 Fixed panels: Content varies by panel. |
| Description | Prepare sequencing libraries for a variety of experiments, including whole-exome, custom, and fixed panel targeted sequencing, from low DNA inputs and a variety of sample types in ~6.5 hours. |
| Hands-on time | ~2 hr, ~2 hr |
| Input quantity | 10-1000 ng high-quality genomic DNA or 50-1000 ng FFPE DNA. (For blood and saliva, see the reference guide). |
| Instruments | MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, MiSeqDx in Research Mode, MiniSeq System, NextSeq 550Dx in Research Mode, NovaSeq X System, NovaSeq 6000Dx in Research Mode, NovaSeq 6000 System, NovaSeq X Plus System |
| Mechanism of action | Bead-bound transposomes and hybrid-capture chemistry |
| Method | Targeted DNA sequencing, Custom sequencing, Exome sequencing, Target enrichment |
| Multiplexing | Up to 384 available unique dual indexes. Pre-enrichment pooling of up to 12-plex is tested. |
| Nucleic acid type | DNA |
| Number of reactions | Custom workflow: 16 or 96 samples |
| On-target reads | ≥85% for exome panel (results from example data set; actual performance may vary) |
| Specialized sample types | Blood, Low-input samples, FFPE tissue, Saliva |
| Species category | Other, Human |
| Technology | Sequencing |
| Uniformity | ≥90% (% coverage at 20x for 4 Gb; for exome panel) |
| Variant class | Single nucleotide polymorphisms (SNPs), Loss of heterozygosity (LOH), Somatic variants, Germline variants, Insertions-deletions (indels), Copy number variants (CNVs) |
Illumina DNA Prep and Enrichment kits require use of an Illumina DNA/RNA UD Indexes Set. Dual indexing is encouraged.
Panels and probes are optional, order separately.
The Flex Lysis Kit complements blood DNA extraction.
The Infinium FFPE QC Kit is required to qualify FFPE samples.
The Infinium MIDI Heatblock Insert is necessary when using the SciGene Hybex Microheating system.
The Illumina Free Adapter Blocking Reagent (optional) is used to reduce index hopping levels.
Illumina Purification Beads are used for DNA purification and/or size selection of DNA fragments based on the beads:sample ratio.
The Illumina DNA Prep with Enrichment combines versatile, simple, and fast library preparation and enrichment from a wide range of DNA inputs and sample types to support broad target enrichment applications encompassing custom panels, fixed panels, and whole-exome panels.
Illumina DNA Prep with Enrichment
| Instrument | Recommended number of samples | Read length |
|---|---|---|
| iSeq 100 System | TruSight Cancer: 4 samples per run (based on 280× mean targeted coverage; 99% target coverage at 20×) |
2 x 100 bp |
| MiniSeq System | TruSight Cancer (samples per run): mid output: 8, high output: 25 (based on 280× mean targeted coverage; 99% target coverage at 20×) |
2 x 100 bp |
| MiSeq System | TruSight Cancer (samples per run): v2 reagents: 15, v3 reagents: 25 (based on 280× mean targeted coverage; 99% target coverage at 20×) |
2 x 100 bp |
| NextSeq 550 System | TruSight One (samples per run): mid output: 12, high output: 36 (based on 120× mean targeted coverage; 95% target coverage at 20×) |
2 x 100 bp |
| NovaSeq 6000 System | Exome sampels per run, by flow cell type) - Illumina DNA Prep with Exome 2.5 Enrichment: SP: 34, S1: 69, S2: 176, S4: 428 based on 50× mean target coverage, 42M reads, 4.2 Gb of data. Note: S4: 428 requires NovaSeq Xp workflow or additional indexes. |
2 x 100 bp |
With targeted resequencing, a subset of genes or a genomic region is isolated and sequenced, which can conserve lab resources.
Our sequencing and microarray technologies support a broad range of cancer genomics research applications, from DNA to RNA analysis, epigenetics, and more.
Complex and genetic disease research
Comprehensive array and next-generation sequencing solutions to accelerate research of various genetic complex diseases.
Library Prep and Array Kit Selector
Find the right sequencing library preparation kit or microarray for your needs. Filter by method, species, and more. Compare, share, and order kits.
A uniform tagmentation reaction mediated by eBLTs followed by a single hybridization reaction enables a fast and flexible workflow.
Illumina DNA Prep with Enrichment is compatible with various Illumina enrichment panels and is optimized for use on low-, mid-, and high-throughput systems.
Illumina DNA Prep with Enrichment provides high coverage uniformity and on-target padded read enrichment for custom, fixed, and exome panels.
Illumina DNA Prep with Enrichment provides low-abundance somatic variant calling for (A, B) cell line FFPE control human reference DNA samples and (C, D) real-world FFPE samples with observed variant frequency showing significant correlation with frequencies from an orthologous sequencing assay.
Illumina® DNA Prep with Enrichment, (S) Tagmentation (96 Samples)
20025524
Includes reagents for preparing and enriching 96 libraries (eight, 12-plex enrichment reactions). Purchase enrichment probe panel, Illumina Purification Beads and index adapters separately.
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Illumina® DNA Prep with Enrichment, (S) Tagmentation (16 Samples)
20025523
Includes reagents for preparing and enriching 16 libraries (16, 1-plex enrichment reactions). Purchase enrichment probe panel, Illumina Purification Beads and index adapters separately.
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Illumina® DNA Prep, (S) Tagmentation (96 Samples)
20025520
Includes reagents for preparing 96 libraries. No enrichment reagents are included. Purchase enrichment probe panel, Illumina Purification Beads and index adapters separately. Enrichment reagents are only orderable with library prep reagents (Illumina DNA Prep with Enrichment, (S) Tagmentation (96 samples)).
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Illumina® DNA Prep, (S) Tagmentation (16 Samples)
20025519
Includes reagents for preparing 16 libraries. No enrichment reagents are included. Purchase enrichment probe panel, Illumina Purification Beads and index adapters separately. Enrichment reagents are only orderable with library prep reagents (Illumina DNA Prep with Enrichment, (S) Tagmentation (16 samples)).
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TruSight Cancer – Enrichment Oligos only (4 or 8 Enrichment Reactions)
FC-121-0202
TruSight Cancer targets 94 genes and 284 SNPs associated with a predisposition towards various cancers and is sufficient for 8 enrichment reactions when paired with Nextera Flex for Enrichment due to a single hybridization workflow and sufficient for 4 enrichment reactions when paired with TruSight Rapid Capture. Library prep, enrichment, and index adapter reagents need to be ordered separately.
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TruSight Hereditary Cancer – Enrichment Oligos Only (8 Enrichment Reactions)
20029551
TruSight Hereditary Cancer – Enrichment Oligos Only (8 Enrichment Reactions)
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TruSight One – Enrichment Oligos only (6 Enrichment Reactions)
20029227
Sufficient for six enrichment reactions when paired with Illumina DNA Prep with Enrichment, (S) Tagmentation. Purchase library prep and enrichment reagents and index adapters separately.
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TruSight One Expanded – Enrichment Oligos only (6 Enrichment Reactions)
20029226
Sufficient for six enrichment reactions when paired with Illumina DNA Prep with Enrichment, (S) Tagmentation. Purchase library prep and enrichment reagents and index adapters separately.
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Illumina Custom Enrichment Panel V2 (32 µl, 120 bp)
20073953
Illumina Custom Enrichment Panel V2 enables 120 bp double-stranded custom panel design from 100 up to 1,000,000 probes using DesignStudio or Concierge Services and provides 32 µl of material (sufficient for 8 enrichment reactions when paired with Illumina DNA Prep with Enrichment). Library prep, enrichment, and index adapter reagents need to be ordered separately.
Illumina Custom Enrichment Panel V2 (384 µl, 120 bp)
20073952
Illumina Custom Enrichment Panel V2 enables 120 bp double-stranded custom panel design from 100 up to 1,000,000 probes using DesignStudio or Concierge Services and provides 384 µl of material (sufficient for 96 enrichment reactions when paired with Illumina DNA Prep with Enrichment). Library prep, enrichment, and index adapter reagents need to be ordered separately.
Illumina Custom Enrichment Panel V2 (1536 µl, 120 bp)
20111339
Illumina Custom Enrichment Panel V2 enables 120 bp double-stranded custom panel design from 100 up to 1,000,000 probes using DesignStudio or Concierge Services and provides 1536 µl of material (sufficient for 384 enrichment reactions when paired with Illumina DNA Prep with Enrichment). Library prep, enrichment, and index adapter reagents need to be ordered separately.
Illumina Custom Enrichment Panel (8 Enrichment Reactions)
20025371
Sufficient for eight enrichment reactions when paired with Illumina DNA Prep with Enrichment. Enables custom panel design between 2K–67K probes using DesignStudio. Purchase library prep and enrichment reagents and index adapters separately.
Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)
20091654
Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)
20091656
Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)
20091658
Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)
20091660
Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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IDT® for Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)
20027213
Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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IDT® for Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)
20027214
Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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IDT® for Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)
20042666
Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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IDT® for Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)
20042667
Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.
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Illumina DNA Prep Enrichment-Customer Site
20028457
A 1.5-day onsite training for the complete Illumina DNA Prep Enrichment library preparation workflow, with detailed hands-on instruction. This training can be delivered with select Illumina fixed panels (Exome or TruSight Cancer), Illumina custom DNA panels, or select third party DNA panels (IDT xGen Exome or Twist Human Core Exome). Participants will learn all steps of the workflow including sample input and library preparation, enrichment, quality control, best practices, and troubleshooting, in addition to training on Illumina-supported sequencing and data analysis tools specific to the Illumina DNA Prep with Enrichment workflow.
Illumina Purification Bead, 100mL
20060057
Includes one, 100-ml container of beads for library clean-up and size selection. Purchase library prep and enrichment reagents, probe panels, and indexes separately.
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Illumina Purification Bead, 400mL
20060058
Includes four, 100-ml container of beads for library clean-up and size selection. Purchase library prep and enrichment reagents, probe panels, and indexes separately.
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Flex Lysis Reagent Kit (96 reactions)
20018706
Includes reagents for processing blood samples with the Illumina DNA Prep and Illumina DNA Prep with Enrichment. Purchase library prep, enrichment, enrichment probe panel, and index adapter reagents separately.
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Infinium FFPE QC Kit (384 reactions)
WG-321-1001
Infinium FFPE QC Kit is an accessory product required to qualify FFPE samples with Nextera Flex for Enrichment. Library prep, enrichment, enrichment probe panel, and index adapter reagents need to be ordered separately.
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Infinium MIDI Heatblock Insert
BD-60-601
Heatblock insert for the SciGene Hybex Microheating system required for the Nextera Flex for Enrichment hybridization steps.
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Illumina® Free Adapter Blocking Reagent (12 Reactions)
20024144
This reagent is used during library preparation to reduce index hopping levels.
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Illumina® Free Adapter Blocking Reagent (48 Reactions)
20024145
This reagent is used during library preparation to reduce index hopping levels.
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The Illumina DNA Prep with Enrichment kit is compatible with high-quality, double-stranded genomic DNA (gDNA) inputs of 10–1000 ng or 50-1000 ng FFPE. For human gDNA samples and other large complex genomes, the recommended minimum gDNA input is 50 ng.
The kit uses a bead-based transposome complex to fragment and tag genomic DNA with adaptors followed by a PCR step that adds indexed adapter sequences to the ends of a DNA fragment. After library prep, targets are enriched by hybridizing biotinylated oligonucleotide probes and capturing the targeted library fragments using Streptavidin Magnetic Beads (SMB). The captured, indexed libraries are eluted from the beads and amplified before sequencing.
Use of frozen or clotted blood with the Flex Lysis Reagent Kit and Blood Lysis protocol with Illumina DNA Prep with Enrichment is not supported or tested by Illumina.
The Blood Lysis protocol with Illumina DNA Prep with Enrichment is optimized for the use with K2-EDTA collection tubes (manufactured by Becton Dickinson). Other blood collection tubes may work, but they have not been validated.
Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.
Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.
Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.
A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.
Focused next-generation sequencing (NGS) panel to assess 15 commonly mutated genes in solid tumors with one simple and rapid workflow.
Targeted custom research panels optimized for sequencing specific targets or genomic content of interest.
A high-performance, fast, and reliable human whole-exome sequencing solution that includes a comprehensive, up-to-date exome enrichment panel.
An efficient, fast, and integrated library preparation workflow that yields highly accurate data for sensitive sequencing applications.
Reagents for the NextSeq 1000/2000 System feature easy-to-use cartridges and multiple flow cell configurations for flexible sequencing options.
Reagent kits that provide increased cluster density and read length for the MiSeq System, improving sequencing quality scores compared to v1 kits.
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