Illumina DNA Prep with Enrichment

A fast, integrated workflow that provides sequencing-ready DNA libraries for a wide range of targeted sequencing applications.

~6.5 hr

Assay time

~2 hr

Hands-on time

10-1000 ng high-quality genomic DNA or 50-1000 ng FFPE DNA. (For blood and saliva, see the reference guide).

Input quantity

See full details in the specifications table

Overview

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.

  • Complete library prep, enrichment, and post-enrichment amplification in only 6.5 hr

  • Enhance library preparation efficiency with integrated protocols for blood and saliva

  • Get consistent library yields with highly uniform insert sizes

Fast, user-friendly workflow

With built-in quantification and library normalization, on-bead tagmentation chemistry combined with a simplified, single hybridization protocol reduces hands-on time to ~2 hr.

Sample input flexibility

Compatible with a broad range of DNA inputs and sample types, including blood, saliva, genomic DNA, and formalin-fixed, paraffin-embedded (FFPE) tissue.

Optimized performance

On-bead tagmentation minimizes bias and opportunities for error, resulting in highly reproducible data across all Illumina sequencing systems.


Illumina DNA Prep product line

Find fast, optimized sequencing library preparation solutions for use in a wide range of applications.


Specifications


Required products

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.

/ Results

Applications

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.

Example workflow



Project recommendations

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×)
TruSight Cardio: 4 samples per run (based on 170× mean targeted coverage; 100% target coverage at 20×)

2 x 100 bp

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×)
TruSight Cardio (samples per run): mid output: 8, high output: 25 (based on 170× mean targeted coverage; 100% target coverage at 20×)

2 x 100 bp

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×)
TruSight Cardio (samples per run): v2 reagents: 15, v3 reagents: 25 (based on 170× mean targeted coverage; 100% target coverage at 20×)
TruSight One (samples per run): v2 reagents: 1, v3 reagents: 3 (based on 120× mean targeted coverage; 95% target coverage at 20×)

2 x 100 bp

2 x 100 bp

2 x 100 bp (up to 2 x 150 bp is possible)

NextSeq 550 System

Exome (samples per run): mid output: 5, high output: 16 (based on 50× mean targeted coverage; 90% target coverage at 20×)

TruSight One (samples per run): mid output: 12, high output: 36 (based on 120× mean targeted coverage; 95% target coverage at 20×)
TruSight One Expanded (samples per run): mid output: 7, high output: 24 (based on 130× mean targeted coverage; 97% target coverage at 20×)

2 x 100 bp
2 x 100 bp (up to 2 x 150 bp is possible)
2 x 100 bp (up to 2 x 150 bp is possible)

NovaSeq 6000 System

Exome (samples per run, by flow cell type): S1: 128, S2: 164, S4: 400 (based on 50× mean targeted coverage; 90% target coverage at 20×; S4 limited by available indexes)

2 x 100 bp


Related applications and methods

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Illumina on-bead tagmentation chemistry

A uniform tagmentation reaction mediated by eBLTs followed by a single hybridization reaction enables a fast and flexible workflow.

Enrichment panel compatibility

Illumina DNA Prep with Enrichment is compatible with various Illumina enrichment panels and is optimized for use on low-, mid-, and high-throughput systems.

High coverage uniformity and padded read enrichment

Illumina DNA Prep with Enrichment provides high coverage uniformity and on-target padded read enrichment for custom, fixed, and exome panels.

Accurate variant calling

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.

Library prep (4)

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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Panel (5)

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 (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.

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Index adapters (8)

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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Services (1)

Illumina DNA Prep with Enrichment Training

20028457

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Accessory products (7)

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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FAQs

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.

/ Results

Order the NovaSeq X Series

Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.

MiSeq Reagent Kit v3

Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.

TruSight Oncology 500

Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.

Illumina DNA Prep

A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.

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