Illumina DNA Prep with Exome 2.5 Enrichment

A high-performance, fast, and reliable human whole-exome sequencing solution that includes a comprehensive, up-to-date exome enrichment panel.

6.5 hr

Assay time

~2 hr

Hands-on time

50-1000 ng high-quality genomic DNA (For direct blood and saliva, see reference guide)

Input quantity

See full details in the specifications table

Overview

Illumina DNA Prep with Exome 2.5 Enrichment offers a cost-effective, reliable solution for human whole-exome sequencing (WES). This kit provides:

  • Focused, comprehensive coverage - maximize sequencing results and get thorough coverage of exomes using a focused, comprehensive, and up-to-date panel

  • Outstanding enrichment performance - decrease costs and increase sample throughput with multiplexing, while achieving high on-target rates and uniform coverage

  • Fast, streamlined workflow - go from DNA to library prep, enrichment, and post-enrichment amplification in only 6.5 hr with a fast, user-friendly workflow that includes built-in library yield normalization and a simplified hybridization protocol

  • Optional mitochondrial genome enrichment - easily add mitochondrial genome coverage with a spike-in panel

  • Automation-friendly workflow - find methods for a range of automation platforms through our partners

Simplified workflow solution from a single vendor

This whole-exome sequencing kit includes library prep and hybridization reagents, clean up/size selection beads, and indexes. The kit also includes the Twist Bioscience for Illumina Exome 2.5 Panel, which offers improved target region coverage for variants reported in public databases. 

Customizable content

Easily add targets to your WES experiment, or boost coverage of critical targets, with a supplementary custom enrichment panel designed for your targets of interest. Add your customized Illumina Custom Enrichment Panel v2 as a spike-in to Illumina DNA Prep with Exome 2.5 Enrichment hybridization reactions. Design your customized WES spike-in panel using DesignStudio, the free assay design tool, or with help from the Illumina Concierge design team.


Specifications


Required products

Illumina DNA Prep with Exome 2.5 Enrichment kits include library prep, enrichment, enrichment probe panel, purification beads, and index adapter reagents. Choose a different index set if preferred. 

The Twist Bioscience for Illumina Mitochondrial Panel is an optional fixed content spike-in panel that allows enrichment and sequencing of mitochondrial DNA variants.  

For direct blood input, the Flex Lysis Reagent Kit is required.

The Infinium MIDI Heatblock Insert fits in the SciGene HybEx Microheating system and is required for the enrichment step. 

Spike-in Panels

Illumina DNA Prep with Exome 2.5 Enrichment Kits may be used with the Twist Bioscience for Illumina Mitochondrial Panel, or Illumina Custom Enrichment Panel v2, as spike-in panels. Custom enrichment panels can be designed through the DesignStudio design tool or Illumina Concierge design team.

/ Results

Applications

The Illumina DNA Prep with Exome 2.5 Enrichment is a fast and comprehensive end-to-end whole-exome sequencing solution that enables support from sample to reporting.

Example workflow

1
Prep

Illumina DNA Prep with Exome 2.5 Enrichment

3
Analyze

Project recommendations

Instrument Recommended number of samples Read length
NextSeq 2000 System

Samples per run (by flow cell type): P2: 19, P3: 57 (based on 50× mean target coverage, 42M reads, 4.2 Gb of data)

2 × 101 bp

NovaSeq 6000 System

Samples per run by flow cell type: 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 × 101 bp


Related applications and methods

Documentation

Product literature

Compare

Illumina DNA Prep with Exome 2.5 Enrichment Illumina DNA Prep with Enrichment
Assay time 6.5 hr ~6.5 hr
Automation details Explore available automation methods Explore available automation methods
Content specifications

37.5 Mb coding content (≥ 99% of RefSeq, CCDS, ClinVar and ACMG pathogenic/likely pathogenic variants, COSMIC Cancer Gene Census), OMIM

Exome: 45 Mb exonic content (≥98% of RefSeq, CCDS, and Ensembl coding content).
Custom: 0.5 - 15 Mb genomic content of interest.
Fixed panels: Content varies by panel.
Description A fast and easy-to-use library prep with enrichment workflow with a focused enrichment probe panel of up-to-date exome content for cost-effective and reliable human whole-exome sequencing.

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, ~2 hr
Input quantity 50-1000 ng high-quality genomic DNA (For direct blood and saliva, see reference guide) 10-1000 ng high-quality genomic DNA or 50-1000 ng FFPE DNA. (For blood and saliva, see the reference guide).
Instruments NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode, NovaSeq X System, NovaSeq 6000 System, NovaSeq X Plus System 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-linked transposome and hybrid-capture chemistry Bead-bound transposomes and hybrid-capture chemistry
Method Targeted DNA sequencing, Exome sequencing, Target enrichment Custom sequencing, Targeted DNA sequencing, Exome sequencing, Target enrichment
Multiplexing Pre-enrichment pooling of up to 12-plex is tested. Kit configuration supports multiplexing up to 192 samples. Up to 384 possible. Up to 384 available unique dual indexes. Pre-enrichment pooling of up to 12-plex is tested.
Nucleic acid type DNA DNA
On-target reads ~ 90% based on average performance from internal testing ≥85% for exome panel (results from example data set; actual performance may vary)
Specialized sample types Blood, Saliva Blood, Low-Input Samples, FFPE Tissue, Saliva
Species category Human Other, Human
Technology Sequencing Sequencing
Uniformity ≥ 91% (% coverage at 20× for 5 Gb) based on average performance from internal testing ≥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) Single nucleotide polymorphisms (SNPs), Loss of heterozygosity (LOH), Somatic variants, Germline variants, Insertions-deletions (indels), Copy number variants (CNVs)

Selection tools:

Figures

Improved performance of Exome 2.5 Panel

Libraries were constructed and enriched using Illumina DNA Prep with Exome 2.5 Enrichment with either the included Exome 2.5 Panel with a 1.5 hr or 16 hr hybridization time or the Illumina Exome Panel (IEP, 20020183) with a 1.5 hr hybridization time. Enriched libraries were sequenced on a NovaSeq 6000 System and analyzed using DRAGEN Enrichment App.

High database target coverage rates in silico

The bed files for the Exome 2.5 Panel and Exome Panel were compared to the listed public databases and the percent overlap was determined and reported.

Excellent coverage of disease-associated variants in public databases

Illumina DNA Prep with Exome 2.5 Enrichment using a 1.5-hr (orange) or 16-hr (blue) hybridization time shows high average percent coverage at ≥ 20× of targets from public databases.

Resources

Exome kits (2)

Illumina DNA Prep with Exome 2.5 Enrichment, (S) Tagmentation Set B (96 Samples, 12-plex)

20077595

Includes Illumina DNA Prep with Enrichment library preparation and enrichment reagents, Twist Bioscience for Illumina Exome 2.0 Plus Panel, Illumina Purification Beads, and IDT for Illumina DNA/RNA UD Indexes Set B, Tagmentation for whole exome enrichment of 96 libraries (eight, 12-plex enrichment reactions).

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Illumina DNA Prep with Exome 2.5 Enrichment, (S) Tagmentation Set D (96 Samples, 12-plex)

20077596

Includes Illumina DNA Prep with Enrichment library preparation and enrichment reagents, Twist Bioscience for Illumina Exome 2.0 Plus Panel, Illumina Purification Beads, and IDT for Illumina DNA/RNA UD Indexes Set D, Tagmentation for whole exome enrichment of 96 libraries (eight, 12-plex enrichment reactions).

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Panel (3)

Twist Bioscience for Illumina Mitochondrial Panel

20093180

Includes Twist Bioscience for Illumina Mitochondrial Panel, 32 ul of reagent for 96 samples (8 hybridization reactions with 12 samples per reaction). This panel can be used with the Exome 2.5 Panel in the Illumina DNA Prep with Exome 2.5 Enrichment kits, for combined enrichment of both human exome plus mitochondrial DNA from whole genome libraries. The Mitochondrial Panel is sold as an accessory for the Exome 2.5 Panel products.

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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.

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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.

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Accessory products (8)

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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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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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 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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Selection summary

Product

Qty

Unit Price

FAQ

Yes, gDNA input of 10-49 ng can be used. However, this protocol does not normalize final pre-enrichment library yields < 50 ng and, therefore, quantification and normalization of libraries before and after enrichment is required.

This protocol has been validated with fresh blood collected in EDTA collection tubes. Other anticoagulants may be used but are not guaranteed when using this kit.

This protocol is validated for saliva collected only in Oragene DNA Saliva collection tubes.

The Twist Bioscience for Illumina Mitochondrial Panel is an optional fixed content panel designed to cover the 16,659 base pairs (bp) and 37 genes of the mitochondrial genome (chrM) and allows enrichment and sequencing of mitochondrial DNA (mtDNA) variants. Use this panel as a spike-in panel in the Illumina DNA Prep with Exome 2.5 Enrichment protocol and add coverage of ChrM to your experiments.

The products previously known as Illumina DNA Prep with Exome 2.0 Plus Enrichment are now called Illumina DNA Prep with Exome 2.5 Enrichment (Cat. No. 20077595 and 20077596). The exome panel oligos have not changed, but the included indexes have been updated to  Illumina DNA/RNA UD Indexes.

/ Results

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