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
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.
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 llumina 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.
What panels do I need?
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.
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
Illumina DNA Prep with Exome 2.5 Enrichment
Illumina Custom Enrichment Panel v2
NextSeq 550 System
NextSeq 1000 and 2000 Systems
NovaSeq 6000 System
NovaSeq X Series
DRAGEN Enrichment
Emedgene
Illumina Connected Insights - Somatic
Not available in all countries. Illumina Connected Insights supports user-defined tertiary analysis through API calls to third-party knowledge sources.
Project recommendations
Instrument: Recommended number of samples
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)
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.
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.
Related applications and methods
Exome sequencing
Whole-exome sequencing is used to investigate protein-coding regions of the genome to uncover genetic influences on disease and population health.
Complex and genetic disease research
Comprehensive array and next-generation sequencing solutions to accelerate research of various genetic complex diseases.
Cancer genomics research
Our sequencing and microarray technologies support a broad range of cancer genomics research applications, from DNA to RNA analysis, epigenetics, and more.
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
Optimized workflows for custom targeted enrichment, from oligo probe design to NGS data analysis
Comprehensive solution, from probe design to data analysis, for multiple targeted sequencing applications. Our custom-designed panels ensure high uniformity and coverage, with enhanced coverage of GC-rich and difficult to sequence areas.
Library prep automation
Reduce hands-on time and minimize errors with high- and low-throughput walk-away automation protocols available through Illumina automation partners.
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). View less
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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). View less
Twist Bioscience for Illumina Mitochondrial Panel
20093180
Twist Bioscience for Illumina Mitochondrial Panel can be used for combined enrichment of both human exome plus mitochondrial DNA from whole exome libraries. Provides 32 ul of material, sufficient for 96 samples when paired with Exome 2.5 Panel in the Illumina DNA Prep with Exome 2.5 Enrichment kits (8 hybridization reactions at 12-plex with up to 4 ul oligo panel per reaction), or a minimum of 64 samples when paired with Exome 2.5 Panel in the lllumina FFPE DNA Prep with Exome 2.5 Enrichment kit (16 hybridization reactions at 4-plex with 2 ul oligo panel per hybridization reaction). View less
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. View less
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. View less
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. View less
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. View less
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. View less
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. View less
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. View less
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. View less
Infinium MIDI Heatblock Insert
BD-60-601
Heatblock insert for the SciGene Hybex Microheating system required for the Nextera Flex for Enrichment hybridization steps. View less
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. View less
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. View less
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Is it possible to use < 50 ng of gDNA with Illumina DNA Prep with Exome 2.5 Enrichment?
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.
What blood collection tubes can be used with Illumina DNA Prep with Exome 2.5 Enrichment?
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.
What saliva collection tubes can be used with Illumina DNA Prep with Exome 2.5 Enrichment?
This protocol is validated for saliva collected only in Oragene DNA Saliva collection tubes.
What is the Twist Bioscience for Illumina Mitochondrial Panel?
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.
What happened to Illumina DNA Prep with Exome 2.0 Plus Enrichment products?
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.
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