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Illumina FFPE DNA Prep with Exome 2.5 Enrichment

A fast, flexible, and scalable human whole-exome sequencing solution with support for low-input samples.

~10 hr

Assay time

~4 hr

Hands-on time

40 ng FFPE

Input quantity

See full details in the specifications table

Overview

Illumina FFPE DNA Prep with Exome 2.5 Enrichment is a sensitive and comprehensive whole-exome sequencing solution that offers a tumor-normal workflow for detecting low-frequency variants from FFPE (formalin-fixed, paraffin-embedded) samples.

The workflow includes unique molecular identifiers (UMIs) for error correction and reduction of false positives, enabling accurate detection of low-frequency mutations.

Key features

  • Comprehensive exome coverage for tumor-normal workflows

  • Streamlined sample-to-insights workflow with automation-friendly fill volumes

  • Accurate detection of low-frequency mutations

High-performance library prep

Illumina FFPE DNA Prep with Exome 2.5 Enrichment detects low-frequency variants, including single nucleotide variants (SNVs), indels, and copy number variants (CNVs). The kit identifies small variants with allele frequencies as low as 5% from only 40 ng FFPE DNA with over 90% variant recall. The Twist Biosciences for Illumina Exome 2.5 Panel content includes biomarkers for tumor mutational burden (TMB), microsatellite instability (MSI), and homologous recombination deficiency (HRD).

Streamlined sample-to-insights workflow

This kit is part of an integrated workflow that starts with FFPE DNA from tumors and matched normal samples. After Illumina sequencing, obtain highly accurate variant calling using the DRAGEN Somatic App.

Fast and scalable

Illumina FFPE DNA Prep with Exome 2.5 Enrichment offers a fast, hybrid-capture workflow for preparing sequencing-ready libraries in ~10 hours, with only 4 hours of hands-on time. Researchers can go from extracted FFPE DNA to sequencing in a single day. The recommended read length is 2 × 151 bp.

Focused, comprehensive coverage

This kit maximizes sequencing results, enabling thorough coverage of exomes using a focused, comprehensive, and up-to-date panel.

Optional mitochondrial and custom spike-in enrichment

Illumina custom v2 probes make it easy to add mitochondrial genome coverage or regions of interest using spike-in panels with up to 10,000 probes.

Same workflow for cfDNA and FFPE samples

Illumina FFPE DNA Prep with Exome 2.5 Enrichment features the same library preparation and enrichment chemistry as Illumina Cell-Free DNA with Enrichment to enable exceptional performance with FFPE samples.

Specifications

Assay time ~10 hr
Cancer type Solid tumor
Description A fast and easy-to-use library prep with an enrichment tumor–normal workflow for accurate and comprehensive whole-exome sequencing and reliable detection of low-frequency mutations from FFPE samples.
Hands-on time ~4 hr
Input quantity 40 ng FFPE DNA
Instruments NextSeq 2000 System, NovaSeq X System, NovaSeq 6000 System, NovaSeq X Plus System
Method Exome sequencing
Nucleic acid type DNA
Specialized sample types Low-input samples, FFPE tissue
Species category Human
Technology Sequencing
Variant class Single nucleotide polymorphisms (SNPs), Somatic variants, Single nucleotide variants (SNVs), Insertions-deletions (indels), Copy number variants (CNVs)

Applications

Illumina FFPE DNA Prep with Exome 2.5 Enrichment is a streamlined, comprehensive sample-to-insights whole-exome sequencing solution that supports low-input samples, including FFPE DNA.

Example workflow

1
Prep
2
Sequence
3
Analyze

Documentation

Product literature
Support documentation

A dedicated support section is not currently available for this product

Compare

Illumina FFPE DNA Prep with Exome 2.5 Enrichment Illumina DNA Prep with Exome 2.5 Enrichment TruSight Oncology 500 Illumina Cell-Free DNA Prep with Enrichment
Assay time ~10 hr 6.5 hr 4–5 days from sample to results 约 8.5–9.5 小时
Description A fast and easy-to-use library prep with an enrichment tumor–normal workflow for accurate and comprehensive whole-exome sequencing and reliable detection of low-frequency mutations from FFPE samples. 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. Assay that enables comprehensive genomic profiling from FFPE tissue and runs on the NextSeq 550 System or NextSeq 550Dx Instrument (in Research Mode) and can batch up to eight samples at a time. A fast, flexible, and scalable cfDNA library preparation kit for highly accurate mutation detection
Hands-on time ~4 hr ~2 hr ~2.5 hr for automated workflow
~10.5 hr for manual workflow 		约 2.5–3 小时
Input quantity 40 ng FFPE DNA 50-1000 ng high-quality genomic DNA (For direct blood and saliva, see reference guide) 40 ng DNA and/or 40 ng RNA 10–30 ng cfDNA
Instruments NextSeq 2000 System, NovaSeq X System, NovaSeq 6000 System, NovaSeq X Plus System NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode, NovaSeq X System, NovaSeq 6000 System, NovaSeq X Plus System NextSeq 550 System, NextSeq 550Dx in Research Mode, NextSeq 500 System NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode, NovaSeq X System, NovaSeq 6000Dx in Research Mode, NovaSeq 6000 System
Nucleic acid type DNA DNA DNA, RNA DNA
Specialized sample types Low-input samples, FFPE tissue Blood, Saliva FFPE tissue Cell-free DNA
Species category Human Human Human Human
Technology Sequencing Sequencing Sequencing Sequencing
Variant class Single nucleotide polymorphisms (SNPs), Somatic variants, Single nucleotide variants (SNVs), 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) Gene fusions, Transcript variants, Single nucleotide variants (SNVs), Insertions-deletions (indels), Copy number variants (CNVs), Loss of heterozygosity (LOH), Somatic variants, Novel transcripts, Single nucleotide polymorphisms (SNPs), Structural variants Gene fusions, Somatic variants, Single nucleotide variants (SNVs), Insertions-deletions (indels), Copy number variants (CNVs)

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Required products

Illumina FFPE DNA Prep with Exome 2.5 Enrichment includes library prep and enrichment reagents. Enrichment probe panels and index adapters are sold separately through Illumina (see below).

To analyze the secondary data on DRAGEN Enrichment and Somatic, you need the following:

  • DRAGEN server license for local analysis, or
  • Subscription to Illumina Connected Analytics and iCredits for cloud analysis, or
  • Subscription to BaseSpace Sequence Hub and iCredits for cloud analysis
  • Illumina UMI DNA/RNA UD v3 Indexes Set A and B

Twist Bioscience for Illumina Exome 2.5 Panel is a comprehensive and up-to-date exome panel that allows uniform coverage for whole-exome sequencing.

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

Illumina Custom Enrichment Panel v2 can be used as spike-in panels, using the DesignStudio Assay Design Tool or with the Illumina Concierge design team.

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Library prep (5)

Illumina® Cell-Free and FFPE DNA Prep, Ligation (16 Samples)

20104105

Includes ligation-based library prep for preparation of 16 libraries with Illumina Qualified Automation Methods, or 24 libraries manually. Enrichment reagents and enrichment panel not included. UMI Index Adapters are purchased separately and required for library preparation. Choose based on prep method. Please note regarding data analysis: Cell-Free DNA: Analyze data on DRAGEN for ILMN Cell-Free DNA Prep with Enrichment App on Illumina Connected Analytics or BaseSpace Sequence Hub at no additional charges. Basic subscription to Cloud platform required. Data storage not included. FFPE DNA: Analysis on DRAGEN Enrichment and Somatic not included.

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Illumina® Cell-Free and FFPE DNA Prep, Ligation (96 Samples)

20104106

Includes ligation-based library prep for preparation of 96 libraries with Illumina Qualified Automation Methods, or 120 libraries manually. Enrichment reagents and enrichment panel not included. UMI Index Adapters are purchased separately and required for library preparation. Choose based on prep method. Please note regarding data analysis: Cell-Free DNA: Analyze data on DRAGEN for ILMN Cell-Free DNA Prep with Enrichment App on Illumina Connected Analytics or BaseSpace Sequence Hub at no additional charges. Basic subscription to Cloud platform required. Data storage not included. FFPE DNA: Analysis on DRAGEN Enrichment and Somatic not included.

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Illumina® Cell-Free and FFPE DNA Prep, Enrichment (16 Reactions)

20104107

Includes fast enrichment reagents for enrichment of Illumina Cell-Free and FFPE DNA Prep libraries for a total of 16 reactions with Illumina Qualified Automation Methods, or 24 reactions manually. Library preparation reagents and enrichment panel not included. UMI Index Adapters are purchased separately and required for library preparation. Choose based on prep method. Cell-Free DNA: 1-4 samples per reaction during enrichment. Analyze data on DRAGEN for ILMN Cell-Free DNA Prep with Enrichment on Illumina Connected Analytics or BaseSpace Sequence Hub at no additional charge. Basic subscription to Cloud platform required. Data storage not included. FFPE DNA: 4 samples per Whole Exome enrichment. Analysis on DRAGEN Enrichment and Somatic not included.

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Illumina® Cell-Free and FFPE DNA Prep with Enrichment, Ligation (192 Samples, 4-plex), Cloud Analysis

20104103

Includes ligation based library prep and fast enrichment reagents for preparation of 192 libraries using Illumina Qualified Automation Methods, or 240 libraries manually, using 4-plex enrichment (pooling of 4 libraries in a single enrichment reaction). UMI Index Adapters are purchased separately and required for library preparation. Choose based on prep method. Enrichment panel not included.  Please note regarding data analysis: Cell-Free DNA: Analyze data on DRAGEN for ILMN Cell-Free DNA Prep with Enrichment on Illumina Connected Analytics or BaseSpace Sequence Hub at no additional charges. Basic subscription to Cloud platform required. Data storage not included. FFPE DNA: Analysis on DRAGEN Enrichment and Somatic not included.

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Illumina® Cell-Free and FFPE DNA Prep with Enrichment, Ligation (192 Samples, 4-plex), On-premises

20104104

Includes ligation based library prep and fast enrichment reagents for preparation of 192 libraries using Illumina Qualified Automation Methods, or 240 libraries manually, using 4-plex enrichment (pooling of 4 libraries in a single enrichment reaction). UMI Index Adapters are purchased separately and required for library preparation. Choose based on prep method. Enrichment panel not included.10,000 Gb, 1 yr DRAGEN Server License included. Illumina DRAGEN v4 Server required for Cell- free DNA analysis.

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Panel (5)

Twist Bioscience® for Illumina Exome 2.5 Panel

20076914

Twist Bioscience for Illumina Exome 2.5 Panel provides 68 µl of material. When paired with Illumina FFPE DNA Prep with Exome 2.5 Enrichment, this volume is sufficient for 20 enrichment reactions at 4- plex for manual workflow. Available by quote only, panel must be sold with library prep reagents. Request pricing for more details.

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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).

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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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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.

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Accessory products (6)

IDT® for Illumina® UMI DNA/RNA UD Indexes Set A, Ligation (96 Indexes, 96 Samples)

20034701

UMI DNA Index Anchors (Plate = 20027219, Box = 20032119) + Nextera Compatible Unique Dual Index A (Sales Kit = 20027213, Plate = 20025019, Box = 20026121)

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IDT® for Illumina® UMI DNA/RNA UD Indexes Set B, Ligation (96 Indexes, 96 Samples)

20034702

UMI DNA Index Anchors (Plate = 20027219, Box = 20032119) + Nextera Compatible Unique Dual Index B (Sales Kit = 20027214, Plate = 20025080, Box = 20026930)

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IDT for Illumina UMI DNA/DNA Index Anchors Set A for Automation

20066404

Includes one box of 96 IDT for Illumina - UMI DNA/RNA UD Indexes Set A for Automation sufficient for labeling 96 samples and one box of 96 IDT for Illumina - UMI DNA Index Anchors for Automation.

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IDT for Illumina UMI DNA/DNA Index Anchors Set B for Automation

20063213

Includes one box of 96 IDT for Illumina - UMI DNA/RNA UD Indexes Set B for Automation sufficient for labeling 96 samples and one box of 96 IDT for Illumina - UMI DNA Index Anchors for Automation.

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Illumina UMI DNA/RNA UD v3 indexes Set A, Ligation (96 indexes, 96 Samples)

20126235

Includes one box of 96 Illumina DNA/RNA UD v3 Indexes Set A sufficient for labeling 96 samples and one box of 96 IDT for Illumina UMI DNA Index Anchors.

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Illumina UMI DNA/RNA UD v3 indexes Set B, Ligation (96 indexes, 96 Samples)

20126237

Includes one box of 96 Illumina DNA/RNA UD v3 Indexes Set B sufficient for labeling 96 samples and one box of 96 IDT for Illumina UMI DNA Index Anchors.

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