Overview
Illumina 5-Base DNA Prep with Enrichment offers a highly sensitive approach for detecting both DNA variants and methylation changes from a single sample preparation and sequencing run. The two-for-one targeted assay uses a cost-effective, library preparation-to-analysis workflow.
High-sensitivity for dual detection of 5-methylcytosine (5mC) and DNA variants
Unbiased capture of methylated and unmethylated targets with optimized panel design
Flexible customization for targeted genome and methylome insights
Optimal library recovery from as little as 1 ng cell-free DNA
Precise 5-base insights from every sequencing read
Detect DNA variants and methylation changes in one assay with an integrated workflow from library prep to analysis—no sample splitting required.
Simultaneously detect low-frequency variants and methylation from low-input samples. Alternatively, reduce sequencing costs by focusing coverage on regions of interest.
Create tailored dual-omic panels for Illumina 5-Base DNA Prep with Enrichment using the intuitive DesignStudio platform.
Applications
Illumina 5-Base DNA Prep with Enrichment enables high-sensitivity, dual detection of DNA variants and methylation from low-input samples in a single, customizable assay while delivering precise 5-base insights with an efficient, cost-effective workflow from library prep to analysis.
Example workflow
Illumina 5-Base DNA Prep with Enrichment
NextSeq 2000 System
NovaSeq X Series
NovaSeq 6000Dx Instrument (RUO mode)
NovaSeq 6000 System
DRAGEN secondary analysis
Related applications and methods
Genome and methylome sequencing
Achieve simultaneous high-accuracy genome and methylome discovery in a single readout with the Illumina 5-base genome solution.
Cancer epigenetics
Explore the benefits of next-generation sequencing and microarrays for analyzing altered methylation patterns and other epigenetic changes in cancer.
Epigenomics
Illumina offers solutions for epigenetic analysis. Use our tools to study epigenetic modifications and their impact on gene regulation.
Figures
Library preparation steps for Illumina 5-Base DNA Prep with Enrichment
Optimized ligation-based library preparation includes a simple, one-step 5mC-to-T base conversion, requires minimal touchpoints, and is completed in fewer than 11 hours. Time includes DNA shearing (if applicable) and library quantification. Normalization and pooling times are not included.
Novel chemistry directly converts 5mC to T in a single enzymatic step
(A) Illumina 5-Base DNA Prep with Enrichment uses a one-step enzymatic process to convert only 5mC to T, yielding greater nucleotide diversity than (B) traditional bisulfite sequencing or on-market enzymatic methylation sequencing (EM-Seq), in which unmethylated C are converted to T.
Resources
Illumina 5-base solution: A comprehensive Workflow Guide
Discover the benefits of high-accuracy dual-omic data with DRAGEN 5-base pipelines and gain insights into the reagents, equipment, and user-supplied consumables required for successful implementation.
Decode DNA and methylation together with the Illumina 5-base solution
Join Fiona Kaper, VP and Head of Assay R&D at Illumina, as she discusses the innovative 5-base solution that simplifies and scales multiomic analysis. Discover how Illumina 5-base chemistry enables dual genomic and epigenomic insights in one assay, providing genetic variant and DNA methylation data with exceptional accuracy, simplicity, and scale.
An introduction to the Illumina 5-base solution
A streamlined, end-to-end NGS library prep and analysis workflow for simultaneous methylation profiling and high-accuracy genetic variant calling.
Illumina® 5-Base DNA Prep with Enrichment (24 Samples)
20140366
Includes library prep, enrichment and methylation detection reagents for preparing 24 libraries (6, 4-plex enrichment reactions) manually. Analyze data on the cloud using DRAGEN apps on Illumina Connected Analytics or BaseSpace Sequence Hub or on premise with DRAGEN Server. Perform data visualization using Illumina connected Multiomics (option). Design panel through DesignStudio. Purchase indexes and enrichment probe panel separately. View less
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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. 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
Illumina® Unique Dual Indexes, LT (48 Indexes, 48 Samples)
20098166
Illumina® Unique Dual Indexes, LT (48 Indexes, 48 Samples) 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
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How does the Illumina 5-Base DNA Prep with Enrichment work?
Illumina 5-Base DNA Prep with Enrichment uses a one-step enzymatic process to convert 5mC to T, yielding greater nucleotide diversity than traditional bisulfite treatment. Optimized ligation-based library preparation is followed by target-capture based enrichment, with customized panel design. When paired with specialized analysis, the solution enables simultaneous detection of 5mC and genomic variants in a single assay.
Why use Illumina 5-Base DNA Prep with Enrichment?
Illumina 5-Base DNA Prep with Enrichment enables high-sensitivity methylation profiling and variant detection in one simple, scalable, and cost-effective workflow, with easy customization of target regions.
What panels can I use with Illumina 5-Base DNA Prep with Enrichment?
Illumina 5-Base DNA Prep with Enrichment requires a custom panel design and is compatible with Illumina Custom Enrichment Panel v2. Panels can be designed and ordered using DesignStudio software. The specialized design algorithm accommodates the 5mC-to-T base conversion for efficient capture of both methylated and nonmethylated targets. Panels made for methods, such as bisulfite sequencing, that convert unmethylated cytosines, are not compatible.
How do I analyze Illumina 5-base DNA data?
DRAGEN secondary analysis uses innovative 5-base algorithms to provide accurate annotation of both genome and methylome from a single dataset. An easy checkbox option activates methylation reporting features within the DRAGEN Enrichment pipeline.
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