Illumina cell-free DNA Prep with Enrichment

A fast, flexible, and scalable cfDNA library preparation kit for highly sensitive mutation detection

~8.5–9.5 hours

Assay time

~2.5–3 hr

Hands-on time

10–30 ng of cfDNA

Input quantity

See full details in the specifications table

Overview

Illumina Cell-Free DNA Prep with Enrichment is a highly sensitive library preparation solution to detect low-abundance mutations from cfDNA samples. The workflow includes unique molecular identifiers (UMIs) for error correction and reduction of false positives, enabling accurate and sensitive detection of low-frequency mutations.

Fast, flexible format

Illumina cell-free DNA Prep with Enrichment is compatible with user-supplied enrichment oligo nucleotides from Illumina or third-party vendors, including single-stranded DNA (ssDNA) from Integrated DNA Technologies (IDT) and double-stranded DNA (dsDNA) from Twist Bioscience, for enhanced content portability. The kit accommodates 55-2000Kb (ssDNA) and 70-2000Kb(dsDNA) panel content, enabling flexible study design. Sequencing-ready libraries are prepared in ~8.5–9.5 hours, with only ~2.5-3 hours of hands-on time, enabling researchers to go from extracted cfDNA to sequencing in a single day. Recommended read length for NextSeq 550 is 2 × 149 bp and for NextSeq 2000 and NovaSeq 6000, it is 2 × 151 bp.

High-performance library prep

Illumina cfDNA Prep with Enrichment detects low-frequency variants, including SNVs, CNVs, Indels as variants, and gene fusions. The kit identifies small variants with allele frequencies as low as 0.2% from only 20 ng cfDNA with ≥90% sensitivity.

Streamlined sample-to-results workflow

This kit is part of an integrated workflow that starts with cfDNA, followed by sequencing on Illumina mid- and high-throughput systems, and highly accurate variant calling using the DRAGEN for ILMN cfDNA Prep with Enrichment App. This user-friendly solution is compatible with liquid-handling automation and accommodates sample multiplexing for scalable efficiency with high data quality.


Specifications


Required products

Index Plates listed above are required to complete the workflow. There are specific SKUs for manual and automation workflow.

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Illumina cell-free DNA Prep with Enrichment Illumina DNA Prep with Enrichment TruSight Oncology 500 ctDNA v2
Analytical sensitivity

Analytical Sensitivity at 20ng: ≥ 90% (SNVs ≥0.2% and indels ≥0.5%)

≥ 95% (small variants, ≥ 0.5% VAF)
Analytical specificity

Analytical Specificity at 20ng: ≥ 99.98% (SNVs ≥0.2% and indels ≥0.5%)

≥ 99.995% (small variants, ≥ 0.5% VAF)
Assay time

~8.5–9.5 hours

~6.5 hr

<4 days from purified nucleic acid to variant report

Hands-on time

~2.5–3 hr

~2 hr

~2.5 hr for library prep and enrichment

Input quantity

10–30 ng of cfDNA

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

20 ng cfDNA (4 ml of plasma)

Instruments NovaSeq 6000Dx Instrument, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode, NextSeq 500 System, NovaSeq 6000 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 NovaSeq 6000 System
Method Target Enrichment, Custom Sequencing, Targeted DNA Sequencing Target Enrichment, Exome Sequencing, Custom Sequencing, Targeted DNA Sequencing Target Enrichment, Targeted DNA Sequencing
Nucleic acid type DNA DNA DNA
Specialized sample types Cell-Free DNA Blood, Low-Input Samples, FFPE Tissue, Saliva Circulating Tumor DNA, Blood
Species category Human Other, Human Human
Technology Sequencing Sequencing Sequencing
Variant class Gene fusions, 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) Single nucleotide variants (SNVs), Insertions-deletions (indels), Copy number variants (CNVs)

*System Compatibility: for NextSeq2000, only P3 flow cell tested

Illumina® cfDNA Prep, Ligation (16 Samples)

20104105

Includes ligation-based library prep for preparation of 16 libraries prepared by automation, or 24 libraries prepared manually. Enrichment reagents not included. Analyze data on Illumina Connected Analytics or BaseSpace Sequence Hub for free. Basic subscription to Cloud platform required. Data storage not included. UMI Index Adapters and Unique Dual Indexes are purchased separately and required for library preparation. Choose UMI Index Adapters and Unique Dual Indexes based on automation or manual workflow. Enrichment Panel Content not included.

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Illumina® cfDNA Prep, Ligation (96 Samples)

20104106

Includes ligation-based library prep for preparation of 96 libraries intended for automation, or 120 libraries prepared manually. Enrichment reagents not included. Analyze data on Illumina Connected Analytics or BaseSpace Sequence Hub for free. Basic subscription to Cloud platform required. Data storage not included. UMI Index Adapters and Unique Dual Indexes are purchased separately and required for library preparation. Choose UMI Index Adapters and Unique Dual Indexes based on automation or manual workflow. Enrichment Panel Content not included.

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Illumina® cfDNA Enrichment (16 Reactions)

20104107

Includes fast enrichment reagents for enrichment of Illumina cfDNA Prep libraries for a total of 16 reactions prepared by automation, or 24 reactions prepared manually. Enrichment plexity of 1-plex and 4-plex recommended (pooling of 4 libraries in a single enrichment). Analyze data on Illumina Connected Analytics or BaseSpace Sequence Hub for free. Basic subscription to Cloud platform required. Data storage not included. UMI Index Adapters and Unique Dual Indexes are purchased separately and required for library preparation. Choose UMI Index Adapters and Unique Dual Indexes based on automation or manual workflow. Enrichment Panel Content not included.

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Illumina® cfDNA 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 prepared by automation, or 240 libraries prepared manually, using 4-plex enrichment (pooling of 4 libraries in a single enrichment). Analyze data on Illumina Connected Analytics or BaseSpace Sequence Hub for free. Basic subscription to Cloud platform required. Data storage not included. UMI Index Adapters and Unique Dual Indexes are purchased separately and required for library preparation. Choose UMI Index Adapters and Unique Dual Indexes based on automation or manual workflow. Enrichment Panel Content not included.

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ILMN cfDNA Prep ENR, On-prem (192/240)

20104104

Includes ligation-based library prep and fast enrichment reagents for preparation of 192 libraries prepared by automation, or 240 libraries prepared manually, using 4-plex enrichment (pooling of 4 libraries in a single enrichment). 10,000 Gb, 1 yr DRAGEN Server License included. Sufficient for analyzing sequencing output for up to 400 kb content at 30,000x sequencing depth. Illumina DRAGEN Server required. UMI Index Adapters and Unique Dual Indexes are purchased separately and required for library preparation. Choose UMI Index Adapters and Unique Dual Indexes based on automation or manual workflow. Enrichment Panel Content not included.

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Accessory products (4)

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

20034701

UMI DNA Index Anchors (Plate = 20031416, Box = 20032620) + 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

IDT for Illumina UMI DNA Index Anchors Set B

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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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