A fast, flexible, and scalable cfDNA library preparation kit for highly sensitive mutation detection
Assay time
Hands-on time
Input quantity
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.
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.
Illumina Cell-Free DNA 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.
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.
| Analytical sensitivity |
Analytical sensitivity at 20ng: ≥ 90% (SNVs ≥0.2% and indels ≥0.5%) |
|---|---|
| Analytical specificity |
Analytical specificity at 20ng: ≥ 99.98% (SNVs ≥0.2% and indels ≥0.5%) |
| Assay time |
~8.5–9.5 hr |
| Hands-on time |
~2.5–3 hr |
| Input quantity |
10–30 ng of cfDNA |
| Instruments | NovaSeq 6000Dx Instrument, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode, NextSeq 500 System, NovaSeq 6000 System |
| Method | Target Enrichment, Custom Sequencing, Targeted DNA Sequencing |
| Nucleic acid type | DNA |
| Specialized sample types | Cell-Free DNA |
| Species category | Human |
| Technology | Sequencing |
| Variant class | Gene fusions, Somatic variants, Single nucleotide variants (SNVs), Insertions-deletions (indels), Copy number variants (CNVs) |
Index Plates listed above are required to complete the workflow. There are specific SKUs for manual and automation workflow.
| 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 hr |
~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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Illumina cfDNA 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 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.
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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Illumina Cell-Free DNA Prep with Enrichment Training - Customer site
20122119
This 2-day introductory course is designed to familiarize new users with the Illumina cfDNA Prep with Enrichment workflow through detailed hands- on instruction. Participants will learn all essential steps in the workflow, including manual library preparation, enrichment, sequencing, and data analysis.
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