20104106, Illumina® Cell-Free and FFPE DNA Prep, Ligation (96 Samples)

Name: Illumina® Cell-Free and FFPE DNA Prep, Ligation (96 Samples)
Brand: Illumina
SKU: 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 additio

Catalog Number: 20104106

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Category

NGS Library Preparation Kits

Pack Sizebox of 96

TagsSequencing kits Library preparation kits

Description

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. Our fastest, highest quality, and most robust sequencing by synthesis chemistry, XLEAP-SBS chemistry is now enabled on the NextSeq 2000 (P4 flow cell) and NovaSeq X Systems.
Illumina Cell-Free DNA Prep with Enrichment has enhanced product attributes that enable greater efficiency for the labs, such as extended shelf life to six months and advanced change notification.

Fast workflow
Illumina Cell-Free DNA Prep with Enrichment offers a fast workflow for preparing sequencing-ready libraries in ~8.5–9.5 hours, with only ~2.5-3 hours of hands-on time. Researchers can go from extracted cfDNA to sequencing in a single day. The recommended read length for sequencing on the NextSeq 550 System is 2 × 149 bp. For sequencing on the NextSeq 2000, NovaSeq 6000, and NovaSeq X Systems, the recommended read length is 2 × 151 bp.

High-performance library prep
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.

Streamlined sample-to-insights workflow
This kit is part of an integrated workflow with option for no manual touchpoints from sequencer to insights that (1) starts with cfDNA, followed by (2) sequencing on Illumina mid- and high-throughput systems, (3) highly accurate variant calling using the DRAGEN for ILMN cfDNA Prep with Enrichment App, and (4) option for variant interpretation through automated draft research report generation using Illumina Connected Insights.

Flexible content options
For enhanced content portability, 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. The kit accommodates 55–2000 Kb (ssDNA) and 70–2000 Kb (dsDNA) panel content, enabling flexible study design.
Illumina Custom Enrichment Panel v2 provides dynamic feedback to optimize target coverage, making it the recommended solution for creating panels specific to your content of interest. DesignStudio software is a free, user-friendly, web-based assay design tool for creating custom sequencing panels.

What panels do I need?
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.

What accessories do I need?
Index plates listed above are required to conplete the workflow. There are specific SKUs for manual and automation workflow. Illumina Custom Enrichment Panel v2 is a 120 bp, double-stranded probe panel designed using DesignStudio and includes enrichment oligos for hybridization capture.

Example workflow
Illumina Cell-Free DNA Prep with Enrichment
Illumina Custom Enrichment Panel v2
NextSeq 550 System
NextSeq 550Dx Instrument (RUO mode)
NextSeq 1000/2000 Systems
NovaSeq 6000 System
NovaSeq X Series
NovaSeq 6000 Dx (RUO Mode)
Variant calling
DRAGEN for ILMN cfDNA Prep with Enrichment
Insights and reporting
Illumina Connected Insights

Related applications and methods
Liquid biopsy research
Researchers can use liquid biopsy NGS assays to detect and characterize tumor-derived biomarkers present in the blood of individuals with cancer.
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.
Target enrichment
Target enrichment captures genomic regions of interest through hybridization. Learn more about target enrichment and how it can be used to assess multiple samples at once.

Resources
Multiomic analysis of liquid biopsy samples Cell-free DNA Prep with Enrichment library prep kit Whole exome sequencing of cfDNA in metastatic prostate cancer – customer presentation
Improved sensitivity for small nucleotide variants with reduced DNA input requirements and reduced hands–on time
Sensitive variant detection with Illumina Cell-Free DNA Prep with Enrichment
Multi-analyte liquid biopsy enables analysis of treatment resistance in prostate cancer.
Illumina presentation recorded at EACR Liquid Biopsies 2024 conference in Lyon. In this brief video (16 min), Anna Babayan outlines solutions available for liquid biopsy research.
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.
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. View less
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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. View less
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. View less
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. View less
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. 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
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) View less
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) View less
IDT for Illumina UMI DNA/RNA 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. View less
IDT for Illumina UMI DNA/RNA 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. View less
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. View less
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. View less
Illumina Cell-Free and FFPE DNA Prep with Enrichment Training - Customer Site
20122119
This 2-day introductory course is designed to familiarize new users with the library prep and enrichment workflow through detailed hands-on instruction, for either Illumina Cell-Free DNA Prep with Enrichment or Illumina FFPE DNA Prep with Exome 2.5 Enrichment. Participants will learn all essential steps in the workflow, including manual library preparation, enrichment, sequencing, and data analysis. Training includes up to 4 attendees. Any necessary panels and reagents need to be purchased separately. View less
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Specifications

General

Assay time	~8.5–9.5 hr
Hands-on time	~2.5–3 hr
Input quantity	10–30 ng cfDNA
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%)
Description	A fast, flexible, and scalable cfDNA library preparation kit for highly accurate mutation detection
Instruments	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
Method	Custom sequencing , Targeted DNA sequencing , Target enrichment
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)

Ordering

Notice

Unless otherwise stated, the minimum order amount is USD 1,000.
For orders below USD 1,000, an additional handling fee may apply, or we may arrange local delivery / local handover where available.
All quotations are subject to final confirmation, including product availability, lead time, batch information, shipping cost, and applicable export or handling requirements.
For quotation requests, please send an RFQ from website or contact:

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