Illumina Complete Long Reads with Enrichment, Human

A cost-effective, flexible, targeted long-read solution to address challenging-to-map regions of the human genome.

~2 days

Assay time

~6 hr

Hands-on time

50 ng DNA recommended; as low as 10 ng DNA

Input quantity

See full details in the specifications table

Overview

Illumina Complete Long Reads with Enrichment, Human enables highly accurate, cost-effective, targeted long reads from low input DNA. This library prep kit adds cost-effective insights by utilizing long reads where they provide the most value by complementing a standard, short-read whole genome with the targeted long-read panel of choice. Note: Analysis requires standard, ≥ 30× short-read WGS data from the same sample to complement the targeted long reads.

Key features

  • Highly flexible, targeted long reads compatible with premanufactured, predesigned, or custom panels

  • Targeted long reads with N50 5-7 kb to provide enhanced coverage of challenging-to-map regions of the human genome

  • Cost-effective insights by providing targeted long reads where they provide the most value

  • Accessible with standard NGS library prep workflow and your Illumina NovaSeq X, NovaSeq 6000, NovaSeq 6000Dx (RUO mode) systems

  • Analyzed in combination with ≥ 30× standard short read human whole genome using a streamlined and comprehensive DRAGEN app


Specifications


Required products

Illumina Complete Long Read Prep with Enrichment, Human includes core reagents for generating targeted long-read libraries. Purchase a probe panel for enrichment, either the premanufactured Human Comprehensive Panel (available to order separately or as part of the kit) or a predesigned or custom panel on the DesignStudio custom assay design tool. 

What accessories do I need?

Illumina unique dual indexes are required, as well as sufficient iCredits to meet data storage and analysis needs based on throughput.

A standard short-read ≥ 30 x whole-genome library from the same sample is required for Illumina Complete Long Read with Enrichment analysis. Illumina DNA PCR-Free Prep is recommended for library preparation of the standard short- read whole genome. Third-party WGS kits are also compatible. Unmarked library does not need to be prepared or sequenced in parallel; FASTQ files from a previously assayed sample can be used.

/ Results

Applications

Example workflow

1
Library preparation

Illumina Complete Long Read Prep with Enrichment, Human

Custom Panel

3
Data analysis

DRAGEN ICLR (Illumina Complete Long Read) with Enrichment App


Project recommendations

Instrument Recommended number of samples Read length
NovaSeq 6000 System

Human Comprehensive Panel: 24 samples per S4 flow cell Large panels (15–25 Mb): ~75 samples per S4 flow cell Medium panels (5–15 Mb): ~187 samples per S4 flow cell Small panels (> 5 Mb): ~375 samples per S4 flow cell

2 × 150

NovaSeq X System

Human Comprehensive Panel: 24 samples per 10B flow cell, 64 samples per 25B flow cell Large panels (15–25 Mb): ~75 samples per 10B flow cell, ~200 samples per 25B flow cell Medium panels (5–15 Mb): ~187 samples per 10B flow cell, ~500 samples per 25B flow cell Small panels (> 5 Mb): ~375 samples per 10B flow cell, ~1000 samples per 25B flow cell

2 × 150

NextSeq 2000 System

Human Comprehensive Panel: 3 samples per P3 flow cell Large panels (15–25 Mb): ~9 samples per P3 flow cell Medium panels (5–15 Mb): ~22 samples per P3 flow cell Small panels (> 5 Mb): ~45 samples per P3 flow cell

2 × 150


Related applications and methods

Documentation

Product literature

Compare

Illumina Complete Long Reads with Enrichment, Human Illumina Complete Long Read Prep, Human Illumina DNA Prep with Exome 2.5 Enrichment Illumina DNA PCR-Free Prep
Assay time ~2 days ~7.5–8.5 hr 6.5 hr ~1.5 hr
Description

Flexible, cost-effective targeted long reads coupled with short-read data for highly accurate WGS. Pair with a predesigned or custom panel to resolve challenging-to-map regions of the genome or add phased sequencing to regions of interest.

Illumina Complete Long Read Prep, Human performs long-read human germline whole-genome sequencing using existing Illumina NovaSeq platforms. 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.

Prepare sequencing libraries for sensitive applications using a unique combination of on-bead tagmentation with PCR-free chemistry which simultaneously eliminates PCR-induced bias and reduces total library prep time to 90 minutes.

Hands-on time

~6 hr

5–6 hr including (PCR and QC) ~2 hr ~45 min
Input quantity

50 ng DNA recommended; as low as 10 ng DNA

50 ng DNA recommended 50-1000 ng high-quality genomic DNA (For direct blood and saliva, see reference guide) 25 ng to 300 ng
Instruments NovaSeq X System, NovaSeq 6000Dx in Research Mode, NovaSeq 6000 System, NovaSeq X Plus System NovaSeq 6000Dx Instrument, 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 MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, NextSeq 550Dx in Research Mode, NovaSeq X System, NextSeq 500 System, NovaSeq 6000 System, NovaSeq X Plus System
Method Custom sequencing, Targeted DNA sequencing, Long-read sequencing, Phased sequencing, Whole-genome sequencing, Target enrichment Long-read sequencing, Whole-genome sequencing Targeted DNA sequencing, Exome sequencing, Target enrichment De novo sequencing, Whole-genome sequencing
Multiplexing

Up to 384 samples per lane (depending on panel target size and sequencing output)

Up to 48 Pre-enrichment pooling of up to 12-plex is tested. Kit configuration supports multiplexing up to 192 samples. Up to 384 possible. Up to 384-plex
Nucleic acid type DNA DNA DNA DNA
Number of reactions 24 or 96 reactions 8 or 24
Specialized sample types Blood, Not FFPE-Compatible, Saliva Blood, Not FFPE-Compatible, Low-Input Samples, Saliva Blood, Saliva Blood, Not FFPE-Compatible, Low-Input Samples, Saliva, Not FFPE-Compatible
Species category Human Human Human Any species, Human
Target insert size

Insert size: 500–700 bp, read length N50 5–7 kb

500–700 bp 450 bp +/- 75 bp
Technology Sequencing Sequencing Sequencing Sequencing
Variant class Single nucleotide polymorphisms (SNPs), Germline variants, Structural variants, Single nucleotide variants (SNVs), Insertions-deletions (indels), Copy number variants (CNVs) Short tandem repeats (STRs), Germline variants, Structural variants, Single nucleotide variants (SNVs), Insertions-deletions (indels) Single nucleotide polymorphisms (SNPs), Loss of heterozygosity (LOH), Somatic variants, Germline variants, Insertions-deletions (indels), Copy number variants (CNVs) Short tandem repeats (STRs), Single nucleotide polymorphisms (SNPs), Somatic variants, Chromosomal abnormalities, Germline variants, Structural variants, Insertions-deletions (indels), Copy number variants (CNVs)

Figures

Targeted long reads enhance accuracy in challenging regions

False negative (FN) plus false positive (FP) variant calls for SNPs and indels in HG002 genic regions targeted by the (A) Human Comprehensive Panel or (B) CMRG panel, using Illumina Complete Long Read Prep with Enrichment (orange) compared to standard short-read WGS (blue).

whole-genome coverage

Cost-effective human whole-genome coverage of challenging regions

Illumina Complete Long Read Prep with Enrichment, Human helps enhance coverage in challenging genic regions to complement standard short-read human WGS. IGV plot of RHCE sequenced using standard short-read WGS and Illumina Complete Long Reads with enrichment. Target regions noted in red.

haplotypes in polymorphic genes

Targeted long reads help resolve haplotypes in polymorphic genes

IGV plot from long-read sequencing using Illumina Complete Long Read Prep with Enrichment, Human. Phasing over a 722 kb region in the MHC locus. A 580 kb region (pink) is encapsulated in one phase block.

haplotypes in polymorphic genes

Targeted long reads help resolve haplotypes in polymorphic genes

IGV plots from long-read sequencing using Illumina Complete Long Read Prep with Enrichment, Human. HLA-C gene is fully phased. Reads are separated by haplotype.

Resources

Library prep (6)

Illumina Complete Long Read Prep with Enrichment, Human (24 samples)

20113832

A library preparation and enrichment solution for long-read human whole- genome sequencing (WGS) applications

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Illumina Complete Long Read Prep with Enrichment, Human (96 samples)

20113833

A library preparation and enrichment solution for long-read human whole- genome sequencing (WGS) applications.

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Illumina Complete Long Read Prep with Enrichment, Human Comprehensive Panel (24 samples)

20113834

A library preparation and enrichment solution with a probe panel designed to address regions that will benefit long-read human whole-genome sequencing (WGS) applications.

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Illumina Complete Long Read Prep with Enrichment, Human Comprehensive Panel (96 samples)

20113835

A library preparation and enrichment solution with a probe panel designed to address regions that will benefit long-read human whole-genome sequencing (WGS) applications.

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Illumina Complete Long Read Prep with Enrichment, HCP-24, S4 Starter Pack

20113838

This package contains 1 ICLR ENR-24 sample kit, 1 HCP-24, 1 NovaSeq 6000 S4 (300) cyc kits, and support 24 analyses

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Illumina Complete Long Read Prep with Enrichment, HCP-24, 10B Starter Pack

20113839

This package contains 1 ICLR ENR-24 sample kit, 1 HCP-24, 1 NovaSeq X 10B (300) cyc kit, and support for 24 analyses

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Panel (2)

Illumina Human Comprehensive Panel (24 samples)

20113836

A hybridization capture probe panel designed to target regions of the human genome that will benefit long-read whole-genome sequencing (WGS) applications

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Illumina Human Comprehensive Panel (96 samples)

20113837

A hybridization capture probe panel designed to target regions of the human genome that will benefit long-read whole-genome sequencing (WGS) applications

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Index adapters (5)

Illumina® Unique Dual Indexes, LT (48 Indexes, 48 Samples)

20098166

Illumina® Unique Dual Indexes, LT (48 Indexes, 48 Samples)

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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.

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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.

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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.

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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.

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Data analysis and storage (3)

Illumina Analytics - 1 iCredit

20042038

iCredits are used for data storage and analysis on either BaseSpace Sequence Hub or Illumina Connected Analytics.

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Illumina Analytics  Starter Pack - 1,000 iCredits

20042039

iCredits are used for data storage and analysis on either BaseSpace Sequence Hub or Illumina Connected Analytics.

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Illumina Analytics  - 5,000 iCredits

20042040

iCredits are used for data storage and analysis on either BaseSpace Sequence Hub or Illumina Connected Analytics.

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Accessory products (2)

Illumina® DNA PCR-Free Prep, Tagmentation (24 Samples)

20041794

Includes reagents and Illumina Purification Beads for preparing 24 libraries. Purchase index adapters separately.

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Illumina® DNA PCR-Free Prep, Tagmentation (96 Samples)

20041795

Includes reagents and Illumina Purification Beads for preparing 96 libraries. Purchase index adapters separately.

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