Illumina Human Comprehensive Panel

Illumina Human Comprehensive Panel

Predesigned, optimized panel to provide enhanced coverage of challenging-to-map regions within protein-coding genes using Illumina Complete Long Reads with Enrichment library prep kit. Analyzed in combination with a required ≥ 30× standard short-read whole 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

The Illumina Human Comprehensive Panel focuses long reads where they provide the greatest value in the genome. Targeted long reads complement highly accurate short-read WGS, creating a comprehensive human whole-genome solution that delivers exceptional small variant accuracy with an F1 score of 99.87% (SNVs +Indels), as measured by the PrecisionFDA1 Truth Challenge v2 benchmarks.

Cost-effective and focused long reads

Illumina Complete Long Read Prep with Enrichment and the Human Comprehensive Panel can help you achieve greater sample throughput than other long-read sequencing solutions when paired with Illumina platforms. Use to augment existing WGS data sets as a reflex tool for broader variant discovery.

Comprehensive and optimized probe panel

The Illumina Human Comprehensive Panel enhances coverage in a broad set of genic regions that benefit from targeted long reads, within >6500 protein coding genes.2 In developing this panel, the full set of over 20,000 protein-coding genes were considered. Genes that are comprehensively covered by short reads alone were excluded. This panel is ready to ship and optimized for use with Illumina Complete Long Read Prep with Enrichment, Human.

  • Highly optimized panel designed to enhance coverage of challenging-to-map areas within protein-coding regions of the genome
  • Broad panel addressing > 6500 genes targeting a total of > 90 Mb using Illumina Complete Long Reads to address regions of low coverage

References

  1. PrecisionFDA. Truth Challenge V2: Calling Variants from Short and Long Reads in Difficult-to-Map Regions. https://precision.fda.gov/challenges/10
  2. Bekritsky MA, Colombo C, Eberle MA. Identifying Genomic Regions with High Quality Single Nucleotide Variant Calling. illumina.com/science/genomics-research/articles/identifying-genomic-regions-with-high-quality-single-nucleotide-.html

Specifications

Assay time ~2 days
Automation capability Liquid Handling Robots
Description

Predesigned and optimized panel to address challenging-to-map regions within 6599 protein-coding genes.
Hands-on time

~6 hr
Input quantity

50 ng DNA recommended; as low as 10 ng DNA
Instruments NovaSeq X System, NovaSeq 6000Dx in Research Mode, NovaSeq 6000 System, NovaSeq X Plus System
Mechanism of action Tagmentation, Land-marking, Bead-linked transposome, Hybrid-capture chemistry
Method Target Enrichment, Whole-Genome Sequencing, Long-Read Sequencing, Targeted DNA Sequencing
Multiplexing

Up to 64 samples
Nucleic acid type DNA
Specialized sample types Blood, Not FFPE-Compatible, Low-Input Samples, Saliva
Species category Human
Technology Sequencing
Variant class Short tandem repeats (STRs), Single nucleotide polymorphisms (SNPs), Germline variants, Structural variants, Insertions-deletions (indels), Copy number variants (CNVs)

Required products

Available to order panel alone or as part of a kit. Requires Illumina Complete Long Read Prep with Enrichment, Human (24 or 96 samples) and Illumina unique dual Indexes. Purchase sufficient iCredits to meet data storage and analysis needs based on throughput.

A standard short-read ≥ 30 × whole-genome library from the same sample is required for Illumina Complete Long Read with Enrichment data analysis. Illumina DNA PCR-Free Prep is recommended for library preparation of the standard short read whole genome. FASTQ files from a previously run sample can be used. 

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Applications

Example workflow

1
Prepare

Recommended : Illumina DNA PCR-Free, Tagmentation

2
Sequence
3
Anlayze

DRAGEN ICLR (Illumina Complete Long Read with Enrichment)

Project recommendations

Instrument Recommended number of samples Read length
NovaSeq 6000 System

24 samples per S4 flow cell, 10 samples per S2 flow cell, 4 samples per S1 flow cell, 2 samples per SP flow cell
A paired PCR-free WGS library is required for analysis (Illumina DNA PCR-Free Prep recommended)

2 × 150

NovaSeq X System

64 samples per 25B flow cell, 24 samples per 10B flow cell, 4 samples per 1.5B flow cell
A paired PCR-free WGS library is required for analysis (Illumina DNA PCR-Free Prep recommended)

2 × 150

Related applications and methods

Human whole-genome sequencing

Human whole-genome sequencing provides the most detailed view into the complex genetic variants that make us unique.

Illumina Complete Long Read Technology

Illumina Complete Long Read technology powers a portfolio of assays that enable highly accurate long and short read sequencing on a single instrument.

Large whole-genome sequencing

Large whole-genome sequencing informs disease research and population genomics studies and reveals disease-associated alleles.

Documentation

Product literature
Support documentation

A dedicated support section is not currently available for this product

Figures

Resolve challenging protein-coding regions using targeted long reads

Illumina Complete Long Read Prep with Enrichment and the Human Comprehensive Panel help enhance coverage in challenging genic regions to complement standard short-read human WGS. IGV plot of STRC sequenced using standard short-read WGS and Illumina Complete Long Reads with enrichment.

Resolve challenging protein-coding regions using targeted long reads

Illumina Complete Long Read Prep with Enrichment and the Human Comprehensive Panel help enhance coverage in challenging genic regions to complement standard short-read human WGS. IGV plot of NEB sequenced using standard short-read WGS and Illumina Complete Long Reads with enrichment.

Targeted long reads enhance accuracy in challenging regions

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

Library prep (8)

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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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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