AmpliSeq for Illumina Custom DNA Panel

Targeted custom research panels optimized for sequencing specific targets or genomic content of interest.

As low as 5 hr (library prep only; doesn't include library quantification, normalization, or pooling time)

Assay time

1.5 hours

Hands-on time

1–100 ng (10 ng recommended per pool)

Input quantity

See full details in the specifications table

The AmpliSeq for Illumina Custom DNA Panel is the recommended replacement for the TruSeq Custom Amplicon and TruSeq Custom Amplicon Low-Input kits, which have been discontinued.

Overview

Accurate data across various sample types

Achieve unmatched data quality with AmpliSeq chemistry and Illumina next-generation sequencing (NGS) technology, even from low-quality starting materials such as formalin-fixed, paraffin-embedded (FFPE) tissues.

Include only the genes and targets of interest

Easily design custom content with DesignStudio, a free, user-friendly, online tool that creates panels optimized for the targets or specific genomic content of interest.

Flexible and tunable designs from 12 to over 12,000 amplicons, and multiple amplicon size options.

Fast, simple workflow

Increased efficiency with a 5.5-hour library preparation workflow with only 1.5 hours of hands-on time.

Scalable solution

Multiple options for sequencing platforms, data analysis, and support meet virtually any throughput requirements.


Specifications


Required products

The AmpliSeq for Illumina Custom workflow requires the Custom Panel, Library PLUS kit, and index adapter.

/ Results

Applications

Example workflow


Related applications and methods

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AmpliSeq for Illumina Custom DNA Panel AmpliSeq for Illumina On-Demand Illumina DNA Prep with Enrichment
Assay time As low as 5 hr (library prep only; doesn't include library quantification, normalization, or pooling time) As low as 5 hr (library prep only; doesn't include library quantification, normalization, or pooling time) ~6.5 hr
Content specifications Custom content of interest - up to 5 Mb Custom content from 1 (24 amplicons) to 500 (15,000 amplicons) genes Exome: 45 Mb exonic content (≥98% of RefSeq, CCDS, and Ensembl coding content).
Custom: 0.5 - 15 Mb genomic content of interest.
Fixed panels: Content varies by panel.
Description A custom research assay that can be used to focus studies on specific genes, regions, or variants of interest with high accuracy. A custom research assay from >5000 pretested genes that can be used to focus studies on specific genes, regions, or variants of interest with high accuracy.

Prepare sequencing libraries for a variety of experiments, including whole-exome, custom, and fixed panel targeted sequencing, from low DNA inputs and a variety of sample types in ~6.5 hours. 

Hands-on time 1.5 hours 1.5 hr ~2 hr, ~2 hr
Input quantity 1–100 ng (10 ng recommended per pool) 1-100 ng DNA 10-1000 ng high-quality genomic DNA or 50-1000 ng FFPE DNA. (For blood and saliva, see the reference guide).
Instruments MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, MiniSeq System, NextSeq 550Dx in Research Mode MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, MiniSeq System, NextSeq 550Dx in Research Mode, NextSeq 500 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
Mechanism of action Multiplex PCR Multiplex PCR Bead-bound transposomes and hybrid-capture chemistry
Method Custom sequencing, Targeted DNA sequencing, Amplicon sequencing, Genotyping by sequencing Targeted DNA sequencing, Amplicon sequencing Custom sequencing, Targeted DNA sequencing, Exome sequencing, Target enrichment
Multiplexing Up to 96-plex Up to 96-plex Up to 384 available unique dual indexes. Pre-enrichment pooling of up to 12-plex is tested.
Nucleic acid type DNA DNA DNA
Number of amplicons 12 to 12,288 amplicons
Number of reactions 750 or 3000 reactions 24 or 96 reactions Custom workflow: 16 or 96 samples
Specialized sample types Blood, FFPE Tissue Blood, FFPE Tissue Blood, Low-Input Samples, FFPE Tissue, Saliva
Species category Any species, Tomato, Bovine, Mouse, Canine, Rice, Ovine, Hamster, Chicken, Porcine, Human, Maize, Soybean Human Other, Human
Species details Compatible with any species; predefined genomes available
Technology Sequencing Sequencing Sequencing

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DNA Amplicon LRM Module

Panel (2)

AmpliSeq™ Custom DNA Panel for Illumina® 

20020495

Custom assay supporting 750 or 3000 samples with < 4999 amplicons. Purchase Library PLUS and index adapters separately.

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AmpliSeq™ Custom DNA Large Panel for Illumina®

20020497

Sufficient for 3000 samples with > 4999 amplicons. Purchase Library PLUS and index adapters separately.

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Library prep (3)

AmpliSeq™ Library PLUS (24 Reactions) for Illumina®

20019101

Includes reagents for preparing 24 libraries. Purchase AmpliSeq for Illumina panel and index adapters separately.

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AmpliSeq™ Library PLUS (96 Reactions) for Illumina®

20019102

Includes reagents for preparing 96 libraries. Purchase AmpliSeq for Illumina panel and index adapters separately.

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AmpliSeq™ Library PLUS (384 Reactions) for Illumina®

20019103

Includes reagents for preparing 384 libraries. Purchase AmpliSeq for Illumina panel and index adapters separately.

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Index adapters (6)

AmpliSeq™ UD Indexes for Illumina® (24 Indexes, 24 Samples)

20019104

Includes 24 indexes sufficient for labeling 24 samples. Purchase library prep and enrichment reagents and probe panels separately.

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AmpliSeq™ CD Indexes Set A for Illumina®

20019105

Includes 96 indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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AmpliSeq™ CD Indexes Set B for Illumina®

20019106

Includes 96 indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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AmpliSeq™ CD Indexes Set C for Illumina®

20019107

Includes 96 indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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AmpliSeq™ CD Indexes Set D for Illumina®

20019167

Includes 96, 8 bp indexes sufficient for labeling 96 samples. Purchase library prep reagents and probe panels separately.

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AmpliSeq™ CD Indexes Set A-D for Illumina® (384 Indexes, 384 Samples)

20031676

Includes four sets of AmpliSeq CD Indexes for Illumina, Set A, Set B, Set C and Set D. Each set contains 96, 8 bp indexes sufficient for labeling 96 samples. Purchase library prep and probe panels separately.

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Accessory products (3)

AmpliSeq™ for Illumina® Sample ID Panel

20019162

Includes eight single nucleotide polymorphism (SNP)-targeting primer pairs and one gender discriminating primer pair sufficient for 96 reactions when paired with AmpliSeq Library PLUS for Illumina. Enables quick and accurate sample identification. Purchase library prep, probe panels, and index adapters separately.

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AmpliSeq™ for Illumina® Direct FFPE DNA

20023378

Includes 24 reactions to prepare DNA from unstained, slide-mounted FFPE tissues for library construction using AmpliSeq for Illumina protocol, without the need for deparaffinization or DNA purification.

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AmpliSeq™ Library Equalizer for Illumina®

20019171

Includes beads and reagents for library normalization when preparing AmpliSeq for Illumina libraries for sequencing.

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Services (2)

AmpliSeq for Illumina DNA Library Prep Training

20023392

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AmpliSeq™ for Illumina®, Sequencing Service

20025874

AmpliSeq for Illumina custom sequencing project in Illumina Lab for 96–384 samples to support research projects (priced per sample). Includes pre-project consult, Illumina scientist support, experimental design, sample shipment coordination, library preparation and sample QC, sequencing, data analysis on BSSH and/or sequencing run files, technology transfer, fixed or custom panel, and consumables. Turnaround time is 6–8 weeks.

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