The AmpliSeq for Illumina sequencing solution offers a highly multiplexed polymerase chain reaction (PCR)-based workflow for use with targets ranging from a few to hundreds of genes in a single run. AmpliSeq for Illumina panels are optimized for clinical cancer research and genetic disease studies.

TruSeq Custom Amplicon v1.5

Focus on key genomic regions of interest with this targeted resequencing solution, useful for very high plexity pools or longer amplicons.Read More...
Select Product(s)

TruSeq Custom Amplicon Kit (96 samples)


Accessory Products
What accessories do I need?

TruSeq Custom Amplicon Index Kit (96 indexes, 384 samples)



TruSeq Custom Amplicon Filter Plate (1 plate)



TruSeq Index Plate Fixture & Collar Kit (2 each)



Infinium FFPE QC Kit (384 reactions)



TruSeq® Custom Amplicon Assay Kit v1.5



Product Highlights

TruSeq Custom Amplicon is a fully customizable, amplicon-based assay for targeted resequencing. The assay enables you to focus interrogation on key regions of genomic interest. Up to 1536 amplicons can be sequenced in a single reaction using a simple workflow. This highly targeted approach enables researchers to efficiently discover, validate, and screen genetic variants.

Requiring as little as 50 ng of input genomic DNA (gDNA), this kit can be used with a wide range of sample types. The ability to multiplex up to 1536 amplicons per reaction allows coverage of up to 650 kb of cumulative sequence. Further, an integrated dual indexing scheme supports up to 96 samples per run, enabling you to fully benefit from desktop sequencer output capabilities.

This assay provides strong performance in difficult to address GC-rich regions, as well as high library yield, uniformity, and stability. Additionally, optimized amplification steps enable sample input requirements to drop from 150 ng to 50 ng.

Simplified Probe Design

Design targeted TruSeq Custom Amplicon oligonucleotide probes with DesignStudio, a free, easy-to-use online tool that provides optimized coverage.

Learn more about DesignStudio Software
Start a project in DesignStudio now (login required)

Simple Data Analysis

Automated data analysis using the BaseSpace TruSeq Amplicon App allows researchers to easily review project data, including variants detected, across multiple runs.

Species Compatibility

TruSeq Custom Amplicon supports human, mouse, rat, and bovine samples. DesignStudio design algorithms are also available for maize, rice, pig, dog, soybean, chicken, and sheep; however, assay performance cannot be guaranteed as the resulting assays have not been tested. In addition, Illumina Concierge services can design custom assays and/or provide assay optimization support for any species of interest.

Inquire about Illumina Concierge services


Find a list of automation vendors with robotic systems compatible with this kit

Frequently Purchased Together


Product Comparison

TruSeq Custom Amplicon v1.5 AmpliSeq for Illumina Custom DNA Panel AmpliSeq for Illumina On-Demand
Assay Time ~8 hours As low as 5 hours (library prep only; doesn't include library quantification, normalization, or pooling time) As low as 5 hours (library prep only; doesn't include library quantification, normalization, or pooling time)
Content Specifications Design custom probes to sequence genomic regions of interest. Content range: 4 – 650 kb Custom content of interest - up to 5 Mb Custom content from 1 (24 amplicons) to 500 (15,000 amplicons) genes
Hands-On Time ~4 hours 1.5 hours 1.5 hrs
Input Quantity 50 – 250 ng high-quality genomic DNA; 250 ng FFPE DNA 1–100 ng (10 ng recommended per pool) 1-100 ng DNA
Mechanism of Action Probe hybridization, extension-ligation, and PCR Multiplex PCR Multiplex PCR
Method Amplicon Sequencing , Custom Sequencing Amplicon Sequencing , Custom Sequencing, Genotyping by Sequencing , Targeted DNA Sequencing Amplicon Sequencing , Targeted DNA Sequencing
Multiplexing 1–96 Up to 96-plex Up to 96-plex
Specialized Sample Types FFPE Tissue Blood, FFPE Tissue FFPE Tissue
Species Category Bovine, Human, Mouse, Other, Rat Any Species, Bovine, Canine, Chicken, Hamster, Human, Maize, Mouse, Ovine, Porcine, Rice, Soybean, Tomato Human

Method-Specific Workflow Example


Customer Stories

Personalized Cancer Therapies through Precision Diagnostics

Dr. Robert Daber uses TruSeq Custom Amplicon to conduct genomic testing that can inform prognosis and therapeutic choices.

Learn More
Restoring and Managing Historical Columbia River Basin Fish Populations with Genomics

Novel GT-Seq method using the HiSeq System reduces genotyping costs and enables analysis of tens of thousands of fish.

Learn More

Supporting Data and Figures

Comparison of TruSeq Custom Amplicon Kits
Technology TruSeq Custom Amplicon v1.5 TruSeq Custom Amplicon Low Input
Amplicon plexity (single pool) Up to 10,000 (via Concierge) Up to 1536
Input requirement 50 ng as low as 10 ng
FFPE Compatibility Yes – 250 ng Yes – 10 ng (FFPE DNA input dependent on quality)
Amplicon size 150, 175, 250, 425 bp 150, 175, 250 bp
Instrument MiniSeq, MiSeq, NextSeq MiniSeq, MiSeq, NextSeq
Read Length Up to 2 x 300 bp Up to 2 x 150 bp
Time 10 hours 6.5 hours
Kit size (samples) 96+ 16, 96+

Two TruSeq Custom Amplicon options for targeted sequencing are available: TruSeq Custom Amplicon Low Input for low-input DNA and FFPE, or TruSeq Custom Amplicon 1.5 for very high plexity pools or longer amplicons. TruSeq Custom Amplicon Low Input enables you to detect and discover high-quality information, even from limited and challenging samples. Use the table to compare assays.

Related Products

AmpliSeq for Illumina Custom DNA Panel

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

TruSeq Custom Amplicon v1.5

Focus on key genomic regions of interest with this targeted resequencing solution, useful for very high plexity pools or longer amplicons.

Nextera XT DNA Library Preparation Kit

Prepare sequencing libraries for small genomes, PCR amplicons, plasmids, or cDNA in as little as 90 minutes, with a low DNA input requirement.