The TruSeq Custom Amplicon Low Input Kit has been discontinued. The AmpliSeq for Illumina Custom DNA Panel is the recommended replacement.

TruSeq Custom Amplicon Low Input Kit (discontinued)

This library prep kit delivers sensitive and specific amplicon sequencing results from both low-input and FFPE DNA samples.Read More...

Achieve high resolution and exceptional accuracy from as little as 1 ng of DNA—Even with complex mixtures or degraded DNA. This kit allows labs to:

  • Perform multiplexing and rapid sample processing
  • Access a wider range of informative single-nucleotide polymorphisms (SNPs) with a single kit
  • Analyze challenging samples

Product Highlights

Low DNA Input and FFPE Compatibility

The TruSeq Custom Amplicon Low Input Library Prep Kit is a fully customizable, amplicon-based assay for targeted resequencing starting from as low as 10 ng of genomic DNA (gDNA). This scalable assay allows researchers to capture multiple targets of interest simultaneously and sequence up to 1536 amplicons in a single pool, using a single reaction. This library prep kit offers the flexibility to accommodate FFPE samples, such as preserved tumor tissue.

Confident Assay Design

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

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

Assess FFPE Sample Quality before Sequencing

The TruSeq FFPE DNA Library Prep QC Kit uses a simple qPCR reaction to determine DNA quality and provide guidance on sequencing parameters. This step ensures that only samples that will achieve the necessary sequencing metrics are prepared, conserving resources that might be used on potentially low-quality, unrecoverable samples. The results of the QC step determine the recommended amount of input DNA. The TruSeq FFPE DNA Library Prep QC Kit can be bundled with the TruSeq Custom Amplicon Low Input Library Prep Kit to maximize lab budgets.

For FFPE applications, we suggest designing your project with 150 bp or 175 bp amplicons since FFPE DNA is highly degraded. TruSeq Custom Amplicon Low Input cannot be used with applications requiring 425 bp amplicons.

Species Compatibility

The TruSeq Custom Amplicon Low Input Library Prep Kit 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 high-throughput automation vendors with robotic systems compatible with this kit

Frequently Purchased Together

Specifications

Product Comparison

TruSeq Custom Amplicon Low Input Kit (discontinued) AmpliSeq for Illumina Custom DNA Panel AmpliSeq for Illumina On-Demand
Assay Time ~6.5 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 ~3.5 hours 1.5 hours 1.5 hrs
Input Quantity 10 ng high-quality genomic DNA; 10 – 100 ng FFPE DNA (depending on QC results) 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 Blood, 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 Low Input TruSeq Custom Amplicon v1.5
Amplicon plexity (single pool) Up to 1536 Up to 10,000 (via Concierge)
Input requirement as low as 10 ng 50 ng
FFPE Compatibility Yes – 10 ng (FFPE DNA input dependent on quality) Yes – 250 ng
Amplicon size 150, 175, 250 bp 150, 175, 250, 425 bp
Instrument MiniSeq, MiSeq, NextSeq MiniSeq, MiSeq, NextSeq
Read Length Up to 2 x 150 bp Up to 2 x 300 bp
Time 6.5 hours 10 hours
Kit size (samples) 16, 96+ 96+

Two amplicon-based options for targeted sequencing are now 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 (discontinued)

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.