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AmpliSeq for Illumina TCR beta-SR Panel

FFPE-compatible panel for measuring T cell diversity and clonal expansion in tumor samples by sequencing T cell receptor beta chain rearrangements.

5.5 – 7.5 hours (library prep only; doesn't include library quantification, normalization, or pooling time)

Assay time

<1.5 hr

Hands-on time

1 ng

Input quantity

See full details in the specifications table

Overview

AmpliSeq for Illumina TCR beta-SR (Short Read) Panel is a highly multiplexed targeted resequencing panel intended for use with multiple sample types, including formalin-fixed paraffin-embedded (FFPE) tumor samples. It is designed to measure T cell diversity and clonal expansion by sequencing T cell receptor (TCR) beta chain rearrangements. You can use a single pool of multiplex PCR primers, library reagents, and sample barcodes to generate libraries from DNA/RNA extracted from FFPE, whole blood, fresh-frozen tissue, or fluorescence activated cell sorting (FACS)-sorted cells.

Key features include:

  • High-value content - Obtain comprehensive coverage of TCR beta chain sequences

  • Simple, streamlined workflow - Prepare sequencing-ready libraries in a single day from FFPE, whole blood, fresh/frozen tissue, or fluorescence-activated cell sorting (FACS) cells

  • Low input requirement - Generate high-quality sequencing libraries from as little as 10 ng of input RNA

The AmpliSeq for Illumina TCR beta-SR Panel is part of an integrated workflow that includes AmpliSeq for Illumina polymerase chain reaction (PCR)-based library preparation, Illumina sequencing by synthesis (SBS) chemistry and next-generation sequencing (NGS) technology, and automated analysis.

This ready-to-use panel saves you the time and effort of identifying targets, designing primers, and optimizing panels. It enables characterization of the hypervariable complementary determining region 3 (CDR3) of the TCR beta chain. This information can help immunology researchers understand immune function, autoimmune diseases, and immune-mediated adverse effects.

Learn More About AmpliSeq for Illumina

Specifications

Assay time 5.5 – 7.5 hours (library prep only; doesn't include library quantification, normalization, or pooling time)
Automation capability Liquid handling robot(s)
Cancer type Solid tumor
Content specifications Sequences TCR beta chain rearrangements, with up to 80 bp read-length amplicons for characterizing CDR3.
Hands-on time <1.5 hr
Input quantity 1 ng
Instruments MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System
Mechanism of action Multiplex PCR
Method Targeted DNA sequencing, Amplicon sequencing, Targeted RNA sequencing
Nucleic acid type DNA, RNA
Number of amplicons Varies
Specialized sample types Blood, FFPE tissue
Species category Human
Target insert size 80 bp
Technology Sequencing
Variant class Transcript variants

Required products

The AmpliSeq for Illumina library preparation workflow requires a panel, library prep reagents (Library PLUS), and indexes. The following products are available for cDNA synthesis, sample identification, and FFPE sample prep:

  • AmpliSeq cDNA Synthesis for Illumina is required to convert total RNA to cDNA when working with AmpliSeq for Illumina RNA Panels.
  • AmpliSeq Library Equalizer for Illumina is an easy-to-use solution for normalizing libraries while using AmpliSeq for Illumina library prep methods.
  • AmpliSeq for Illumina Direct FFPE DNA allows for DNA preparation and library construction from FFPE tissues using the AmpliSeq for Illumina protocol without the need for deparaffinization or DNA purification.
/ Results

Applications

Example workflow

1
Prep

AmpliSeq for Illumina TCR beta-SR Panel

AmpliSeq for Illumina Library PLUS

AmpliSeq for Illumina CD Indexes

AmpliSeq for Illumina cDNA Synthesis

2
Sequence

Project recommendations

Instrument Recommended number of samples Read length
MiniSeq System

Samples per run will depend on sample type.

2 × 151 bp
MiSeq System

Samples per run will depend on sample type.

2 × 151 bp
NextSeq 550 System

Samples per run will depend on sample type.

2 × 151 bp

Related applications and methods

Amplicon sequencing

Ultra-deep sequencing of PCR amplicons enables analysis of specific genomic regions of interest. Learn more about amplicon sequencing and find comprehensive solutions.

Cancer genomics research

Our sequencing and microarray technologies support a broad range of cancer genomics research applications, from DNA to RNA analysis, epigenetics, and more.

Immunogenomics research

Gain insight into the immune repertoire, disease mechanisms, and the functional impact of immune-related genetic variation with NGS and array solutions.

Documentation

Product literature
Support documentation

Compare

AmpliSeq for Illumina TCR beta-SR Panel AmpliSeq for Illumina Immune Repertoire Plus, TCR beta Panel
Assay time 5.5 – 7.5 hours (library prep only; doesn't include library quantification, normalization, or pooling time) 5.5 – 7.5 hours (library prep only; doesn't include library quantification, normalization, or pooling time)
Automation capability Liquid handling robot(s)
Cancer type Solid tumor
Content specifications Sequences TCR beta chain rearrangements, with up to 80 bp read-length amplicons for characterizing CDR3. RNA evaluation of TCRβ chain rearrangements, including CDR1, CDR2, and CDR3 (with up to 400 bp read-length amplicons)
Hands-on time <1.5 hr < 1.5 hr
Input quantity 1 ng 10～1,000 ng
Instruments MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System
Mechanism of action Multiplex PCR Multiplex PCR
Method Targeted DNA sequencing, Amplicon sequencing, Targeted RNA sequencing Amplicon sequencing, Targeted RNA sequencing
Nucleic acid type DNA, RNA RNA
Number of amplicons Varies
Specialized sample types Blood, FFPE tissue Blood
Species category Human Human
Target insert size 80 bp
Technology Sequencing Sequencing
Variant class Transcript variants Transcript variants

Selection tools:

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Panel (1)

AmpliSeq™ for Illumina® TCR beta-SR Panel

20031675

Sufficient for 24 DNA or RNA samples when paired with AmpliSeq Library PLUS for Illumina. Includes AmpliSeq dNTP Mix for Illumina. Purchase library prep, index adapters, and accessory products 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™ cDNA Synthesis for Illumina®

20022654

Includes reaction mix and enzyme blend to convert total RNA to cDNA when working with AmpliSeq for Illumina RNA Panels (eg, AmpliSeq for Illumina Immune Response, Immune Repertoire Plus, TCR beta Panel, Myeloid, Transcriptome Human Gene Expression, Focus, and Comprehensive Panel v3 as well as Custom or Community RNA Panels). Number of reactions vary by panel (eg, 100 reactions per kit for AmpliSeq for Illumina Immune Response, Focus, Comprehensive Panel v3, and Custom panels and 200 reactions per kit for AmpliSeq for Illumina Transcriptome Human Gene Expression, Myeloid, Immune Repertoire Plus, and TCR beta Panels).

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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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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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