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FFPE-compatible panel for measuring T cell diversity and clonal expansion in tumor samples by sequencing T cell receptor beta chain rearrangements.
Assay time
Hands-on time
Input quantity
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.
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.
Assay time | 5.5 – 7.5 hours (library prep only; doesn't include library quantification, normalization, or pooling time) |
---|---|
Automation capability | Liquid handling robots |
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 |
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 for Illumina TCR beta-SR Panel
AmpliSeq for Illumina Library PLUS
AmpliSeq for Illumina CD Indexes
AmpliSeq for Illumina cDNA Synthesis
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 |
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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 robots | ||||
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 |
Library Prep and Array Kit Selector
Find the right sequencing library preparation kit or microarray for your needs. Filter by method, species, and more. Compare, share, and order kits.
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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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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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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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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