Oncomine™ TCR Beta-LR Assay - FAQs

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14 product FAQs found

What control do you recommend using with the Oncomine TCR Beta-LR Assay?

We recommend using T Cell Leukemia (Jurkat) Total RNA (Cat. No. AM7858) as a control. T cell Leukemia (Jurkat) Total RNA is derived from a cell line consisting of a single T cell clonotype. Running the Oncomine TCR Beta-LR Assay on Jurkat Total RNA should enable detection of a single clonotype.

Are there any BED files for the Oncomine TCR Beta-LR Assay?

Unlike other AmpliSeq panels, there are no BED files and no reference is needed. All downstream analysis takes place in Ion Reporter Software.

Can I quantitate the Oncomine TCR Beta-LR Assay library with the Ion Library Equalizer Kit?

We have tested the Ion Library Equalizer Kit with this kit for library quantitation and it does function, but manually balancing library input into the Ion Chef instrument is preferred.

What version of Torrent Suite Software and Ion Reporter Software can be used with the Oncomine TCR Beta-LR Assay?

Torrent Suite Software 5.6 and Ion Reporter Software 5.6 are needed to generate reports. In Torrent Suite Software 5.6, two Planned Run templates are provided for use with the Oncomine TCR Beta-LR Assay.

Can I run the Oncomine TCR Beta-LR Assay on the Ion PGM System?

The Oncomine TCR Beta-LR Assay has been developed and verified for use on the Ion GeneStudio S5 Series System. The assay can be used with the Ion PGM System, however, this instrument configuration is not supported.

What are the components of the Oncomine TCR Beta-LR Assay?

Here are the components of the Oncomine TCR Beta-LR Assay:

- Oncomine TCR Beta‑LR Panel
- Ion AmpliSeq Library Kit Plus
- Ion Select Barcode Adapters

What is the concentration of the primer pool in the Oncomine TCR Beta-LR Assay?

The primer pool is at 5X concentration.

What are the amplicon read lengths in the Oncomine TCR Beta-LR Assay?

The Oncomine TCR Beta-LR Assay enables long-read RNA sequencing (up to 400 bp amplicon length) for complete characterization of the T cell receptor Beta (TCR Beta) chain, including all three complementarity-determining regions (CDR1, 2, and 3) of the variable gene. This enables allele-specific interrogation of TCR Beta to potentially predict drug-mediated adverse events.

How many primer pools does the Oncomine TCR Beta-LR Assay kit contain?

The primers are provided as a single pool.

With the Oncomine TCR Beta-LR Assay, how many samples can I multiplex on each chip?

Up to 16 samples can be multiplexed on an Ion 530 chip, up to 4 samples can be multiplexed on an Ion 520 chip, and up to 4 samples can be multiplexed on an Ion 318 chip.

What research sample types are compatible with the Oncomine TCR Beta-LR Assay?

A variety of research sample types including fresh-frozen tissue, whole blood, and sorted T cells are compatible with the Oncomine TCR Beta-LR Assay.

Why are immunologists and immuno-oncologists interested in T cell repertoire sequencing research?

T cell repertoire sequencing helps:

- To characterize diversity and study features of T lymphocytes in blood and infiltrated tumors
- To study variable gene polymorphisms implicated in autoimmune disease or immune-mediated adverse events
- To study the production and function of therapeutic or engineered T cells

How many samples can I analyze with the Oncomine TCR Beta-LR Assay?

This kit is good for 24 samples.

What does the Oncomine TCR Beta-LR Assay measure?

The Oncomine TCR Beta-LR Assay is an RNA-based next-generation sequencing (NGS) research assay that enables the characterization of the T cell receptor Beta (TCR Beta) sequences including all three complementarity-determining regions (CDR1, 2, and 3) of the variable gene. The assay measures T cell repertoire diversity as well as clonal expansion, and allows for identification of allele-specific polymorphisms.