AIRR-seq Spike-in Control Standards

DriverMap AIR RNA Spike-in Controls for Adaptive Immune Receptor Repertoire Sequencing

A collection of synthetic mRNA constructs to be used as universal controls for both commercial and home-brewed AIRR-seq assays based on multiplex RT-PCR or 5’-RACE (SMART) PCR techniques

These first-in-kind RNA spike-in controls are designed to ensure consistent and reproducible T-cell Receptor (TCR) and B-cell Receptor (BCR) clonotype profiling using multiplex RT-PCR such as Cellecta´s DriverMap AIR Assay or 5´-RACE /SMART PCR.

The RNA standards contain nearly full-length V(D)JC structures that represent all seven TCR (TRB, TRA, TRG, TRD) and BCR (IGH, IGK, and IGL) chains:

39 TCR constructs, each representing unique TRBs, TRAs, TRGs, and TRDs are shown. Each construct has 3 variations in the CDR3 region (*) that differ by 3 nucleotides in fixed positions

48 BCR mRNA spike-in constructs for IGH, IGK and IGL chains are shown. Each construct has three variations in the CDR3 region (*) that differ by three nucleotides in a fixed position.

Product Formats

DriverMap AIR RNA Spike-in controls are available as Premixed Control or as Sets of Isoform Pools for use in TCR- or BCR-NGS-based AIRR profiling:

  • Premixed Control:
Mix of 39 TCR constructs with each of 13 TCR isoforms containing  three CDR3 variants for each isoform. (Cat #: DMAIR-HTR-SC-M)
Mix of 48 BCR constructs with each of 16 BCR Isoforms containing three CDR3 variants for each isoform (Cat #: DMAIR-HBR-SC-M)
The three CD3 variants from each isoform are mixed in a 16:4:1 ratio present in three discrete concentrations of 4000, 1000 and 250 RNA molecules (i.e., UMIs)/µl.

  • Sets of Isoform Pools:
13 TCR isoform pools (Cat #: DMAIR-HTR-SC-P), 16 BCR isoform pools (Cat #: DMAIR-HBR-SC-P). Each pool has three constructs with the same V(D)JC isoform receptor structure, and each construct has a unique CDR3 sequence. The sequences of the three CD3 variant constructs within each pool differ from each other by 3 unique single-nucleotide mutations, and the three variants are mixed at a 1:1:1 ratio, each with 2,500 RNA molecules/µl.

Applications for DriverMap AIR RNA Spike-in Controls

  • Ensure Sensitivity and Specificity: Premixed Control may be spiked into your experimental sample to measure the accuracy and linear range of your PCR assay.
  • Error Quantification: Premixed Control may be used to assess sequencing errors introduced at the RT, PCR and NGS stages.
  • Sample Quality Control: Isoform Pool Sets or Premixed Control may be used to assess sample quality such as in degraded FFPE samples.
  • Cross-Contamination Detection: Isoform Pool Sets can measure cross-contamination between different samples.

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