2. Experimental Design Strategies

The main objective of the DriverMap AIR assays is to:

• Characterize the global AIR repertoire in normal and pathological conditions
• Identify activated subsets of TCR and BCR clonotypes due to the adaptive immune response
• Identify disease- or pathogen-specific TCR and BCR clonotypes (both CDR3—or CDR1-CDR2-CDR3—sequences and chain-pairing)
• Characterize the phenotype of antigen-specific, activated T and B cells
  

Currently, most available AIR technologies are based on the amplification of TCR and BCR sequences followed by NGS but provide only partial immune receptor repertoire information [1-7,18] while being characterized by significant systematic biases [8, 14]. The following sections will provide practical guidelines for selecting the best design strategy for AIR experiments.