1.2. DriverMap™ AIR DNA Profiling

The DriverMap™ AIR DNA profiling assay is a multiplex PCR assay that uses the same set of 315 forward primers designed for the FR3 region and 100 reverse primers designed for the J region of seven immune receptor genes (Fig. 3).

Fig 3. gDNA structure and position of PCR primers to amplify CDR3 regions from gDNA template in the AIR DNA assay.

Similar to the AIR-RNA assay, it allows you to amplify all these seven chains encoded by the TCR and BCR genes. As there is a significant difference in the number of T and B cells present in biological samples, the preferred strategy for balanced immune receptor profiling from DNA is to amplify the TCR and BCR chains separately (Fig 4).

Fig.4. Outline of AIR DNA multiplex-PCR technology. Step1: Reverse gene-specific primers (GSP) with UMI targeting TCR or BCR J-region isoforms (in separate reactions) are annealed to single, complementary DNA strand (top strand) and extended with DNA polymerase. Step 2: Forward GSPs are annealed to extended DNA template and after extension by DNA polymerase generate CDR3 regions flanking from both sides by universal anchor sequences (AP1 and AP2). Step 3: In the first PCR step, anchored universal primers (AP1 and AP2) amplify CDR3 DNA fragments. Step 4: The second PCR step amplifies CDR3 fragments using indexed primers. The indexed amplified products (separately for TCR and BCR) are combined in equal amounts and analyzed by NGS.