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3 Adaptive immune receptor repertoire profiling for biomarker discovery
  1. Alex Chenchik,
  2. Mikhail Makhanov,
  3. Dongfang Hu,
  4. Tianbing Liu and
  5. Lester Kobzik
  1. Cellecta, Inc., Mountain View, CA, USA


Background Adaptive Immune Receptor (AIR) Repertoire profiling and characterization of antigen-activated immune cells is essential for the discovery of novel prognostic and predictive biomarkers and for studying immune response mechanisms in cancer, auto-immune and other diseases.

Methods To facilitate these studies, we developed a novel technology for combined, unbiased profiling of all human TCR and BCR variable regions; and phenotypic characterization of immune cells in bulk, sorted fraction and single immune cells (figure 1). This method involves multiplex RT-PCR amplification and sequencing of CDR3 regions of TCR and BCR genes along with immunophenotyping with a set 500 highly expressed T- and B-cell subtyping and activation marker genes. Bioinformatic analysis of next-generation sequencing (NGS) data allows comprehensive AIR repertoire profiling, identification of antigen-activated TCR and BCR clonotypes, and detailed phenotypic characterization of T and B cells induced by adaptive immune responses.

Results Preliminary phenotypic AIR profiling studies in metastatic tumor samples and Humira®-treated rheumatoid arthritis cases indicate that AIR immunophenotyping technology has unparalleled throughput and sensitivity for the discovery of immunity biomarkers.

Abstract 3 Figure 1

Integrated AIR repertoire profiling & immunophenotypingFig. 1 The workflow illustrates integrated adaptive immune receptor (AIR) repertoire profiling and immunophenotyping directly in sorted cells without RNA purification using multiplex RT-PCR. High-resolution immunophenotyping (matching) of top TCR/BCR clonotypes is based on the expression of 300 key cell typing and activation T and B markers. Candidates were selected from a set of 3000 candidate genes described in >100 public databases, commercial assays, and peer-reviewed publications

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