Abstract
Single-cell next-generation sequencing assays are powerful tools to understand the nature of the immune cells that drive disease pathogenesis. In this brief review we explain the value of performing assays at single-cell resolution to better understand the pathogenesis of allergy, asthma, and other lung diseases. We explain the challenges in performing single-cell studies of airways and lung samples from patients with lung diseases. A major limitation comes from the amount of diseased tissue that can be used for research purposes. Finally, we discuss which sequencing strategies can be used to successfully investigate airway and lung diseases at single-cell resolution.