Additionally, we developed an analysis pipeline for the assignment of putative clonotypes based on simultaneous expression of alpha and beta variable TCR chains (TCRVβ/Vα pairs) at the single-cell level.<h4>Findings</h4>Our approach captured specific immune cell distributions in relation to the individual sample clonality, as well as regional dominance of certain TCRVβ/Vα pairs in surgical non-small cell lung cancer (NSCLC) specimens and matching lymph node samples. The gene discussed is COX5A; the disease is non-small cell lung carcinoma.