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Background  Immunohistochemistry (IHC) for programmed cell death ligand 1 (PD-L1) displays staining diversity. We compared IHC staining of PD-L1 in gastric cancer (GC) by using three commercially available antibody clones, and analyzed the correlation with the prognosis.    Methods  IHC using PD-L1 antibodies (clones SP142, 28–8 and E1L3N) in 315 formalin-fixed paraffin-embedded samples was qualitatively compared at the 1, 5 and 10% cut-off by two pathologists on total, tumor and immune/stromal cells. We used computer – assisted scoring to quantitatively analyze and compare the “H-score” of PD-L1 expression in 66 samples on total cells. The antibody clone SP142 was selected to investigate the infiltration of PD-L1 + CD8 +  T cells using automated quantitative immunofluorescence analyses ( n  = 50) and the prognostic significance. The prognoses were assessed by log-rank test.    Results  PD-L1 clones SP142 and 28–8 displayed great concordance by qualitative (κ = 0.816, 0.810 for total cells and tumor cells at the 5% cut-off) and quantitative analyses (R 2  = 0.7991, 0.8187 for positive percentage and “H-score”). PD-L1 clone SP142 showed the highest positivity in immune/stromal cells staining (18.41%) compared to 28–8 (7.62%), while clone E1L3N showed poor staining in both tumor and immune/stromal cells. Clone SP142, but not 28–8 and E1L3N, predicted a worse prognosis at the 5% cut-off ( p  = 0.0243). Both the clone SP142 and 28–8 had high inter-pathologist correlation for tumor staining (R 2  = 0.9805 and R 2  = 0.9853), but a moderate correlation for stromal/immune cell staining (R 2  = 0.5653 and R 2  = 0.5745). Furthermore, a higher density of PD-L1 + CD8 +  T cells was correlated with a shorter survival time (R 2  = 0.0909,  p  = 0.0352).    Conclusions  PD-L1 antibody clone SP142 was superior in cell staining, particularly in immune/stromal cell and prognosis. These findings are important for selection of PD-L1 antibody clones in the future diagnostic test.    Electronic supplementary material  The online version of this article (10.1186/s13000-018-0766-0) contains supplementary material, which is available to authorized users.

PD-L1 expression and the prognostic significance in gastric cancer: a retrospective comparison of three PD-L1 antibody clones (SP142, 28–8 and E1L3N)