Survival curves using the Kaplan Meier method were generated and log-rank tests applied using the TMA data viewer within QuPath, and independently verified using R (version 3.2.2)30 with the ‘Survival’ package (version 2.38–3)31 . For the calculation of disease-specific survival, deaths from other causes were treated as censored events. Median cutoff values were used in all cases, except for p53 where an experienced pathologist (MBL) selected two biologically-plausible cutoffs (H-scores 10 and 160) to separate extreme positive and extreme negative cases from those with intermediate (‘wild-type’) expression, based upon viewing all TMA cores post-analysis ranked by H-score. Stratification based on tertiles is also provided in the Supplementary Materials for PD-L1.
For TMA analysis, up to three tissue cores were available from each tumor, all selected from the same paraffin block representing the central tumor region. A single patient biomarker score was defined as the median of all available scores for the corresponding patient and biomarker. The median was chosen to aid the robustness of the measurement in a high-throughput setting, and reduce the likelihood of basing the score for any individual patient on an outlier that may have been caused by a tissue or staining artefact.
For TMA analysis, up to three tissue cores were available from each tumor, all selected from the same paraffin block representing the central tumor region. A single patient biomarker score was defined as the median of all available scores for the corresponding patient and biomarker. The median was chosen to aid the robustness of the measurement in a high-throughput setting, and reduce the likelihood of basing the score for any individual patient on an outlier that may have been caused by a tissue or staining artefact.
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