Peter van Mourik

144 Chapter 7 Evaluation of clinical treatment For all treatments both the patients and those who were involved in clinical data collection were blinded for the magnitude of the in vitro drug response of the patients’ organoids and vice versa. The ppFEV 1 was measured according to ATS- ERS standards 23,24 . The SCC was measured using the Macroduct® system and performed according to the most recent version of the standard operating procedure of the European Cystic Fibrosis Society-Clinical Trial Network. Quantification and statistical analysis The primary outcome of the study was the correlation (Pearson) between the in vitro organoid and in vivo effects (change in ppFEV 1 and SCC) plus the predictive capacity of the organoid model, in patients that had a baseline ppFEV 1 between 40 and 90 percent. When a change in ppFEV 1 or SCC was missing, a patient was excluded from that part of the analysis. In a secondary analysis, we calculated the correlation and predictive capacity for patients that had a baseline ppFEV 1 of <40 or >90 percent as well as for the total group of patients that was treated. Finally we used the wilcoxon signed rank test to examined the clinical response of patients with at least one rare CFTR mutation (non- F508del or S1251N ) who had a response in their rectal organoids (area under the curve (AUC) at 0.128 µM forsklin >1000) to the CFTR modulating drug. Receiver operating characteristic (ROC) curves were generated to evaluate the predictive capacity of organoid FIS for clinical responses. A Youden index was used to select the organoid cut-off point with the most optimal combination of sensitivity and specificity from the ROC-curves 25 . A leave-one-out cross validation further validated our findings 26 . As some patients were treated with two CFTR modifying treatments, we controlled for repeated measurements when calculating correlations and ROC-curves to evaluate a potential bias 27,28 . Because of the limited number of patients, no further subgroup analysis were performed. Statistical analysis were performed using GraphPad Prism 7.02, IBM SPSS Statistics version 22 and R-studio version 0.99.441. Additional resources The clinical trial registry numbers and Institutional Review Board (IRB) numbers of the two trials in which the patients with an S1251N mutation were treated with genistein plus curcumin and ivacaftor are NTR4585/METC14-268/G-M and NTR4873/METC14-514/M respectively. Additional information on these trials can be found on http://www.trialregister.nl/trialreg/index.asp. The IRB code of the HUB-CF organoid biobank is 14-008.