scAmpi-A versatile pipeline for single-cell RNA-seq analysis from basics to clinics.

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique to decipher tissue composition at the single-cell level and to inform on disease mechanisms, tumor heterogeneity, and the state of the immune microenvironment. Although multiple methods for the computational analysis of scRNA-seq data exist, their application in a clinical setting demands standardized and reproducible workflows, targeted to extract, condense, and display the clinically relevant information. To this end, we designed scAmpi (Single Cell Analysis mRNA pipeline), a workflow that facilitates scRNA-seq analysis from raw read processing to informing on sample composition, clinically relevant gene and pathway alterations, and in silico identification of personalized candidate drug treatments. We demonstrate the value of this workflow for clinical decision making in a molecular tumor board as part of a clinical study.

Implementation of an IT-guided checklist to improve the quality of medication history records at hospital admission.

Background Medication discrepancies often occur at transition of care such as hospital admission and discharge. Obtaining a complete and accurate medication history on admission is essential as further treatment is based on it. Objective The goal of this study was to reduce the proportion of patients with at least one medication discrepancy in the medication history at admission by implementing an IT-guided checklist. Setting Surgery ward focused on vascular and visceral surgery at a Swiss Cantonal Hospital. Method The study was divided into two phases, before and after implementation of an IT-guided checklist. For both phases a pharmacist collected and compared the medication history (defined as gold standard) with that of the admitting physician. Medication discrepancies were subdivided in omissions and commissions, incorrect medications or dose changes, and incorrect dosage forms or strength. Main outcome measure The proportion of patients with at least one medication discrepancy in the medication history before and after intervention was assessed. Results Out of 415 admissions, 228 patients that met the inclusion criteria were enrolled in the study, 113 before and 115 patients after intervention. After intervention, medication discrepancies declined from 69.9 to 29.6% (p < 0.0001) of patients, the mean medication discrepancy per patient was reduced from 2.3 to 0.6 (p < 0.0001), and the most common error, omission of a regularly used medication, was reduced from 76.4 to 44.1% (p < 0.001). Conclusion The implementation of the IT-guided checklist is associated with a significant reduction of medication discrepancies at admission and potentially improves the medication safety for the patient.