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

• DOI: 10.1371/journal.pcbi.1010097
• Publication Date: 2022-06-03T17:56:08Z
• Authors: Anne Bertolini; Michael Prummer; Mustafa Anil Tuncel; Ulrike Menzel; María Lourdes Ros...; Jack Kuipers; Daniel Johannes S...; ; Niko Beerenwinkel; Franziska Singer
• Keywords: 0303 health sciences; QH301-705.5; Sequence Analysis, RNA; Gene Expression Profiling; 2804 Cellular and Molecular Neuroscience; 610 Medicine & health; Workflow; 3. Good health; 03 medical and health sciences; 1105 Ecology, Evolution, Behavior and Systematics; 1311 Genetics; 10049 Institute of Pathology and Molecular Pathology; Exome Sequencing; 1312 Molecular Biology; Biology (General); Single-Cell Analysis; 2303 Ecology; Software; 2611 Modeling and Simulation; 1703 Computational Theory and Mathematics; Research Article

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.