GxP-Ready Single-Cell RNA-seq and Spatial Transcriptomics End-to-End Pipeline for Clinical Research

Area of Science:

• Genomics
• Computational Biology
• Biotechnology

Background:

• Single-cell/nucleus RNA-sequencing and Spatial Transcriptomics offer deep insights into cellular heterogeneity and tissue architecture.
• Clinical adoption of these powerful omics tools is limited by regulatory hurdles like data integrity, reproducibility, and scalability.

Purpose of the Study:

• To develop a modular, GxP-ready computational pipeline for integrated single-cell and spatial omics data analysis.
• To facilitate the use of advanced omics technologies in clinical and regulated research settings.

Main Methods:

• Development of NNclinSSOAP (Novo Nordisk Clinical Single-cell Spatial Omics Analytical Pipeline), a Nextflow-based end-to-end computational workflow.
• Integration of established single-cell RNA sequencing analysis with a novel pipeline for Xenium spatial transcriptomics data.
• Implementation of features ensuring data integrity, traceability, and scalability for high-performance computing (HPC) environments.

Main Results:

• NNclinSSOAP transforms raw RNA sequencing and Xenium spatial data into annotated single-cell objects and spatially resolved tissue maps.
• The pipeline is designed for mechanistic studies and clinical endpoint generation, supporting large-scale dataset processing.
• A demo case demonstrates the pipeline's usability, executable within 1.5 hours on a standard laptop, with open-source code and data.

Conclusions:

• NNclinSSOAP provides a robust, compliant, and scalable solution for analyzing single-cell and spatial transcriptomics data in regulated environments.
• The pipeline enhances the potential of omics technologies for clinical research and disease understanding.
• Open-source availability promotes broader adoption and reproducibility in the scientific community.