Quality Assurance of Data Imported from the Genomic Data Commons (GDC) into the Xena Browser

The Xena Browser is a web-based tool that enables researchers to visualize and analyze cancer functional genomics data by integrating genomic, clinical, and survival data from different sources, including the Genomic Data Commons (GDC). To ensure the integrity of the data imported from the GDC via the Xena GDC Extract Transform Load (ETL) pipeline, automated quality assurance testing code has been developed here to validate this data. This testing code utilizes orthogonal data retrieval and comparison methods, independently verifying genomic, clinical, and survival data against data retrieved from the GDC. Multiple methods are implemented to accomplish this, such as rounding optimizations for gene expression data, handling multiple data values for single samples, addressing inconsistencies in the clinical and mutation files, and creating a logger file to document all inconsistencies. The testing code has been rigorously tested using flawed data and files to ensure its effectiveness in identifying errors. This automated approach not only saves time in QAing this data but also ensures the quality of important cancer functional genomics data for research purposes