Privacy preserving validation for multiomic prediction models. Issue 3 (6th April 2022)

• Record Type: Journal Article
• Authors: Ahmed, Talal; Carty, Mark A; Wenric, Stephane; Dry, Jonathan R; Salahudeen, Ameen A; Khan, Aly A; Lefkofsky, Eric; Stumpe, Martin C; Pelossof, Raphael
• Is Part Of: Briefings in bioinformatics. Volume 23:Issue 3(2022)
• Publication Date: 2022-04-06
• Subjects: privacy -- translational research -- reproducibility -- model validation -- machine learning -- transcriptomics; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbac110
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Reproducibility of results obtained using ribonucleic acid (RNA) data across labs remains a major hurdle in cancer research. Often, molecular predictors trained on one dataset cannot be applied to another due to differences in RNA library preparation and quantification, which inhibits the validation of predictors across labs. While current RNA correction algorithms reduce these differences, they require simultaneous access to patient-level data from all datasets, which necessitates the sharing of training data for predictors when sharing predictors. Here, we describe SpinAdapt, an unsupervised RNA correction algorithm that enables the transfer of molecular models without requiring access to patient-level data. It computes data corrections only via aggregate statistics of each dataset, thereby maintaining patient data privacy. Despite an inherent trade-off between privacy and performance, SpinAdapt outperforms current correction methods, like Seurat and ComBat, on publicly available cancer studies, including TCGA and ICGC. Furthermore, SpinAdapt can correct new samples, thereby enabling unbiased evaluation on validation cohorts. We expect this novel correction paradigm to enhance research reproducibility and to preserve patient privacy.