Mantis-ml: Disease-Agnostic Gene Prioritization from High-Throughput Genomic Screens by Stochastic Semi-supervised Learning.
AuthorVitsios, D; Petrovski, S
Source TitleAmerican Journal of Human Genetics
University of Melbourne Author/sPetrovski, Slave
AffiliationMedicine (Austin & Northern Health)
Document TypeJournal Article
CitationsVitsios, D. & Petrovski, S. (2020). Mantis-ml: Disease-Agnostic Gene Prioritization from High-Throughput Genomic Screens by Stochastic Semi-supervised Learning.. Am J Hum Genet, 106 (5), pp.659-678. https://doi.org/10.1016/j.ajhg.2020.03.012.
Access StatusOpen Access
Open Access at PMChttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212270
Access to large-scale genomics datasets has increased the utility of hypothesis-free genome-wide analyses. However, gene signals are often insufficiently powered to reach experiment-wide significance, triggering a process of laborious triaging of genomic-association-study results. We introduce mantis-ml, a multi-dimensional, multi-step machine-learning framework that allows objective assessment of the biological relevance of genes to disease studies. Mantis-ml is an automated machine-learning framework that follows a multi-model approach of stochastic semi-supervised learning to rank disease-associated genes through iterative learning sessions on random balanced datasets across the protein-coding exome. When applied to a range of human diseases, including chronic kidney disease (CKD), epilepsy, and amyotrophic lateral sclerosis (ALS), mantis-ml achieved an average area under curve (AUC) prediction performance of 0.81-0.89. Critically, to prove its value as a tool that can be used to interpret exome-wide association studies, we overlapped mantis-ml predictions with data from published cohort-level association studies. We found a statistically significant enrichment of high mantis-ml predictions among the highest-ranked genes from hypothesis-free cohort-level statistics, indicating a substantial improvement over the performance of current state-of-the-art methods and pointing to the capture of true prioritization signals for disease-associated genes. Finally, we introduce a generic mantis-ml score (GMS) trained with over 1,200 features as a generic-disease-likelihood estimator, outperforming published gene-level scores. In addition to our tool, we provide a gene prioritization atlas that includes mantis-ml's predictions across ten disease areas and empowers researchers to interactively navigate through the gene-triaging framework. Mantis-ml is an intuitive tool that supports the objective triaging of large-scale genomic discovery studies and enhances our understanding of complex genotype-phenotype associations.
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