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- Title
MAGPIE: accurate pathogenic prediction for multiple variant types using machine learning approach.
- Authors
Liu, Yicheng; Zhang, Tianyun; You, Ningyuan; Wu, Sai; Shen, Ning
- Abstract
Identifying pathogenic variants from the vast majority of nucleotide variation remains a challenge. We present a method named Multimodal Annotation Generated Pathogenic Impact Evaluator (MAGPIE) that predicts the pathogenicity of multi-type variants. MAGPIE uses the ClinVar dataset for training and demonstrates superior performance in both the independent test set and multiple orthogonal validation datasets, accurately predicting variant pathogenicity. Notably, MAGPIE performs best in predicting the pathogenicity of rare variants and highly imbalanced datasets. Overall, results underline the robustness of MAGPIE as a valuable tool for predicting pathogenicity in various types of human genome variations. MAGPIE is available at https://github.com/shenlab-genomics/magpie.
- Subjects
MAGPIES; MACHINE learning; ORTHOGONALIZATION; HUMAN genome; INDEPENDENT sets; FORECASTING
- Publication
Genome Medicine, 2024, Vol 16, Issue 1, p1
- ISSN
1756-994X
- Publication type
Article
- DOI
10.1186/s13073-023-01274-4