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Last Posted: Aug 08, 2023
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Deep learning model improves COPD risk prediction and gene discovery.
et al. Nat Genet 2023 4

Liability scores for chronic obstructive pulmonary disease obtained from our deep learning model improve genetic association discovery and risk prediction. We trained our model using full spirograms and noisy medical record labels obtained from self-reporting and hospital diagnostic codes, and demonstrated that the machine-learning-based phenotyping approach can be generalized to diseases that lack expert-defined annotations.

Inference of chronic obstructive pulmonary disease with deep learning on raw spirograms identifies new genetic loci and improves risk models.
Justin Cosentino et al. Nat Genet 2023 4

Here we train a deep convolutional neural network on noisy self-reported and International Classification of Diseases labels to predict COPD case–control status from high-dimensional raw spirograms and use the model’s predictions as a liability score. The machine-learning-based (ML-based) liability score accurately discriminates COPD cases and controls and predicts COPD-related hospitalization without any domain-specific knowledge.

Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.
Nick Shrine et al. Nature genetics 2023 3 (3) 410-422

Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by =2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups.

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