DeepRisk: A deep learning approach for genome-wide assessment of common disease risk

Jiajie Peng, Zhijie Bao, Jingyi Li, Ruijiang Han, Yuxian Wang, Lu Han, Jinghao Peng, Tao Wang, Jianye Hao, Zhongyu Wei, Xuequn Shang

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

The potential for being able to identify individuals at high disease risk solely based on genotype data has garnered significant interest. Although widely applied, traditional polygenic risk scoring methods fall short, as they are built on additive models that fail to capture the intricate associations among single nucleotide polymorphisms (SNPs). This presents a limitation, as genetic diseases often arise from complex interactions between multiple SNPs. To address this challenge, we developed DeepRisk, a biological knowledge-driven deep learning method for modeling these complex, nonlinear associations among SNPs, to provide a more effective method for scoring the risk of common diseases with genome-wide genotype data. Evaluations demonstrated that DeepRisk outperforms existing PRS-based methods in identifying individuals at high risk for four common diseases: Alzheimer's disease, inflammatory bowel disease, type 2 diabetes, and breast cancer.

Original languageEnglish
Pages (from-to)752-760
Number of pages9
JournalFundamental Research
Volume4
Issue number4
DOIs
StatePublished - Jul 2024

Keywords

  • Common disease risk
  • Deep learning
  • Disease prevention
  • Disease risk prediction
  • Polygenic risk score

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