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DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell

Guangsheng Pei1, Ruifeng Hu1, Peilin Jia1

  • 1Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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|May 28, 2021
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Summary

DeepFun is a new web server that assesses the function of non-coding genetic variants using a convolutional neural network (CNN). It provides tissue-specific functional predictions for genetic variants identified in genome-wide association studies (GWAS).

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Most genetic variants from genome-wide association studies (GWAS) are in non-coding DNA.
  • Understanding the function of these non-coding variants is crucial for disease research.

Purpose of the Study:

  • To develop a user-friendly web server, DeepFun, for assessing the functional activity of non-coding genetic variants.
  • To provide tissue- and cell type-specific functional predictions for genetic variants.

Main Methods:

  • Utilized a convolutional neural network (CNN) framework.
  • Integrated extensive epigenomics annotations from ENCODE and Roadmap projects, including DNase I accessibility, histone modifications, and transcription factor binding profiles across 225 tissues/cell types.
  • Developed a web server accessible at https://bioinfo.uth.edu/deepfun/.

Main Results:

  • DeepFun offers enhanced functional assessment for non-coding variants in a tissue-specific manner.
  • Independent validations using GWAS datasets confirmed DeepFun's ability to predict variant effects and visualize potential regulatory motifs.
  • The server expands the capabilities of existing variant prioritization tools.

Conclusions:

  • DeepFun is a valuable tool for predicting the functional impact of non-coding genetic variants.
  • The web server facilitates research in genetics, functional genomics, and disease studies.
  • It enables a more precise understanding of genetic variation in non-coding regions.