VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in genome-wide association studies: Applied to Alzheimer's disease

Qiao Liu, Chen Chen, Annie Gao, Hanghang Tong, Lei Xie

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

It is a grand challenge to reveal the causal effects of DNA variants in complex phenotypes. Although statistical techniques can establish correlations between genotypes and phenotypes in Genome-Wide Association Studies (GWAS), they often fail when the variant is rare. The emerging Network-based Association Studies aim to address this shortcoming in statistical analysis, but are mainly applied to coding variations. Increasing evidences suggest that non-coding variants play critical roles in the etiology of complex diseases. However, few computational tools are available to study the effect of rare non-coding variants on phenotypes. Here we have developed a multiscale modeling variant-to-function-to-network framework VariFunNet to address these challenges. VariFunNet first predict the functional variations of molecular interactions, which result from the non-coding variants. Then we incorporate the genes associated with the functional variation into a tissue-specific gene network, and identify subnetworks that transmit the functional variation to molecular phenotypes. Finally, we quantify the functional implication of the subnetwork, and prioritize the association of the non-coding variants with the phenotype. We have applied VariFunNet to investigating the causal effect of rare non-coding variants on Alzheimer's disease (AD). Among top 21 ranked causal non-coding variants, 16 of them are directly supported by existing evidences. The remaining 5 novel variants dysregulate multiple downstream biological processes, all of which are associated with the pathology of AD. Furthermore, we propose potential new drug targets that may modulate diverse pathways responsible for AD. These findings may shed new light on discovering new biomarkers and therapies for the prevention, diagnosis, and treatment of AD. Our results suggest that multiscale modeling is a potentially powerful approach to studying causal genotype-phenotype associations.

Original languageEnglish (US)
Title of host publicationProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages2177-2182
Number of pages6
Volume2017-January
ISBN (Electronic)9781509030491
DOIs
StatePublished - Dec 15 2017
Event2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States
Duration: Nov 13 2017Nov 16 2017

Other

Other2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
CountryUnited States
CityKansas City
Period11/13/1711/16/17

Fingerprint

Genome-Wide Association Study
Alzheimer Disease
Genes
Phenotype
Genetic Association Studies
Biological Phenomena
Gene Regulatory Networks
Molecular interactions
Biomarkers
Pathology
Statistical methods
DNA
Association reactions
Tissue
Pharmaceutical Preparations
Therapeutics

Keywords

  • complex disease
  • network robustness
  • RNA binding
  • single nucleotide polymorphism
  • systems biology
  • transcription factor

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Liu, Q., Chen, C., Gao, A., Tong, H., & Xie, L. (2017). VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in genome-wide association studies: Applied to Alzheimer's disease. In Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 (Vol. 2017-January, pp. 2177-2182). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2017.8217995

VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in genome-wide association studies : Applied to Alzheimer's disease. / Liu, Qiao; Chen, Chen; Gao, Annie; Tong, Hanghang; Xie, Lei.

Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Vol. 2017-January Institute of Electrical and Electronics Engineers Inc., 2017. p. 2177-2182.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Liu, Q, Chen, C, Gao, A, Tong, H & Xie, L 2017, VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in genome-wide association studies: Applied to Alzheimer's disease. in Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. vol. 2017-January, Institute of Electrical and Electronics Engineers Inc., pp. 2177-2182, 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, United States, 11/13/17. https://doi.org/10.1109/BIBM.2017.8217995
Liu Q, Chen C, Gao A, Tong H, Xie L. VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in genome-wide association studies: Applied to Alzheimer's disease. In Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Vol. 2017-January. Institute of Electrical and Electronics Engineers Inc. 2017. p. 2177-2182 https://doi.org/10.1109/BIBM.2017.8217995
Liu, Qiao ; Chen, Chen ; Gao, Annie ; Tong, Hanghang ; Xie, Lei. / VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in genome-wide association studies : Applied to Alzheimer's disease. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Vol. 2017-January Institute of Electrical and Electronics Engineers Inc., 2017. pp. 2177-2182
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