Reaching the end-game for GWAS: Machine learning approaches for the prioritization of complex disease loci
Open accessAbstract
Genome-wide association studies (GWAS) have revealed thousands of genetic loci that underpin the complex biology of many human traits. However, the strength of GWAS - the ability to detect genetic association by linkage disequilibrium (LD) - is also its limitation. Whilst the ever-increasing study size and improved design have augmented the power of GWAS to detect effects, differentiation of causal variants or genes from other highly correlated genes associated by LD remains the real challenge. This has severely hindered the biological insights and clinical translation of GWAS findings. Although thousands of disease susceptibility loci have been reported, causal genes at these loci remain elusive. Machine learning (ML) techniques offer an opportunity to dissect the heterogeneity of variant and gene signals in the post-GWAS analysis phase. ML models for GWAS prioritization vary greatly in their complexity, ranging from relatively simple logistic regression approaches to more complex ensemble models such as random forests and gradient boosting, as well as deep learning models, i.e., neural networks. Paired with functional validation, these methods show important promise for clinical translation, providing a strong evidence-based approach to direct post-GWAS research. However, as ML approaches continue to evolve to meet the challenge of causal gene identification, a critical assessment of the underlying methodologies and their applicability to the GWAS prioritization problem is needed. This review investigates the landscape of ML applications in three parts: selected models, input features, and output model performance, with a focus on prioritizations of complex disease associated loci. Overall, we explore the contributions ML has made towards reaching the GWAS end-game with consequent wide-ranging translational impact.
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Combining ML with progressive feature elimination can identify the main predictors, enhance classification, and provide a top assortment of features to classify outcomes.
“Combining ML with progressive feature elimination can identify the main predictors, enhance classification, and provide a top assortment of features to classify outcomes (Montavon et al., 2018; Nicholls et al., 2020).”
From Multiclass characterization of frontotemporal dementia variants via multimodal brain network computational inference (2023) · cites this paper as Nicholls et al., 2020
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Artificial intelligence for dementia genetics and omics
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- Authors
- Nicholls, H. L., John, C. R., Watson, D. S., Munroe, P. B., Barnes, M. R., & Cabrera, C. P.
- Affiliations
- Queen Mary University of London (GB)
- Corresponding author
- Barnes, Michael R.
- Cabrera, Claudia P.
- ORCID
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2020-04-15
- Volume
- 11
- Pages
- 350-350
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC7174742
- OpenAlex
- W3016610742
- Cited by
- 155
- References
- 71
- Citations by year
- 2026: 10 · 2025: 21 · 2024: 23 · 2023: 33 · 2022: 36 · 2021: 23 · 2020: 9
- FWCI
- 3.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UCL Discovery (University College London) (submittedVersion)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion, cc-by)
- Funders
- National Institute for Health and Care Research
- British Heart Foundation (FS/18/64/34185C)
- Barts and The London School of Medicine and Dentistry
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- causal variant identification, linkage disequilibrium, machine learning, random forest, gradient boosting, deep learning, ensemble learning, post-GWAS analysis, functional validation, clinical translation
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