Genome-wide association neural networks identify genes linked to family history of Alzheimer's disease
Upamanyu Ghose, William Sproviero, Laura Winchester, Najaf Amin, Taiyu Zhu, Danielle Newby, Brittany S Ulm, Angeliki Papathanasiou et al.. Briefings in bioinformatics, 2024-11-22
Topic: Genetics and APOE
Augmenting traditional genome-wide association studies (GWAS) with advanced machine learning algorithms can allow the detection of novel signals in available cohorts. We introduce "genome-wide association neural networks (GWANN)" a novel approach that uses neural networks (NNs) to perform a gene-level association study with family history of Alzheimer's disease (AD). In UK Biobank, we defined cases (n = 42 110) as those with AD or family history of AD and sampled an equal number of controls. The data was split into an 80:20 ratio of training and testing samples, and GWANN was trained on the former followed by identifying associated genes using its performance on the latter. Our method identified 18 genes to be associated with family history of AD. APOE, BIN1, SORL1, ADAM10, APH1B, and SPI1 have been identified by previous AD GWAS. Among the 12 new genes, PCDH9, NRG3, ROR1, LINGO2, SMYD3, and LRRC7 have been associated with neurofibrillary tangles or phosphorylated tau in previous studies. Furthermore, there is evidence for differential transcriptomic or proteomic expression between AD and healthy brains for 10 of the 12 new genes. A series of post hoc analyses resulted in a significantly enriched protein-protein interaction network (P-value < 1 × 10-16), and enrichment of relevant disease and biological pathways such as focal adhesion (P-value = 1 × 10-4), extracellular matrix organization (P-value = 1 × 10-4), Hippo signaling (P-value = 7 × 10-4), Alzheimer's disease (P-value = 3 × 10-4), and impaired cognition (P-value = 4 × 10-3). Applying NNs for GWAS illustrates their potential to complement existing algorithms and methods and enable the discovery of new associations without the need to expand existing cohorts.
Cite this study APA, Vancouver, BibTeX · download .bib or .ris
APA 7th
Ghose, U., Sproviero, W., Winchester, L., Amin, N., Zhu, T., Newby, D., et al. (2024). Genome-wide association neural networks identify genes linked to family history of Alzheimer's disease. Briefings in bioinformatics. https://doi.org/10.1093/bib/bbae704
Vancouver
Ghose U, Sproviero W, Winchester L, Amin N, Zhu T, Newby D, et al. Genome-wide association neural networks identify genes linked to family history of Alzheimer's disease. Briefings in bioinformatics. 2024. doi:10.1093/bib/bbae704. PMID: 39775791.
BibTeX
@article{ghose2024-39775791,
author = {Ghose, Upamanyu and Sproviero, William and Winchester, Laura and Amin, Najaf and Zhu, Taiyu and Newby, Danielle and Ulm, Brittany S and Papathanasiou, Angeliki and others},
title = {{Genome-wide association neural networks identify genes linked to family history of Alzheimer's disease}},
journal = {Briefings in bioinformatics},
year = {2024},
doi = {10.1093/bib/bbae704},
pmid = {39775791},
url = {https://doi.org/10.1093/bib/bbae704}
}
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Key findings
- Our method identified 18 genes to be associated with family history of AD.
- Among the 12 new genes, PCDH9, NRG3, ROR1, LINGO2, SMYD3, and LRRC7 have been associated with neurofibrillary tangles or phosphorylated tau in previous studies.
- A series of post hoc analyses resulted in a significantly enriched protein-protein interaction network (P-value < 1 × 10-16), and enrichment of relevant disease and biological pathways such as focal adhesion (P-value = 1 × 10-4), extracellular matrix organization (P-value = 1 × 10-4), Hippo signaling (P-value = 7 × 10-4), Alzheimer's disease (P-value = 3 × 10-4), and impaired cognition (P-value = 4 × 10-3).
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Study details
- Participants42
- Evidence strengthLow
How this study scored 50/100
Published in a peer-reviewed journal. Scored zero for study design, effect reported and randomised / blinded because the record does not state it. We have no data on journal's citation record, times cited, citations per year, impact for its field and year, cited by studies here, still being cited, senior author's track record, institution's track record, multi-centre collaboration and free to read, so those were left out: it earned 28 of the 56 points we could judge it on, which is 50 out of 100.
| Component | Points | Why |
|---|---|---|
| Journal tier | 7 / 10 | Tier 3 — peer-reviewed journal (Briefings in bioinformatics) |
| Journal's citation record | — / 4 | No journal record from OpenAlex — left out of this score |
| Study design | 0 / 12 | No study design recorded — scores zero, not guessed (not stated in the record — scored 0) |
| Strength of evidence | 1 / 5 | Rated “low” in our summary |
| Peer-review validation | 10 / 10 | Peer-reviewed. Published as an article in a named peer-reviewed journal. |
| How recent | 4 / 5 | 2024 — within 3 year(s) of the newest study here |
| Sample size | 1 / 4 | 42 participants |
| Effect reported | 0 / 3 | No effect size reported — scores zero (not stated in the record — scored 0) |
| Studied in people | 3 / 3 | Studied in people (participant count stated) |
| Randomised / blinded | 0 / 2 | No randomisation or blinding stated — scores zero (not stated in the record — scored 0) |
| Times cited | — / 7 | No citation count (not found in OpenAlex) — left out of this score |
| Citations per year | — / 5 | No citation count or no year — left out of this score |
| Impact for its field and year | — / 6 | No field-weighted citation impact (OpenAlex has none yet) — left out of this score |
| Cited by studies here | — / 6 | Not yet checked against this library's citation graph — left out of this score |
| Still being cited | — / 4 | No yearly citation counts — left out of this score |
| Senior author's track record | — / 4 | Senior author's record not available — left out of this score |
| Institution's track record | — / 3 | No institution listed in OpenAlex — left out of this score |
| Multi-centre collaboration | — / 3 | Institutions not listed — left out of this score |
| Indexed in PubMed | 2 / 2 | Indexed in PubMed (PMID 39775791) |
| Free to read | — / 2 | Access not recorded — left out of this score |
| Points | 28 / 56 | Scored on 10 of 20 parts. We have no data for the rest, so they are left out: 28 of the 56 points we could judge it on is 50 out of 100. |
| Total | 50 / 100 | — |
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