CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses
Yang Z, Wang C, Liu L, Khan A, Lee A, Vardarajan B, Mayeux R, Kiryluk K et al.. Nature genetics, 2023-05-11
Topic: Risk, prevention and care in population studies
Fine-mapping is commonly used to identify putative causal variants at genome-wide significant loci. Here we propose a Bayesian model for fine-mapping that has several advantages over existing methods, including flexible specification of the prior distribution of effect sizes, joint modeling of summary statistics and functional annotations and accounting for discrepancies between summary statistics and external linkage disequilibrium in meta-analyses. Using simulations, we compare performance with commonly used fine-mapping methods and show that the proposed model has higher power and lower false discovery rate (FDR) when including functional annotations, and higher power, lower FDR and higher coverage for credible sets in meta-analyses. We further illustrate our approach by applying it to a meta-analysis of Alzheimer's disease genome-wide association studies where we prioritize putatively causal variants and genes.
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APA 7th
Yang, Z., Wang, C., Liu, L., Khan, A., Lee, A., Vardarajan, B., et al. (2023). CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses. Nature genetics. https://doi.org/10.1038/s41588-023-01392-0
Vancouver
Yang Z, Wang C, Liu L, Khan A, Lee A, Vardarajan B, et al. CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses. Nature genetics. 2023. doi:10.1038/s41588-023-01392-0. PMID: 37169873.
BibTeX
@article{yang2023-37169873,
author = {Yang, Z. and Wang, C. and Liu, L. and Khan, A. and Lee, A. and Vardarajan, B. and Mayeux, R. and Kiryluk, K. and others},
title = {{CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses}},
journal = {Nature genetics},
year = {2023},
doi = {10.1038/s41588-023-01392-0},
pmid = {37169873},
url = {https://doi.org/10.1038/s41588-023-01392-0}
}
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Key findings
- Fine-mapping is commonly used to identify putative causal variants at genome-wide significant loci.
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Study details
- Study designmeta-analysis
- Evidence strengthHigh
How this study scored 71/100
Published in a leading specialty journal, and it is a meta-analysis pooling many studies. Scored zero for sample size, effect reported and studied in people 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 and multi-centre collaboration, so those were left out: it earned 41 of the 58 points we could judge it on, which is 71 out of 100.
| Component | Points | Why |
|---|---|---|
| Journal tier | 9 / 10 | Tier 2 — leading specialty journal (Nature genetics) |
| Journal's citation record | — / 4 | No journal record from OpenAlex — left out of this score |
| Study design | 12 / 12 | A meta-analysis pooling many studies |
| Strength of evidence | 5 / 5 | Rated “high” in our summary |
| Peer-review validation | 10 / 10 | Peer-reviewed. Published as an article in a named peer-reviewed journal. |
| How recent | 3 / 5 | 2023 — within 6 year(s) of the newest study here |
| Sample size | 0 / 4 | Participant count not stated — scores zero (not stated in the record — scored 0) |
| Effect reported | 0 / 3 | No effect size reported — scores zero (not stated in the record — scored 0) |
| Studied in people | 0 / 3 | Not stated whether this was studied in people — scores zero (not stated in the record — scored 0) |
| Randomised / blinded | 0 / 2 | A review of other studies — randomisation is not credited here |
| 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 37169873) |
| Free to read | 0 / 2 | Behind a paywall — scores zero |
| Points | 41 / 58 | Scored on 11 of 20 parts. We have no data for the rest, so they are left out: 41 of the 58 points we could judge it on is 71 out of 100. |
| Total | 71 / 100 | — |
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