Bayesian multivariant fine mapping using the Laplace prior

Walters, Kevin and Yaacob, Hannuun (2023) Bayesian multivariant fine mapping using the Laplace prior. Genetic Epidemiology, 47 (3). pp. 249-260. ISSN 0741-0395, DOI

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Currently, the only effect size prior that is routinely implemented in a Bayesian fine-mapping multi-single-nucleotide polymorphism (SNP) analysis is the Gaussian prior. Here, we show how the Laplace prior can be deployed in Bayesian multi-SNP fine mapping studies. We compare the ranking performance of the posterior inclusion probability (PIP) using a Laplace prior with the ranking performance of the corresponding Gaussian prior and FINEMAP. Our results indicate that, for the simulation scenarios we consider here, the Laplace prior can lead to higher PIPs than either the Gaussian prior or FINEMAP, particularly for moderately sized fine-mapping studies. The Laplace prior also appears to have better worst-case scenario properties. We reanalyse the iCOGS case-control data from the CASP8 region on Chromosome 2. Even though this study has a total sample size of nearly 90,000 individuals, there are still some differences in the top few ranked SNPs if the Laplace prior is used rather than the Gaussian prior. R code to implement the Laplace (and Gaussian) prior is available at .

Item Type: Article
Uncontrolled Keywords: Bayesian; Fine mapping; Laplace prior; Multi-SNP
Subjects: Q Science > QA Mathematics
Q Science > QH Natural history > QH301 Biology
Divisions: Faculty of Business and Economics
Depositing User: Ms Zaharah Ramly
Date Deposited: 04 Jul 2023 06:44
Last Modified: 04 Jul 2023 06:44

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