Credible set is sensitive to imputation quality and missing variants Article Swipe
Yanyu Liang
,
Adam Auton
,
Xin Wang
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.08.28.610135
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.08.28.610135
Bayesian fine-mapping to obtain credible sets has been widely applied post GWAS to pinpoint causal variants. The calculation of credible sets generally assumes that all variants have been equally well genotyped, which is often not the case when a GWAS has been run on imputed data. In this work, we investigate the behavior of credible sets in imputed datasets utilizing ‘held out’ genotyped variants to measure accuracy. We show, via simulation, that: i) the coverage of credible sets decreases when using imputed variants in GWAS; ii) rare causal variants often fail to be tagged in credible sets when they are not present in the GWAS variant set. We develop a reweighting approach to take imputation quality into account during fine-mapping that only requires summary statistics, and demonstrate the approach with real data.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.08.28.610135
- https://www.biorxiv.org/content/biorxiv/early/2024/08/29/2024.08.28.610135.full.pdf
- OA Status
- green
- References
- 19
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4402075297
All OpenAlex metadata
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https://openalex.org/W4402075297Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2024.08.28.610135Digital Object Identifier
- Title
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Credible set is sensitive to imputation quality and missing variantsWork title
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-08-29Full publication date if available
- Authors
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Yanyu Liang, Adam Auton, Xin WangList of authors in order
- Landing page
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https://doi.org/10.1101/2024.08.28.610135Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2024/08/29/2024.08.28.610135.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2024/08/29/2024.08.28.610135.full.pdfDirect OA link when available
- Concepts
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Imputation (statistics), Missing data, Computer science, Data mining, Statistics, MathematicsTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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19Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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