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gaow / mvarbvs

Multivariate Bayesian variable selection via variational inference
https://gaow.github.io/mvarbvs/
MIT License
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Existing (eQTL) fine mapping methods #11

Open gaow opened 7 years ago

gaow commented 7 years ago

This ticket keeps track of existing eQTL fine mapping methods -- please use new comment for additional references so that I can be notified to add here and to my mendeley:

  1. Davis, Joe R., et al. "An efficient multiple-testing adjustment for eQTL studies that accounts for linkage disequilibrium between variants." The American Journal of Human Genetics 98.1 (2016): 216-224.

  2. Wen, Xiaoquan, Francesca Luca, and Roger Pique-Regi. "Cross-population joint analysis of eQTLs: fine mapping and functional annotation." PLoS Genet 11.4 (2015): e1005176.

  3. Chen, Wenan, et al. "Incorporating Functional Annotations for Fine-Mapping Causal Variants in a Bayesian Framework Using Summary Statistics." Genetics 204.3 (2016): 933-958.

  4. Hormozdiari, Farhad, et al. "Identifying causal variants at loci with multiple signals of association." Genetics 198.2 (2014): 497-508. -- this is eCAVIAR

  5. Constraints on eQTL fine mapping in the presence of multi-site local regulation of gene expression https://doi.org/10.1101/084293

  6. Lewin, Alex, et al. "MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues." Bioinformatics 32.4 (2016): 523-532. this is a modular multivariate, multiple regression framework similar to ours though not the data driven nature and applications.

More generic (in application) fine mapping methods

  1. Servin, Bertrand, and Matthew Stephens. "Imputation-based analysis of association studies: candidate regions and quantitative traits." PLoS Genet 3.7 (2007): e114.

  2. Benner, Christian, et al. "FINEMAP: efficient variable selection using summary data from genome-wide association studies." Bioinformatics 32.10 (2016): 1493-1501.

stephens999 commented 7 years ago

fine mapping isn't specific to eQTLs so you probably want to extend to fine mapping generally?

eg Servin + Stephens

software FINEMAP? http://www.christianbenner.com/

On Wed, May 10, 2017 at 10:41 PM, gaow notifications@github.com wrote:

This ticket keeps track of existing eQTL fine mapping methods -- please use new comment for additional references so that I can be notified to add here and to my mendeley:

1.

Davis, Joe R., et al. "An efficient multiple-testing adjustment for eQTL studies that accounts for linkage disequilibrium between variants." The American Journal of Human Genetics 98.1 (2016): 216-224. APA 2.

Wen, Xiaoquan, Francesca Luca, and Roger Pique-Regi. "Cross-population joint analysis of eQTLs: fine mapping and functional annotation." PLoS Genet 11.4 (2015): e1005176. APA 3.

Chen, Wenan, et al. "Incorporating Functional Annotations for Fine-Mapping Causal Variants in a Bayesian Framework Using Summary Statistics." Genetics 204.3 (2016): 933-958. 4.

Hormozdiari, Farhad, et al. "Identifying causal variants at loci with multiple signals of association." Genetics 198.2 (2014): 497-508. -- this is eCAVIAR 5.

Constraints on eQTL fine mapping in the presence of multi-site local regulation of gene expression https://doi.org/10.1101/084293

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gaow commented 7 years ago

Thanks @stephens999! yes it should be a generic list. I updated the list.