Abbreviation

• APA: alternative polyadenylation
• 3'aQTL: 3′UTR alternative polyadenylation quantitative trait loci

This pipeline describes the step-by-step methods for analyzing dynamics alternative polyadenylation events across population-scale samples and performing association analysis between common genetic variants and APA usages to obtain a map of genetic regulation of APA.

The scripts in this repository have been tested on 89 samples from Geuvadis RNA-seq Project and GTEx Project. For conditions to reuse of these scripts please refer to LICENSE file.

Details on how to prepare environment and use the script can be found on GitHub wiki pages for this repository.

This pipeline relies on Dapars2 for APA quantification, Matrix-eQTL for association mapping, and SuSieR for fine-mapping.

Xudong Zou, Ruofan Ding, Wenyan Chen, Gao Wang, Shumin Cheng, Wei Li, Lei Li

Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China

• Code and Execution:

Using population-scale transcriptomic and genomic data to map 3' UTR alternative polyadenylation quantitative trait loci

Xudong Zou, Ruofan Ding, Wenyan Chen, Gao Wang, Shumin Cheng, Qin Wang, Wei Li, Lei Li. STAR Protocols,3(3):101566 (2022). DOI: https://doi.org/10.1016/j.xpro.2022.101566 https://www.sciencedirect.com/science/article/pii/S2666166722004464?via%3Dihub

• The first 3'aQTL atlas of human tissues:

An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability

Lei Li, Kai-Lieh Huang, Yipeng Gao, Ya Cui, Gao Wang, Nathan D. Elrod, Yumei Li, Yiling Elaine Chen, Ping Ji, Fanglue Peng, William K. Russell, Eric J. Wagner & Wei Li. Nature Genetics,53,994-1005 (2021). DOI:https://doi.org/10.1038/s41588-021-00864-5

https://www.nature.com/articles/s41588-021-00864-5

For any issues, please create a GitHub Issue.

This work was supported by National Natural Science Foundation of China (no. 32100533) and startup funds from Shenzhen Bay Laboratory to L.L.