X-Wing (Cross-population Weighting) is a cross-population polygenic prediction framework only using GWAS summary statistics. It contains three methods:
LOGODetect(LOcal Genetic cOrrelation DETECTor) (Also see here)PANTHER(Polygenic prediction using Bayesian ANnoTation-dependent HorsEshoe Regression)LEOPARD(LinEar cOmbination of PRS using gwAs summaRy statistics Data)
The X-Wing software can perform four tasks:
- Improve genetic risk prediction in ancestrally diverse populations using
X-Wing. - Identify small genome segments harboring cross-population local genetic correlation signals using
LOGODetect. - Incorporate annotation into single and cross-population polygenic prediction using
PANTHER. - Estimate the linear combination weights for multiple PRS by GWAS summary statistics alone using
LEOPARD.
The layout of the scripts is
Please see the wiki for the detailed manual of X-Wing.
- May 26, 2022: Initial release.
Part of the code is adapted from PRS-CSx (https://github.com/getian107/PRScsx) and XPASS (https://github.com/YangLabHKUST/XPASS). We thank Dr. Tian Ge and Dr. Mingxuan Cai for sharing their code.
The X-Wing posterior SNP effect size estimates in our manusciript are available at here.
If you use X-Wing, please cite
Miao, J., Guo, H., Song, G., Zhao, Z., Hou, L., & Lu, Q. (2022). Quantifying portable genetic effects and improving cross-ancestry genetic prediction with GWAS summary statistics. bioRxiv, 2022.2005.2026.493528.
For questions and comments, please open a Github issue (preferred) or contact Jiacheng Miao at jmiao24@wisc.edu or Hanmin Guo at ghm17@mails.tsinghua.edu.cn.