This paper introduces SBayesAPP, a Bayesian model that estimates annotation-stratified pleiotropy and co-polygenicity between complex traits using GWAS summary statistics, revealing cell-type-specific genetic correlations.

World Congress on Genetics Applied to Livestock Production (WCGALP) · Feb 26, 2026Peer-reviewedGenomics

Transcriptional and translational genetic control in blood contributes significantly to complex trait heritability and polygenic prediction

Shouye Liu, Xiaoyu Qian, Yang Wu, Zhili Zheng, Michael Edward Goddard, Jian Yang, Peter M. Visscher, Jian Zeng

The paper evaluates the contribution of expression, splicing, and protein QTL in blood to SNP-based heritability and polygenic prediction across 27 traits, finding they capture significant portions of genetic variation.

medRxiv · May 24, 2025 · PreprintGenetic & Genomic Medicine

Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

Zhili Zheng, Shouye Liu, Julia Sidorenko, Ying Wang, Tian Lin, Loïc Yengo, Patrick Turley, Alireza Ani, Rujia Wang, Ilja Maria Nolte, Harold Snieder, LifeLines Cohort Study, Raul Aguirre-Gamboa, Patrick Deelen, Lude Franke, , Jian Zeng

This paper introduces SBayesRC, a method that improves polygenic prediction of complex traits by integrating GWAS summary statistics with functional genomic annotations, showing significant accuracy gains across ancestries.

Nature Genetics · Apr 30, 2024Peer-reviewedGenetics

mBAT-combo: a more powerful test to detect gene-trait associations from GWAS data

Ang Li, Shouye Liu, Andrew Bakshi, Longda Jiang, Wenhan Chen, Zhili Zheng, Patrick F. Sullivan, Peter M. Visscher, Naomi R. Wray, Jian Yang, Jian Zeng

mBAT-combo improves gene-trait association detection in GWAS by accounting for SNP effect directions, revealing masking effects in complex traits.

The American Journal of Human Genetics · Jan 1, 2023Peer-reviewedGenetics