X-LDR: an atlas of linkage disequilibrium across species
To reach a genomic scale illustration for linkage disequilibrium (LD), we introduce X-LDR, a stochastic algorithm for biobank-scale data ([Formula: see text], n the sample size, m the number of SNPs, and B iterations). X-LDR can scale the entire genome to high-resolution LD grids, such as nearly 9 million LD grids for UK Biobank ([Formula: see text] and [Formula: see text] million). Various characteristics of LD are discovered in terms of their biological annotation. We also present an unprecedented LD atlas for 25 reference populations that contours the diversity of interspecies LD. The algorithms have been implemented in C++.
Authors
- Shizhou Yu (ORCID: https://orcid.org/0000-0002-2162-3819)
- Guo‐Bo Chen (ORCID: https://orcid.org/0000-0001-5475-8237)
- T. J. Zhu (ORCID: https://orcid.org/0009-0000-1863-7024)
- Hou‐Feng Zheng (ORCID: https://orcid.org/0000-0001-5681-8598)
- Qi-Xin Zhang
- Xin Jin (ORCID: https://orcid.org/0000-0001-6461-6005)
- Wenjing Zhang (ORCID: https://orcid.org/0000-0002-7492-7904)
- Zhe Zhang (ORCID: https://orcid.org/0000-0001-7338-7718)
- Xing Huang (ORCID: https://orcid.org/0000-0002-8886-2777)
- Feng Lin (ORCID: https://orcid.org/0000-0003-2035-2743)
- Guo‐An Qi (ORCID: https://orcid.org/0000-0002-2412-3932)
- Haiming Xu
- Mengyuan Yang (ORCID: https://orcid.org/0009-0005-2342-0993)
Institutions
- BGI Group (China) (CN)
- South China Agricultural University (CN)
- Zhejiang Chinese Medical University (CN)
- China Tobacco (CN)
- Westlake University (CN)
- Soochow University (CN)
- Tobacco Research Institute (CN)
- Second Affiliated Hospital of Soochow University (CN)
- Hangzhou Medical College (CN)
- BGI Research (CN)
- Zhejiang University (CN)
Publication Details
- Journal
- Genome biology
- Published
- 2025-11-20
- DOI
- https://doi.org/10.1186/s13059-025-03863-5
- Primary Topic
- Genetic Associations and Epidemiology
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Westlake University
- National Natural Science Foundation of China
- Zhejiang University
- China National Tobacco Corporation