Protocol: Estimating cross-ancestry local genetic correlation using Logica
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Updated: May 12, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
Boran Gao1, Zheng Li2, Xiang Zhou3
1Department of Statistics, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
Abstract:
Here, we present a reproducible protocol for estimating cross-ancestry local genetic correlation using Logica, a likelihood-based framework that employs summary statistics from genome-wide association studies (GWASs) and ancestry-specific linkage disequilibrium (LD). We describe steps for estimating locus-level heritability and cross-ancestry genetic correlation and outlining required inputs. We then detail analytical procedures to enable accurate and scalable inference of shared genetic architecture. For complete details on the use and execution of this protocol, please refer to Gao et al.1.
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