期刊
CELL GENOMICS
卷 2, 期 12, 页码 -出版社
ELSEVIER
DOI: 10.1016/j.xgen.2022.100210
关键词
-
资金
- NIH [DP5 OD024582]
- Nakajima Foundation Fellowship
- Masason Foundation
Heterogeneity can affect the calibration of meta-analysis fine-mapping, and a new method called SLALOM has been proposed to identify suspicious loci. 67% of loci in meta-analyses showed suspicious patterns, indicating caution is needed when interpreting fine-mapping results from heterogeneous cohorts.
Meta-analysis is pervasively used to combine multiple genome-wide association studies (GWASs). Fine -mapping of meta-analysis studies is typically performed as in a single-cohort study. Here, we first demon-strate that heterogeneity (e.g., of sample size, phenotyping, imputation) hurts calibration of meta-analysis fine-mapping. We propose a summary statistics-based quality-control (QC) method, suspicious loci analysis of meta-analysis summary statistics (SLALOM), that identifies suspicious loci for meta-analysis fine-mapping by detecting outliers in association statistics. We validate SLALOM in simulations and the GWAS Catalog. Applying SLALOM to 14 meta-analyses from the Global Biobank Meta-analysis Initiative (GBMI), we find that 67% of loci show suspicious patterns that call into question fine-mapping accuracy. These predicted suspicious loci are significantly depleted for having nonsynonymous variants as lead variant (2.73; Fisher's exact p = 7.3 3 10-4). We find limited evidence of fine-mapping improvement in the GBMI meta-analyses compared with individual biobanks. We urge extreme caution when interpreting fine-mapping results from meta-analysis of heterogeneous cohorts.
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