ArticleBioinformatics advances2026
Removing array-specific batch effects in GWAS mega-analyses by applying a two-step imputation workflow.
Article in Bioinformatics advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
- Effects of BACE2 polymorphisms on verbal memory in the general population.European archives of psychiatry and clinical neuroscience · 2026Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: Combining genetic data from different genotyping arrays (mega-analysis) increases statistical power but introduces array-specific batch effects that may bias results. This project developed a two-step genotype imputation workflow addressing this bias in studies using multiple genotyping platforms.Genotype data of 10 647 individuals generated using five different arrays were included. The two-step method involved creating intermediate array-type specific panels, which were then imputed against the 1000 Genomes reference panel. Batch effects were assessed using genetic principal component analysis of the combined imputed dataset. Performance was evaluated by comparing imputation quality and allele frequency differences between the two-step and the conventional array-specific imputation. Additionally, concordance with a whole-genome-sequenced subgroup was examined. Genome-wide association analysis on goiter risk and thyroid gland volume was conducted to compare outcomes between both imputation approaches.The workflow eliminated array-driven batch effect from the first 20 PCs and showed high correlation with the conventional approach for allele frequencies ( Availability and implementation: The study provides a workflow for high-quality imputation results without batch effects, fostering genetic analysis involving multiple genotyping arrays.
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Registered trials
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