ArticleCommunications biology2023
Accuracy of haplotype estimation and whole genome imputation affects complex trait analyses in complex biobanks.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it, 17 citations in OpenAlex.
- Correcting for Genomic Inflation Leads to Loss of Power in Large-Scale Genome-Wide Association Study Meta-Analysis.Genetic epidemiology · 2025Pooled it
- Selphi, a tool for improving genotype imputation accuracy.Scientific reports · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- The relationship between genotype- and phenotype-based estimates of genetic liability to psychiatric disorders, in practice and in theory.American journal of human genetics · 2026Article
- Ambiguities faced by parents who received a genetic diagnosis for autistic offspring with intellectual disabilities.Journal of community genetics · 2025Article
- Establishing Best Practices for Clinical GWAS: Tackling Imputation and Data Quality Challenges.International journal of molecular sciences · 2025Review
- Leveraging haplotype information in heritability estimation and polygenic prediction.Nature communications · 2025Article
- Impact of Receiving Genetic Diagnoses on Parents' Perceptions of Their Children with Autism and Intellectual Disability.Journal of autism and developmental disorders · 2025Article
- Analysis of exonic deletions in a large population study provides novel insights into NRXN1 pathology.NPJ genomic medicine · 2024Article
- The Evolution of Genetic Variability at theGenes · 2024Article
- Article
- Views of Genetic Testing for Autism Among Autism Self-Advocates: A Qualitative Study.AJOB empirical bioethicsArticle
Corrections and comments
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Authors and funding
14 authors at 7 institutions in 3 countries.
Funding
Abstract
Sample recruitment for research consortia, biobanks, and personal genomics companies span years, necessitating genotyping in batches, using different technologies. As marker content on genotyping arrays varies, integrating such datasets is non-trivial and its impact on haplotype estimation (phasing) and whole genome imputation, necessary steps for complex trait analysis, remains under-evaluated. Using the iPSYCH dataset, comprising 130,438 individuals, genotyped in two stages, on different arrays, we evaluated phasing and imputation performance across multiple phasing methods and data integration protocols. While phasing accuracy varied by choice of method and data integration protocol, imputation accuracy varied mostly between data integration protocols. We demonstrate an attenuation in imputation accuracy within samples of non-European origin, highlighting challenges to studying complex traits in diverse populations. Finally, imputation errors can bias association tests, reduce predictive utility of polygenic scores. Carefully optimized data integration strategies enhance accuracy and replicability of complex trait analyses in complex biobanks.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.