ArticleNature communications2021
Variant-specific inflation factors for assessing population stratification at the phenotypic variance level.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 21 citations in OpenAlex.
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- Estimating population structure using epigenome-wide methylation data.Briefings in bioinformatics · 2026Article
- Identification of Novel Susceptibility Genes for Early-Onset Colorectal Cancer Through Germline Rare Variant Burden Testing.Cancers · 2025Article
- Interpretable machine learning analysis of clinicopathological and immunonutritional biomarkers for predicting lymph node metastasis in gastric cancer.Scientific reports · 2025Article
- Genotypic and phenotypic consequences of domestication in dogs.bioRxiv : the preprint server for biology · 2025Article
- Estimating population structure using epigenome-wide methylation data.medRxiv : the preprint server for health sciences · 2025Article
- Perceived indoor thermal environment and depressive symptoms among older adults in the Japan Gerontological Evaluation Study.Scientific reports · 2025Article
- Carbon reduction strategies for logistics based on emission prediction under multi-scenarios in coastal developed region.Carbon balance and management · 2025Article
- A grip strength prediction tool for older adults based on logistic regression: construction, validation, and clinical application value.Scientific reports · 2025Article
- Advancements in genetic research by the Hispanic Community Health Study/Study of Latinos: A 10-year retrospective review.HGG advances · 2025Review
- Associations between accelerometer-measured physical activity and sedentary behaviour with physical function among older women: a cross-sectional study.BMC public health · 2024Article
- Intracranial Volume Is Driven by Both Genetics and Early Life Exposures: The SOL-INCA-MRI Study.Ethnicity & disease · 2024Article
- A benchmark study on current GWAS models in admixed populations.Briefings in bioinformatics · 2023Article
- Evaluating the use of blood pressure polygenic risk scores across race/ethnic background groups.Nature communications · 2023Article
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Authors and funding
16 authors at 20 institutions in 5 countries.
Funding
Abstract
In modern Whole Genome Sequencing (WGS) epidemiological studies, participant-level data from multiple studies are often pooled and results are obtained from a single analysis. We consider the impact of differential phenotype variances by study, which we term 'variance stratification'. Unaccounted for, variance stratification can lead to both decreased statistical power, and increased false positives rates, depending on how allele frequencies, sample sizes, and phenotypic variances vary across the studies that are pooled. We develop a procedure to compute variant-specific inflation factors, and show how it can be used for diagnosis of genetic association analyses on pooled individual level data from multiple studies. We describe a WGS-appropriate analysis approach, implemented in freely-available software, which allows study-specific variances and thereby improves performance in practice. We illustrate the variance stratification problem, its solutions, and the proposed diagnostic procedure, in simulations and in data from the Trans-Omics for Precision Medicine Whole Genome Sequencing Program (TOPMed), used in association tests for hemoglobin concentrations and BMI.
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