ArticlePloS one2018
The impact of a fine-scale population stratification on rare variant association test results.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- BeyondFrontiers in genetics · 2026Review
- Identification of MAPK10 as a Candidate Gene for High Milk Production in Water Buffaloes Through a Genome-Wide Association Study.Animals : an open access journal from MDPI · 2025Article
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- Appraisal of the causal effect ofmedRxiv : the preprint server for health sciences · 2024Article
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- Integrative Analysis of Germline Rare Variants in Clear and Non-clear Cell Renal Cell Carcinoma.European urology open science · 2024Article
- Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data.PLoS computational biology · 2023Article
- A comparison between similarity matrices for principal component analysis to assess population stratification in sequenced genetic data sets.Briefings in bioinformatics · 2023Article
- Risk and protection of different rare protein-coding variants of complement component C4A in age-related macular degeneration.Frontiers in genetics · 2023Article
- Clarifying the causes of consistent and inconsistent findings in genetics.Genetic epidemiology · 2022Review
- Importance of Including Non-European Populations in Large Human Genetic Studies to Enhance Precision Medicine.Annual review of biomedical data science · 2022Review
- Recent advances and challenges of rare variant association analysis in the biobank sequencing era.Frontiers in genetics · 2022Review
- Taking population stratification into account by local permutations in rare-variant association studies on small samples.Genetic epidemiology · 2021Article
- Controlling for human population stratification in rare variant association studies.Scientific reports · 2021Article
- Exploring the Causality Between Hypothyroidism and Non-alcoholic Fatty Liver: A Mendelian Randomization Study.Frontiers in cell and developmental biology · 2021Article
- Genetic Determinants of Antibody-Mediated Immune Responses to Infectious Diseases Agents: A Genome-Wide and HLA Association Study.Open forum infectious diseases · 2020Article
- Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.Science (New York, N.Y.) · 2020Article
- The genetic history of France.European journal of human genetics : EJHG · 2020Article
- Genome-wide Association Study for Vitamin D Levels Reveals 69 Independent Loci.American journal of human genetics · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Population stratification is a well-known confounding factor in both common and rare variant association analyses. Rare variants tend to be more geographically clustered than common variants, because of their more recent origin. However, it is not yet clear if population stratification at a very fine scale (neighboring administrative regions within a country) would lead to statistical bias in rare variant analyses. As the inclusion of convenience controls from external studies is indeed a common procedure, in order to increase the power to detect genetic associations, this problem is important. We studied through simulation the impact of a fine scale population structure on different rare variant association strategies, assessing type I error and power. We showed that principal component analysis (PCA) based methods of adjustment for population stratification adequately corrected type I error inflation at the largest geographical scales, but not at finest scales. We also showed in our simulations that adding controls obviously increased power, but at a considerably lower level when controls were drawn from another population.
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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 Socratic graph.