ArticleGenetic epidemiology2017
Improving power for rare-variant tests by integrating external controls.
Article in Genetic epidemiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed.
- CCAFE: Estimating case and control allele frequencies from GWAS summary statistics.HGG advances · 2026Article
- Replication of a GWAS signal nearBlood neoplasia · 2025Article
- Public platform with 39,472 exome control samples enables association studies without genotype sharing.Nature genetics · 2024Article
- Integrating External Controls by Regression Calibration for Genome-Wide Association Study.Genes · 2024Article
- Case-only exome variation analysis of severe alcohol dependence using a multivariate hierarchical gene clustering approach.PloS one · 2023Article
- Article
- Opportunities and challenges for the use of common controls in sequencing studies.Nature reviews. Genetics · 2022Review
- Integrating external controls in case-control studies improves power for rare-variant tests.Genetic epidemiology · 2022Article
- A data harmonization pipeline to leverage external controls and boost power in GWAS.Human molecular genetics · 2022Article
- Recent advances and challenges of rare variant association analysis in the biobank sequencing era.Frontiers in genetics · 2022Review
- Summix: A method for detecting and adjusting for population structure in genetic summary data.American journal of human genetics · 2021Article
- Novel score test to increase power in association test by integrating external controls.Genetic epidemiology · 2021Article
- Analysis in case-control sequencing association studies with different sequencing depths.Biostatistics (Oxford, England) · 2020Article
- Association of Breast and Ovarian Cancers With Predisposition Genes Identified by Large-Scale Sequencing.JAMA oncology · 2019Article
- ProxECAT: Proxy External Controls Association Test. A new case-control gene region association test using allele frequencies from public controls.PLoS genetics · 2018Article
- Complex-Trait Prediction in the Era of Big Data.Trends in genetics : TIG · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Due to the drop in sequencing cost, the number of sequenced genomes is increasing rapidly. To improve power of rare-variant tests, these sequenced samples could be used as external control samples in addition to control samples from the study itself. However, when using external controls, possible batch effects due to the use of different sequencing platforms or genotype calling pipelines can dramatically increase type I error rates. To address this, we propose novel summary statistics based single and gene- or region-based rare-variant tests that allow the integration of external controls while controlling for type I error. Our approach is based on the insight that batch effects on a given variant can be assessed by comparing odds ratio estimates using internal controls only vs. using combined control samples of internal and external controls. From simulation experiments and the analysis of data from age-related macular degeneration and type 2 diabetes studies, we demonstrate that our method can substantially improve power while controlling for type I error rate.
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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.