ArticleGenetics2018
Improved Use of Small Reference Panels for Conditional and Joint Analysis with GWAS Summary Statistics.
Article in Genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 2 of them syntheses that pooled it.
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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, 2 syntheses or guidelines pooled it.
- Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.Journal of advanced research · 2025Pooled it
- A gene based combination test using GWAS summary data.BMC bioinformatics · 2023Pooled it
- Cross-tissue transcriptome-wide association studies identify genetic susceptibility genes for prostate cancer.BMC cancer · 2025Article
- Cross-tissue transcriptome-wide analysis reveals novel insights into thyroid cancer etiology.Discover oncology · 2025Article
- Unveiling novel susceptibility genes and drug targets for basal cell carcinoma by a cross-tissue transcriptome-wide association study.Discover oncology · 2025Article
- A cross-tissue transcriptome-wide association study identified susceptibility genes for age-related macular degeneration.Scientific reports · 2025Article
- ON BLOCKWISE AND REFERENCE PANEL-BASED ESTIMATORS FOR GENETIC DATA PREDICTION IN HIGH DIMENSIONS.Annals of statistics · 2024Article
- Article
- A cross-tissue transcriptome-wide association study identifies new susceptibility genes for frailty.Frontiers in genetics · 2024Article
- Inferring a directed acyclic graph of phenotypes from GWAS summary statistics.bioRxiv : the preprint server for biology · 2023Article
- A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes.Journal of advanced research · 2022Article
- Gene-based association tests using GWAS summary statistics and incorporating eQTL.Scientific reports · 2022Article
- Implicating causal brain imaging endophenotypes in Alzheimer's disease using multivariable IWAS and GWAS summary data.NeuroImage · 2020Article
- A powerful and versatile colocalization test.PLoS computational biology · 2020Article
- Shared genetic etiology underlying Alzheimer's disease and major depressive disorder.Translational psychiatry · 2020Article
- Novel susceptibility genes for varicose veins revealed by a cross-tissue transcriptome-wide association study.Science progressArticle
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Due to issues of practicality and confidentiality of genomic data sharing on a large scale, typically only meta- or mega-analyzed genome-wide association study (GWAS) summary data, not individual-level data, are publicly available. Reanalyses of such GWAS summary data for a wide range of applications have become more and more common and useful, which often require the use of an external reference panel with individual-level genotypic data to infer linkage disequilibrium (LD) among genetic variants. However, with a small sample size in only hundreds, as for the most popular 1000 Genomes Project European sample, estimation errors for LD are not negligible, leading to often dramatically increased numbers of false positives in subsequent analyses of GWAS summary data. To alleviate the problem in the context of association testing for a group of SNPs, we propose an alternative estimator of the covariance matrix with an idea similar to multiple imputation. We use numerical examples based on both simulated and real data to demonstrate the severe problem with the use of the 1000 Genomes Project reference panels, and the improved performance of our new approach.
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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.