ArticleGigaScience2022
EraSOR: a software tool to eliminate inflation caused by sample overlap in polygenic score analyses.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Reconstructing SNP allele and genotype frequencies from GWAS summary statistics.Scientific reports · 2022Pooled it
- Article
- Genomic structural equation modelling of 12 cancers identifies a latent pan-cancer susceptibility factor and shared determinants of carcinogenesis.EBioMedicine · 2026Article
- Methods for modeling gene-environment interplay using polygenic risk scores.Statistical applications in genetics and molecular biology · 2026Review
- GRPa-PRS: A risk stratification method to identify genetically-regulated pathways in polygenic diseases.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Article
- Addressing overfitting bias due to sample overlap in polygenic risk scoring.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Benchmarking Alzheimer's disease prediction: personalised risk assessment using polygenic risk scores across various methodologies and genome-wide studies.Alzheimer's research & therapy · 2025Article
- A review of methods and software for polygenic risk score analysis.PeerJ. Computer science · 2025Article
- Striking Departures from Polygenic Architecture in the Tails of Complex Traits.bioRxiv : the preprint server for biology · 2024Article
- Genetic risk factors underlying white matter hyperintensities and cortical atrophy.Nature communications · 2024Article
- Inflation of polygenic risk scores caused by sample overlap and relatedness: Examples of a major risk of bias.American journal of human genetics · 2024Article
- Genetic determinants of obesity in Korean populations: exploring genome-wide associations and polygenic risk scores.Briefings in bioinformatics · 2024Article
- Dementias Platform UK: Bringing genetics into life.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Article
- Addressing overlapping sample challenges in genome-wide association studies: Meta-reductive approach.PloS one · 2024Article
- Genetic risk for hospitalization of African American patients with severe mental illness reveals HLA loci.Frontiers in psychiatry · 2024Article
- Addressing Overlapping Sample Challenges in Genome-Wide Association Studies: Meta-Reductive Approach.bioRxiv : the preprint server for biology · 2023Article
- Overestimated prediction using polygenic prediction derived from summary statistics.BMC genomic data · 2023Article
- A genetically informed Registered Report on adverse childhood experiences and mental health.Nature human behaviour · 2023Article
- EraSOR: a software tool to eliminate inflation caused by sample overlap in polygenic score analyses.GigaScience · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundPolygenic risk score (PRS) analyses are now routinely applied across biomedical research. However, as PRS studies grow in size, there is an increased risk of sample overlap between the genome-wide association study (GWAS) from which the PRS is derived and the "target sample," in which PRSs are computed and hypotheses are tested. Despite the wide recognition of the sample overlap problem, its potential impact on the results from PRS studies has not yet been quantified, and no analytical solution has been provided.
findingsHere, we first conduct a comprehensive investigation into the scale of the sample overlap problem, finding that PRS results can be substantially inflated even in the presence of minimal overlap. Next, we introduce a method and software, EraSOR (Erase Sample Overlap and Relatedness), which eliminates the inflation caused by sample overlap (and close relatedness) in almost all settings tested here.
conclusionsEraSOR could be useful in PRS studies (with target sample >1,000) similar to those investigated here, either (i) to mitigate the potential effects of known or unknown intercohort overlap and close relatedness or (ii) as a sensitivity tool to highlight the possible presence of sample overlap before its direct removal, when possible, or else to provide a lower bound on PRS analysis results after accounting for potential sample overlap.
Indexed as
Identifiers
What OpenQuestion holds
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.