ArticleBioinformatics (Oxford, England)2024
The GenoPred pipeline: a comprehensive and scalable pipeline for polygenic scoring.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Rare extreme polygenic risk scores strongly indicate Alzheimer's disease risk.medRxiv : the preprint server for health sciences · 2026Article
- Evidence standards for multi-ancestry polygenic prediction.Genome biology · 2026Review
- Polygenic background contributes to GCK-MODY clinical presentation and glycaemic variability.Diabetologia · 2026Article
- Metabolomic ageing across mental and behavioural disorders.BMJ mental health · 2026Article
- Association and risk prediction of 19 complex diseases with polygenic scores and socioeconomic status.Communications medicine · 2026Article
- Trans-ancestry genome-wide association meta-analysis of antidepressant response to selective serotonin reuptake inhibitors in clinical studies of depression.medRxiv : the preprint server for health sciences · 2026Article
- PolyGenie: a reproducible Nextflow pipeline for phenome-wide association studies using polygenic risk scores.NAR genomics and bioinformatics · 2026Article
- Splitting schizophrenia: divergent cognitive and educational outcomes revealed by genomic structural equation modelling.Molecular psychiatry · 2026Article
- Metabolomic ageing (MileAge) in mid-life predicts incident vascular, unspecified and all-cause dementia.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Genetic Impacts on Variability of Body Fat Distribution Uncover Gene-Environment and Gene-Gene Interactions.bioRxiv : the preprint server for biology · 2026Article
- Polygenic risk scores: Navigating the future of precision medicine through economic, ethical, and scientific advancements.iScience · 2026Review
- Leveraging global genetics resources to enhance polygenic prediction across ancestrally diverse populations.HGG advances · 2025Article
- Latent class growth mixture modeling of HbA1C trajectories identifies individuals at high risk of developing complications of type 2 diabetes mellitus in the UK Biobank.BMJ open diabetes research & care · 2025Article
- Common genetic variants modify disease risk and clinical presentation in monogenic diabetes.Nature metabolism · 2025Article
- LDAK-KVIK performs fast and powerful mixed-model association analysis of quantitative and binary phenotypes.Nature genetics · 2025Article
- PGSFusion streamlines polygenic score construction and epidemiological applications in biobank-scale cohorts.Genome medicine · 2025Article
- Antidepressant Switching as a Proxy Phenotype for Drug Nonresponse: Investigating Clinical, Demographic, and Genetic Characteristics.Biological psychiatry global open science · 2025Article
- Evaluating metabolome-wide causal effects on risk for psychiatric and neurodegenerative disorders.BMC medicine · 2025Article
- Sociodemographic, clinical, and genetic factors associated with self-reported antidepressant response outcomes in the UK Biobank.Psychological medicine · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
motivationPolygenic scoring is an approach for estimating an individual's likelihood of a given outcome. Polygenic scores are typically calculated from genome-wide association study (GWAS) summary statistics and individual-level genotype data for the target sample. Going from genotype to interpretable polygenic scores involves many steps and there are many methods available, limiting the accessibility of polygenic scores for research and clinical application. Additional challenges exist for studies in ancestrally diverse populations. We have implemented the leading polygenic scoring methodologies within an easy-to-use pipeline called GenoPred.
resultsHere, we present the GenoPred pipeline, an easy-to-use, high-performance, reference-standardized, and reproducible workflow for polygenic scoring. It requires minimal inputs and offers various configuration options to cater to a range of use cases. GenoPred implements a comprehensive set of analyses, including genotype and GWAS quality control, target sample ancestry inference, polygenic score file generation using a range of leading methods, and target sample scoring. GenoPred standardizes the polygenic scoring process using reference genetic data, providing interpretable polygenic scores. The pipeline is applicable to GWAS and targets data from any population within the reference, facilitating studies of diverse ancestry. GenoPred is a Snakemake pipeline with associated Conda software environments, ensuring reproducibility. We apply the pipeline to UK Biobank data demonstrating the pipeline's simplicity, efficiency, and performance. The GenoPred pipeline provides a novel resource for polygenic scoring, integrating a range of complex processes within an easy-to-use framework. GenoPred widens access to the leading polygenic scoring methodology and their application to studies of diverse ancestry. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at https://github.com/opain/GenoPred.
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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 OpenQuestion graph.