Evidence map›Paper›PMID 40715455›Full record

ArticleNature biotechnology2026

Single-cell polygenic risk scores dissect cellular and molecular heterogeneity of complex human diseases.

Sai Zhang, Hantao Shu, Jingtian Zhou, Jasper Rubin-Sigler, Xiaoyu Yang, Yuxi Liu, Johnathan Cooper-Knock, Emma Monte, Chenchen Zhu, Sharon Tu and 8 more

Abstract read
In one paragraph

Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Medea: An omics AI agent for therapeutic discovery.bioRxiv : the preprint server for biology · 2026
    Article
  8. Article
  9. Article
  10. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Sai Zhang *Department of Epidemiology, University of Florida, Gainesville, FL, USA. sai.zhang@ufl.edu.ORCID http://orcid.org/0000-0001-5996-6086
Hantao Shu *Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.ORCID http://orcid.org/0000-0002-7306-5644
Jingtian Zhou *Arc Institute, Palo Alto, CA, USA.
Jasper Rubin-SiglerDepartment of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA.
Xiaoyu YangInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Yuxi LiuInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Johnathan Cooper-KnockSheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK.
Emma MonteDepartment of Genetics, Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Chenchen ZhuDepartment of Genetics, Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Sharon TuDepartment of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA.
Han LiInstitute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.ORCID http://orcid.org/0000-0002-7380-6174
Mingming TongDepartment of Genetics, Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-8422-5108
Joseph R EckerGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-5799-5895
Justin K IchidaDepartment of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA.
Yin ShenInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-9901-5613
Jianyang ZengSchool of Engineering, Research Center for Industries of the Future, Westlake University, Hangzhou, China. zengjy@westlake.edu.cn.ORCID http://orcid.org/0000-0003-0950-7716
Philip S TsaoVA Palo Alto Healthcare System, Palo Alto, CA, USA. ptsao@stanford.edu.ORCID http://orcid.org/0000-0001-7274-9318
Michael P SnyderDepartment of Genetics, Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA. mpsnyder@stanford.edu.ORCID http://orcid.org/0000-0003-0784-7987

Funding

Stanford Islet Research CoreP30DK116074 · NIDDK · STANFORD UNIVERSITY · PI Seung K Kim · 2017 to 2026
$19.5M
Elucidate the roles of Alzheimer's disease risk genes and variants in gene expression and AD-related phenotypesRF1AG079557 · NIA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GAN, LI, SHEN, YIN · 2022 to 2025
$6.1M
Study of Selective Cell and System Vulnerability in Alzheimer's DiseaseR01AG079291 · NIA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Li Gan, Yun Li · 2023 to 2026
$5.4M
NIDDK NIH HHS P30 DK116074U.S. Department of Health & Human Services | National Institutes of Health (NIH) 1R01NS131409U.S. Department of Health & Human Services | National Institutes of Health (NIH) 2R01NS097850U.S. Department of Health & Human Services | National Institutes of Health (NIH) 5P50HG007735U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01AG079291U.S. Department of Health & Human Services | National Institutes of Health (NIH) RF1AG079557
6 · The paper itself

Abstract

Polygenic risk scores (PRSs) predict an individual's genetic risk for complex diseases, yet their utility in elucidating disease biology remains limited. We introduce scPRS, a graph neural network-based framework that computes single-cell-resolved PRSs by integrating reference single-cell chromatin accessibility profiles. scPRS outperforms traditional PRS approaches in genetic risk prediction, as demonstrated across multiple diseases including type 2 diabetes, hypertrophic cardiomyopathy, Alzheimer disease and severe COVID-19. Beyond risk prediction, scPRS prioritizes disease-critical cells and, when combined with a layered multiomic analysis, links risk variants to gene regulation in a cell-type-specific manner. Applied to these diseases, scPRS fine-maps causal cell types and cell-type-specific variants and genes, demonstrating its ability to bridge genetic risk with cell-specific biology. scPRS provides a unified framework for genetic risk prediction and mechanistic dissection of complex diseases, laying a methodological foundation for single-cell genetics.

Indexed as

Genetic Predisposition to DiseaseMultifactorial InheritanceSingle-Cell AnalysisAlzheimer DiseaseCardiomyopathy, HypertrophicChromatinCOVID-19Diabetes Mellitus, Type 2Genetic Risk ScoreGenome-Wide Association StudyHumansNeural Networks, ComputerRisk FactorsSARS-CoV-2Chromatin

Identifiers

PMID40715455
PMCPMC13180658

What OpenQuestion holds

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Registered trials

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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.