Evidence map›Paper›PMID 41372418›Full record

ArticleNature2026

Causal modelling of gene effects from regulators to programs to traits.

Mineto Ota, Jeffrey P Spence, Tony Zeng, Emma Dann, Nikhil Milind, Alexander Marson, Jonathan K Pritchard

Abstract read
In one paragraph

Article in Nature, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing 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

20 citing papers in PubMed.

  1. AlphaGenome Atlas:medRxiv : the preprint server for health sciences · 2026
    Article
  2. Genome-scale perturbation signatures from primary human CD4bioRxiv : the preprint server for biology · 2026
    Article
  3. Article
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  16. medRxiv : the preprint server for health sciences · 2026
    Article
  17. Article
  18. Review
  19. Article
  20. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Mineto OtaDepartment of Genetics, Stanford University, Stanford, CA, USA. mineto-ota@g.ecc.u-tokyo.ac.jp.ORCID 0000-0003-4552-8573
Jeffrey P SpenceDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0002-3199-1447
Tony ZengDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0002-6509-9879
Emma DannDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0002-7400-7438
Nikhil MilindDepartment of Genetics, Stanford University, Stanford, CA, USA.
Alexander MarsonGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. alex.marson@gladstone.ucsf.edu.ORCID 0000-0002-2734-5776
Jonathan K PritchardDepartment of Genetics, Stanford University, Stanford, CA, USA. pritch@stanford.edu.ORCID 0000-0002-8828-5236

Funding

Integration of genetic association mapping and functional data to elucidate genetic mechanisms of diseaseR01HG008140 · NHGRI · STANFORD UNIVERSITY · PI JONATHAN K PRITCHARD · 2016 to 2026
$7.3M
Predicting context-specific molecular and phenotypic effects of genetic variation through the lens of the cis-regulatory codeU01HG012069 · NHGRI · STANFORD UNIVERSITY · PI Anshul Kundaje · 2021 to 2026
$3.9M
New methods for constructing and evaluating polygenic scoresR01HG011432 · NHGRI · STANFORD UNIVERSITY · PI PRITCHARD, JONATHAN K · 2020 to 2023
$3.3M
Bayesian estimation of gene effects on traits from coding variantsR01HG014005 · NHGRI · STANFORD UNIVERSITY · PI JONATHAN K PRITCHARD · 2025 to 2026
$1.3M
NHGRI NIH HHS R01 HG008140NHGRI NIH HHS R01 HG011432NHGRI NIH HHS R01 HG014005NHGRI NIH HHS U01 HG012069
6 · The paper itself

Abstract

Genetic association studies provide a unique tool for identifying candidate causal links from genes to human traits and diseases. However, it is challenging to determine the biological mechanisms underlying most associations, and we lack genome-scale approaches for inferring causal mechanistic pathways from genes to cellular functions to traits. Here we propose approaches to bridge this gap by combining quantitative estimates of gene-trait relationships from loss-of-function burden tests

Indexed as

CausalityGene Expression RegulationGenetic Association StudiesModels, GeneticAnimalsGene Regulatory NetworksGenome-Wide Association StudyHumansLoss of Function MutationPhenotypeQuantitative Trait, HeritableQuantitative Trait Loci

Identifiers

PMID41372418
PMCPMC12893915

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.