Evidence map›Paper›PMID 41292636›Full record

ArticlemedRxiv : the preprint server for health sciences2025

Editing stem cell genomes at scale to measure variant effects in diverse cell and genetic contexts.

Shawn Fayer, Riddhiman K Garge, Melissa Hopkins, Clayton E Friedman, Abby V McGee, Joshua Rico, Rachel L Powell, Evan McDermot, Nahum T Smith, Sriram Pendyala and 11 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors.

Shawn FayerDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0003-1883-9069
Riddhiman K GargeDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0002-6774-0172
Melissa HopkinsDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0009-0009-2029-7351
Clayton E FriedmanInstitute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, USA.ORCID 0000-0003-4211-886X
Abby V McGeeDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0001-9294-7039
Joshua RicoInstitute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.ORCID 0009-0004-3779-0963
Rachel L PowellDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0003-4791-6692
Evan McDermotDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0009-0000-6257-9845
Nahum T SmithDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Sriram PendyalaDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0003-3395-3417
Marcy E RichardsonAmbry Genetics, Aliso Viejo, CA, USA.
Erica D SmithAmbry Genetics, Aliso Viejo, CA, USA.ORCID 0000-0002-5424-580X
B Monica BowenAmbry Genetics, Aliso Viejo, CA, USA.ORCID 0000-0002-3148-5667
Rebecca ResnickDepartment of Medicine, Division of Cardiology, University of Washington, Seattle, WA, USA.ORCID 0000-0001-5804-4418
Pankhuri GuptaDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0009-0002-5802-1296
Andrew B StergachisDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0002-1299-3674
Casey GiffordInstitute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.ORCID 0000-0002-7757-573X
Sudarshan PinglayDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Kai-Chun YangInstitute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, USA.ORCID 0000-0001-5429-6853
Douglas M FowlerDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0001-7614-1713
Lea M StaritaDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0003-2870-5099

Funding

Vector and Transgenic Mouse CoreP30DK017047 · NIDDK · UNIVERSITY OF WASHINGTON · PI Sakeneh Zraika · 1986 to 2026
$41.4M
INTERDISCIPLINARY TRAINING IN GENOMIC SCIENCEST32HG000035 · NHGRI · UNIVERSITY OF WASHINGTON · PI Bruce Colston Trapnell · 1995 to 2026
$24.2M
Technology to understand genetic variant effects in contextRM1HG010461 · NHGRI · UNIVERSITY OF WASHINGTON · PI Douglas M Fowler, Bruce Colston Trapnell · 2019 to 2026
$18.9M
Advancing the implementation of variant-level functional data into clinical databases and clinical practiceR01HG013025 · NHGRI · UNIVERSITY OF WASHINGTON · PI Lea Starita, Andrew Ben Stergachis · 2023 to 2026
$3.1M
NHGRI NIH HHS R01 HG013025NHGRI NIH HHS RM1 HG010461NHGRI NIH HHS T32 HG000035NIDDK NIH HHS P30 DK017047
6 · The paper itself

Abstract

Multiplexed assays of variant effect (MAVEs) systematically measure variant function but have been limited to cancer cell lines rather than disease-relevant cell types. We developed saturation genome editing in human iPSCs (iPSC-SGE) to introduce variant libraries into a single allele of a target gene while programming the genetic background of the second allele, enabling variant assessment across differentiated cell types and genetic contexts at scale. We edited 1,137 variants into

Identifiers

PMID41292636
PMCPMC12642741

What OpenQuestion holds

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LicenceCC BY
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.