Evidence map›Paper›PMID 40631108›Full record

ArticlebioRxiv : the preprint server for biology2025

Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.

Sriram Pendyala, Katie Partington, Nicholas Bradley, Abbye E McEwen, Gwenneth Straub, Hyeon-Jin Kim, Shawn Fayer, Daniel Lee Holmes, Katherine A Sitko, Allyssa J Vandi and 10 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

20 authors.

Sriram PendyalaDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0003-3395-3417
Katie PartingtonDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0009-0009-1502-7154
Nicholas BradleyDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0009-0001-2056-1679
Abbye E McEwenDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0001-7187-7975
Gwenneth StraubDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0009-0007-6050-8729
Hyeon-Jin KimDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0001-6938-4602
Shawn FayerDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0003-1883-9069
Daniel Lee HolmesDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0002-0489-4043
Katherine A SitkoDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0009-0008-5810-9590
Allyssa J VandiDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0009-0001-6781-416X
Rachel L PowellDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0003-4791-6692
Clayton E FriedmanInstitute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, USA.ORCID 0000-0003-4211-886X
Evan McDermotDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0009-0000-6257-9845
Nishka KishoreDonnelly Centre, University of Toronto, Toronto, ON, Canada.ORCID 0000-0002-9219-4310
Frederick P RothDonnelly Centre, University of Toronto, Toronto, ON, Canada.ORCID 0000-0002-6628-649X
Alan F RubinBioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.ORCID 0000-0003-1474-605X
Kai-Chun YangInstitute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, USA.ORCID 0000-0001-5429-6853
Lea M StaritaDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0003-2870-5099
William S NobleDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0001-7283-4715
Douglas M FowlerDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0001-7614-1713

Funding

University of Washington Medical Scientist Training Program: MD/PhDT32GM007266 · NIGMS · UNIVERSITY OF WASHINGTON · PI HORWITZ, MARSHALL S. · 1985 to 2023
$30.4M
Technology to understand genetic variant effects in contextRM1HG010461 · NHGRI · UNIVERSITY OF WASHINGTON · PI Douglas M Fowler, Bruce Colston Trapnell · 2019 to 2026
$18.9M
Systematically mapping variant effects for cardiovascular genesR01HL164675 · NHLBI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI ASHLEY, EUAN A, RODEN, DAN M · 2022 to 2025
$8.1M
University of Washington Medical Scientist Training ProgramT32GM153182 · NIGMS · UNIVERSITY OF WASHINGTON · PI MARSHALL S. HORWITZ · 2024 to 2026
$5.3M
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
Deep mutational scanning of MYH7 in genome-edited cardiomyocytesR01HL171174 · NHLBI · UNIVERSITY OF WASHINGTON · PI Kai-Chun Daniel Yang · 2024 to 2026
$2.6M
New approaches for investigating the causes and consequences of cellular heterogeneityR35GM152106 · NIGMS · UNIVERSITY OF WASHINGTON · PI Douglas M Fowler · 2024 to 2026
$1.8M
High-Throughput Studies of MYH7 Variant Cardiomyocytes to Identify Pathogenic Variants and Factors Governing Variable Expressivity of Hypertrophic CardiomyopathyK99HL177347 · NHLBI · UNIVERSITY OF WASHINGTON · PI Clayton E Friedman · 2025 to 2026
$252k
BLRD VA I01 BX006428BLRD VA IK2 BX004642NHGRI NIH HHS R01 HG013025NHGRI NIH HHS RM1 HG010461NHLBI NIH HHS K99 HL177347NHLBI NIH HHS R01 HL164675NHLBI NIH HHS R01 HL171174NIGMS NIH HHS R35 GM152106NIGMS NIH HHS T32 GM007266NIGMS NIH HHS T32 GM153182
6 · The paper itself

Abstract

Genetic variants often produce complex phenotypic effects that confound current assays and predictive models. We developed Variant in situ sequencing (VIS-seq), a pooled, image-based method that measures variant effects on molecular and cellular phenotypes in diverse cell types. Applying VIS-seq to ~3,000

Identifiers

PMID40631108
PMCPMC12236469

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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.