Evidence map›Paper›PMID 38314955›Full record

ArticleCurrent protocols2024

Transcriptome-Wide Association Studies (TWAS): Methodologies, Applications, and Challenges.

Patrick Evans, Taylor Nagai, Anuar Konkashbaev, Dan Zhou, Ela W Knapik, Eric R Gamazon

Abstract read
In one paragraph

Article in Current protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing 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

13 citing papers in PubMed.

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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

6 authors.

Patrick EvansDivision of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee.
Taylor NagaiDivision of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee.
Anuar KonkashbaevDivision of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee.
Dan ZhouDivision of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee.
Ela W KnapikDivision of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee.
Eric R GamazonDivision of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee.ORCID https://orcid.org/0000-0003-4204-8734

Funding

Overall: Eunice Kennedy Shriver Intellectual and Developmental Disabilities Research Center at VanderbiltP50HD103537 · NICHD · VANDERBILT UNIVERSITY MEDICAL CENTER · PI Jeffrey L Neul · 2020 to 2026
$10.3M
Discovering Biology for Neuropsychiatric Diseases Through Omics Studies on ComorbiditiesR01MH113362 · NIMH · VANDERBILT UNIVERSITY MEDICAL CENTER · PI COX, NANCY J, KNAPIK, ELA W · 2017 to 2021
$3.9M
Gene Expression Regulation in Brains of East Asian, African, and European Descent Explains Schizophrenia GWAS in Diverse Populations.R01MH126459 · NIMH · UPSTATE MEDICAL UNIVERSITY · PI Chunyu Liu · 2022 to 2026
$3.7M
Haplotype-aware models of gene and isoform expression with application to genetic studies of disease in diverse populationsR01GM140287 · NIGMS · SEATTLE CHILDREN'S HOSPITAL · PI GAMAZON, ERIC R, MOHAMMADI, PEJMAN · 2021 to 2024
$2.8M
Functional Genomics: A Phenome-wide SurveyR35HG010718 · NHGRI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI GAMAZON, ERIC R · 2019 to 2023
$2.2M
Advancing Multi-Omics and Electronic Health Records Computational MethodologiesR01HG011138 · NHGRI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI GAMAZON, ERIC R · 2020 to 2024
$1.6M
Advancing drug repositioning and development for Alzheimer's Disease using functional genomics and computational phenomicsR56AG068026 · NIA · VANDERBILT UNIVERSITY MEDICAL CENTER · PI GAMAZON, ERIC R · 2021 to 2022
$1.5M
NHGRI NIH HHS R01 HG011138NHGRI NIH HHS R01HG011138NHGRI NIH HHS R35 HG010718NHGRI NIH HHS R35HG010718NIA NIH HHS R56 AG068026NIA NIH HHS R56AG068026NICHD NIH HHS P50 HD103537NIGMS NIH HHS R01 GM140287NIGMS NIH HHS R01GM140287NIH HHSNIMH NIH HHS R01 MH113362NIMH NIH HHS R01 MH126459NIMH NIH HHS R01MH126459
6 · The paper itself

Abstract

Transcriptome-wide association study (TWAS) methodologies aim to identify genetic effects on phenotypes through the mediation of gene transcription. In TWAS, in silico models of gene expression are trained as functions of genetic variants and then applied to genome-wide association study (GWAS) data. This post-GWAS analysis identifies gene-trait associations with high interpretability, enabling follow-up functional genomics studies and the development of genetics-anchored resources. We provide an overview of commonly used TWAS approaches, their advantages and limitations, and some widely used applications. © 2024 Wiley Periodicals LLC.

Indexed as

Genome-Wide Association StudyTranscriptomeComputer SimulationPhenotypeQuantitative Trait Locicomplex traitselectronic health recordsjoint-tissue imputation (JTI)PrediXcansingle-cell transcriptomicstranscriptome-wide association studies (TWAS)

Identifiers

PMID38314955
PMCPMC10846672

What OpenQuestion holds

Textmetadata
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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.