Evidence map›Paper›PMID 40894657›Full record

ArticlebioRxiv : the preprint server for biology2025

Quantification method affects replicability of eQTL analysis, colocalization, and TWAS.

S Taylor Head, Sean T Bresnahan, Nolan Cole, William Wu, Arjun Bhattacharya

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

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

5 authors.

S Taylor HeadDepartment of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID 0000-0002-1761-1145
Sean T BresnahanDepartment of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID 0000-0001-6685-1930
Nolan ColeDepartment of Biostatistics, University of Washington, Seattle, WA, USA.
William WuDepartment of BioSciences, Rice University, Houston, TX, USA.
Arjun BhattacharyaDepartment of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID 0000-0003-1196-4385

Funding

Alternative splicing and isoform expression as mediators for the genetic etiology of breast cancerR21CA293419 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI BHATTACHARYA, ARJUN, LINDSTROEM, SARA · 2024 to 2024
$407k
NCI NIH HHS R21 CA293419
6 · The paper itself

Abstract

eQTL mapping and TWAS are widely used to contextualize GWAS, yet the impact of RNA-seq processing choices remains unexplored. We find that RNA-seq quantification method and transcriptomic reference substantially affect eQTL detection and gene expression prediction with significant downstream impact on colocalization and TWAS results. Our findings demonstrate that seemingly minor methodological decisions substantially affect these common analyses, highlighting the need for standardized practices to ensure reproducible genetic association studies.

Identifiers

PMID40894657
PMCPMC12393437

What OpenQuestion holds

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LicenceCC BY-NC
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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.