Evidence map›Paper›PMID 40119139›Full record

ArticleNPJ precision oncology2025

Comparative analysis of RNA expression in a single institution cohort of pediatric cancer patients.

Yvonne A Vasquez, Holly C Beale, Lauren Sanders, A Geoffrey Lyle, Ellen T Kephart, Katrina Learned, Drew Thompson, Jennifer Peralez, Amy Li, Min Huang and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in NPJ precision oncology, 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

16 authors.

Yvonne A Vasquez *Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
Holly C Beale *Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
Lauren SandersUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
A Geoffrey LyleDepartment of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
Ellen T KephartUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Katrina LearnedUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Drew ThompsonDepartment of Biomolecular Engineering, School of Engineering, University of California, Santa Cruz, CA, USA.
Jennifer PeralezStanford University School of Medicine, Stanford, CA, USA.
Amy LiStanford University School of Medicine, Stanford, CA, USA.
Min HuangStanford University School of Medicine, Stanford, CA, USA.
Kimberly A Pyke-GrimmStanford University School of Medicine, Stanford, CA, USA.
Sofie R SalamaDepartment of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
David HausslerUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Isabel BjorkUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
L Spunt SheriStanford University School of Medicine, Stanford, CA, USA.
Olena M VaskeDepartment of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA. olena@ucsc.edu.

Funding

Training Program in Molecular, Cell, and Developmental BiologyT32GM133391 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Needhi Bhalla · 2019 to 2026
$3.0M
American Association for Cancer Research NextGen Award for Transformative Cancer ResearchNIGMS NIH HHS T32 GM133391St. Baldrick's Foundation Emily Beazley Kures for Kids
6 · The paper itself

Abstract

With the low incidence of mutations in pediatric cancers, alternate genomic approaches are needed to identify therapeutic targets. Our study, the Comparative Analysis of RNA Expression to Improve Pediatric and Young Adult Cancer Treatment, was conducted by the UC Santa Cruz Treehouse Childhood Cancer Initiative and Stanford University School of Medicine. RNA sequencing data from 33 children and young adults with a relapsed, refractory or rare cancer underwent CARE analysis to reveal activated cancer driver pathways and nominate treatments. We compare our pipeline to other gene expression outlier detection approaches and discuss challenges for clinical implementation. Of our 33 patients, 31 (94%) had findings of potential clinical significance. Findings were implemented in 5 patients, 3 of which had defined clinical benefit. We demonstrate that comparator cohort composition determines which outliers are detected. This study highlights the clinical utility and challenges of implementing comparative RNA sequencing analysis in the clinic.

Identifiers

PMID40119139
PMCPMC11928651

What OpenQuestion holds

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LicenceCC BY
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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.