Evidence map›Paper›PMID 40145859›Full record

ArticleGenes, chromosomes & cancer2025

Genome-Wide DNA Methylation and Copy Number Alterations in Gastrointestinal Stromal Tumors.

Tony G Kleijn, Baptiste Ameline, Roos F Bleckman, Wierd Kooistra, Evert van den Broek, Gilles F H Diercks, Bettien M van Hemel, Bert Timmer, Wim Timens, Gursah Kats-Ugurlu and 8 more

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Article in Genes, chromosomes & cancer, 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

18 authors.

Tony G KleijnDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Baptiste AmelineBone Tumor Reference Center at the Institute for Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.
Roos F BleckmanDepartment of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Wierd KooistraDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Evert van den BroekDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Gilles F H DiercksDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Bettien M van HemelDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Bert TimmerDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Wim TimensDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Gursah Kats-UgurluDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Léon C van KempenDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Boudewijn van EttenDepartment of Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Ed SchuuringDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Albert J H SuurmeijerDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Jacco J de HaanDepartment of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Daniel BaumhoerBone Tumor Reference Center at the Institute for Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.
Anna K L ReynersDepartment of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Arjen H G ClevenDepartment of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Funding

UMCG Cancer Research Fund
6 · The paper itself

Abstract

Gastrointestinal stromal tumors (GISTs) span a broad clinical spectrum, from indolent neoplasms to life-threatening metastatic tumors. A persistent limitation of current risk stratification systems is that a subset of GISTs is graded as low-risk but nevertheless metastasizes. Therefore, new predictive factors that improve risk stratification are needed. In this exploratory study, we investigated the potential of genome-wide DNA methylation profiling and copy number variation (CNV) analysis as additional prognostic tools for GISTs. We collected a cohort of 28 patients with GIST diagnosed between 2001 and 2022, with available follow-up and molecular data. This included 15 patients without progressive disease (seven low-risk and eight moderate- to high-risk GISTs) and 13 with progressive disease. Among those with progression, eight experienced recurrence or metastasis post-surgery (one low-risk, seven high-risk GISTs), while five had metastatic disease at initial diagnosis. Risk stratification was determined according to Miettinen's criteria. Genome-wide DNA methylation data and CNV plots were generated from imatinib-naïve primary GISTs using the Illumina Infinium MethylationEPIC BeadChip array. Unsupervised cluster analysis revealed distinct DNA methylation patterns predominantly associated with anatomical location and genotype. Differential DNA methylation analysis comparing primary gastric GISTs associated with and without progressive disease showed 8 differentially methylated regions spanning the coding and promoter areas of 6 genes. CNV analysis demonstrated that GISTs associated with progressive disease had the most CNVs, whereas low-risk, non-progressive GISTs had the fewest. Despite the limited sample size, this exploratory study indicates that genome-wide DNA methylation profiling and CNV analysis could enhance GIST risk stratification.

Indexed as

DNA Copy Number VariationsDNA MethylationGastrointestinal NeoplasmsGastrointestinal Stromal TumorsAdultAgedAged, 80 and overFemaleGenome-Wide Association StudyHumansMaleMiddle AgedPrognosiscopy number variationDNA methylationgastrointestinal stromal tumor (GIST)profiling

Identifiers

PMID40145859
PMCPMC11949093

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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.