biostudies-literatureUnknown64(3)Kleijn TGUMCG Cancer Research FundGastrointestinal 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 diseGenes, chromosomes & cancere70046https://www.ebi.ac.uk/biostudies/studies/S-EPMC11949093biostudies-literatureGenome-Wide DNA Methylation and Copy Number Alterations in Gastrointestinal Stromal Tumors.PMC11949093van den Broek Evan Hemel BMTimmer Bvan Kempen LCCleven AHGKats-Ugurlu GDiercks GFHSchuuring Evan Etten BSuurmeijer AJHAmeline BKooistra WReyners AKLBleckman RFTimens Wde Haan JJBaumhoer DKleijn TGfalseGenome-Wide DNA Methylation and Copy Number Alterations in Gastrointestinal Stromal Tumors.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 dise2025-01-01T00:00:00Z2025 Mar2025-07-13T03:04:45.084Z2025-07-13T03:04:45.084ZS-EPMC119490934014585910.1002/gcc.70046