ArticleBMC genomics2015
A survey of tandem repeat instabilities and associated gene expression changes in 35 colorectal cancers.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 35 citations in OpenAlex.
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- Tumor mutational burden predicts neoantigen profiles and immunotherapy response in microsatellite stable tumors across different cancer types.Frontiers in immunology · 2025Article
- RNA-Binding S1 Domain in Bacterial, Archaeal and Eukaryotic Proteins as One of the Evolutionary Markers of Symbiogenesis.International journal of molecular sciences · 2024Article
- Lynch syndrome-associated and sporadic microsatellite unstable colorectal cancers: different patterns of clonal evolution yield highly similar tumours.Human molecular genetics · 2024Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Detecting microsatellite instability by length comparison of microsatellites in the 3' untranslated region with RNA-seq.Briefings in bioinformatics · 2024Article
- Short tandem repeat mutations regulate gene expression in colorectal cancer.Scientific reports · 2024Article
- Diversity and features of proteins with structural repeats.Biophysical reviews · 2023Review
- Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species.Journal of evolutionary biology · 2023Review
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- Detection of Urinary Molecular Marker Test in Urothelial Cell Carcinoma: A Review of Methods and Accuracy.Diagnostics (Basel, Switzerland) · 2022Review
- Microsatellite Instability Analysis (MSA) for Bladder Cancer: Past History and Future Directions.International journal of molecular sciences · 2021Review
- Abundancy of polymorphic CGG repeats in the human genome suggest a broad involvement in neurological disease.Scientific reports · 2021Article
- Glioblastoma signature in the DNA of blood-derived cells.PloS one · 2021Article
- Beyond Microsatellite Instability: Intrinsic Disorder as a Potential Link Between Protein Short Tandem Repeats and Cancer.Frontiers in bioinformatics · 2021Article
- Article
- Polymorphisms in the Bovine Tumour Necrosis Factor Receptor Type Two Gene (TNF-RII) and Cell Subpopulations Naturally Infected with Bovine Leukaemia Virus.Journal of veterinary research · 2019Article
- Estimation of duplication history under a stochastic model for tandem repeats.BMC bioinformatics · 2019Article
- Establishment of a detection assay for DNA endonuclease activity and its application in the screening and prognosis of malignant lymphoma.BMC biochemistry · 2018Article
- Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes.Genome biology and evolution · 2017Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundColorectal cancer is a major contributor to cancer morbidity and mortality. Tandem repeat instability and its effect on cancer phenotypes remain so far poorly studied on a genome-wide scale.
resultsHere we analyze the genomes of 35 colorectal tumors and their matched normal (healthy) tissues for two types of tandem repeat instability, de-novo repeat gain or loss and repeat copy number variation. Specifically, we study for the first time genome-wide repeat instability in the promoters and exons of 18,439 genes, and examine the association of repeat instability with genome-scale gene expression levels. We find that tumors with a microsatellite instable (MSI) phenotype are enriched in genes with repeat instability, and that tumor genomes have significantly more genes with repeat instability compared to healthy tissues. Genes in tumor genomes with repeat instability in their promoters are significantly less expressed and show slightly higher levels of methylation. Genes in well-studied cancer-associated signaling pathways also contain significantly more unstable repeats in tumor genomes. Genes with such unstable repeats in the tumor-suppressor p53 pathway have lower expression levels, whereas genes with repeat instability in the MAPK and Wnt signaling pathways are expressed at higher levels, consistent with the oncogenic role they play in cancer.
conclusionsOur results suggest that repeat instability in gene promoters and associated differential gene expression may play an important role in colorectal tumors, which is a first step towards the development of more effective molecular diagnostic approaches centered on repeat instability.
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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.