ArticleGenes, chromosomes & cancer2016
Genomic aberrations frequently alter chromatin regulatory genes in chordoma.
Article in Genes, chromosomes & cancer, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 76 citations in OpenAlex.
- The copy-number events in skull base chordoma stratify tumours into four biologically coherent groups.Neoplasia (New York, N.Y.) · 2026Article
- Atypical notochordal cell tumors: an alternative diagnosis when diagnostic criteria are not straightforward : Short title: atypical notochordal cell tumor.Virchows Archiv : an international journal of pathology · 2026Article
- TP53 mutations as drivers of chordoma progression and hallmarks of aggressive chordoma.Acta neuropathologica communications · 2025Article
- Epigenetic roles of chromatin remodeling complexes in bone biology and the pathogenesis of bone‑related disease (Review).International journal of molecular medicine · 2025Review
- The TBXT rs2305089 SNP links the benign notochordal cell tumour and chordoma.The Journal of pathology · 2025Article
- Conventional Spinal Chordomas: Investigation of SMARCB1/INI1 Protein Expression, Genetic Alterations inCancers · 2024Article
- A retrospective study on the mechanism underlying quick transfer from response to resistance in a repeated recurrent chordoma patient with molecular alterations treated with Palbociclib.Journal of cancer research and clinical oncology · 2024Article
- Article
- DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment.Acta neuropathologica communications · 2023Article
- SMARCB1/INI1 loss in skull base conventional chordomas: a clinicopathological and molecular analysis.Frontiers in oncology · 2023Article
- SETD2-H3K36ME3: an important bridge between the environment and tumors.Frontiers in genetics · 2023Review
- Rare germline variants in PALB2 and BRCA2 in familial and sporadic chordoma.Human mutation · 2022Article
- OligoTRAFTACs: A generalizable method for transcription factor degradation.RSC chemical biology · 2022Article
- DNA methylation-based prognostic subtypes of chordoma tumors in tissue and plasma.Neuro-oncology · 2022Article
- A chronicle review of new techniques that facilitate the understanding and development of optimal individualized therapeutic strategies for chordoma.Frontiers in oncology · 2022Review
- Article
- Selinexor inhibits growth of patient derived chordomasFrontiers in oncology · 2022Article
- Emerging target discovery and drug repurposing opportunities in chordoma.Frontiers in oncology · 2022Review
- Recurrent loss of chromosome 22 and SMARCB1 deletion in extra-axial chordoma: A clinicopathological and molecular analysis.Genes, chromosomes & cancer · 2021Article
- H3K36 trimethylation-mediated biological functions in cancer.Clinical epigenetics · 2021Review
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Authors and funding
14 authors at 2 institutions in 1 country.
Funding
Abstract
Chordoma is a rare primary bone neoplasm that is resistant to standard chemotherapies. Despite aggressive surgical management, local recurrence and metastasis is not uncommon. To identify the specific genetic aberrations that play key roles in chordoma pathogenesis, we utilized a genome-wide high-resolution SNP-array and next generation sequencing (NGS)-based molecular profiling platform to study 24 patient samples with typical histopathologic features of chordoma. Matching normal tissues were available for 16 samples. SNP-array analysis revealed nonrandom copy number losses across the genome, frequently involving 3, 9p, 1p, 14, 10, and 13. In contrast, copy number gain is uncommon in chordomas. Two minimum deleted regions were observed on 3p within a ∼8 Mb segment at 3p21.1-p21.31, which overlaps SETD2, BAP1 and PBRM1. The minimum deleted region on 9p was mapped to CDKN2A locus at 9p21.3, and homozygous deletion of CDKN2A was detected in 5/22 chordomas (∼23%). NGS-based molecular profiling demonstrated an extremely low level of mutation rate in chordomas, with an average of 0.5 mutations per sample for the 16 cases with matched normal. When the mutated genes were grouped based on molecular functions, many of the mutation events (∼40%) were found in chromatin regulatory genes. The combined copy number and mutation profiling revealed that SETD2 is the single gene affected most frequently in chordomas, either by deletion or by mutations. Our study demonstrated that chordoma belongs to the C-class (copy number changes) tumors whose oncogenic signature is non-random multiple copy number losses across the genome and genomic aberrations frequently alter chromatin regulatory genes. © 2016 Wiley Periodicals, Inc.
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