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Clear Cell Chondrosarcoma With Somatic VHL Inactivation: A Case Report With Integrated Genomic and Transcriptomic

Lalit R Patel1, Philip Wong2, Shervin Oskouei3

  • 1Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.

Genes, Chromosomes & Cancer
|May 5, 2026
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Summary
This summary is machine-generated.

This study identifies somatic VHL inactivation in clear cell chondrosarcoma (CCC), a rare bone tumor. This finding expands the known genomic landscape of CCC and suggests VHL pathway dysregulation in tumorigenesis.

Keywords:
COL2A1IDH1/2VHLclear cell chondrosarcomagenomic profiling

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Area of Science:

  • Oncology
  • Genetics
  • Molecular Biology

Background:

  • Clear cell chondrosarcoma (CCC) is a rare, low-grade malignant bone tumor, distinct from IDH-mutated conventional chondrosarcomas.
  • The genomic profile of CCC is largely uncharacterized, with no prior demonstration of somatic VHL alterations.
  • While VHL disease association is known, somatic VHL mutations in CCC were not previously established.

Purpose of the Study:

  • To molecularly characterize a recurrent clear cell chondrosarcoma.
  • To investigate the genomic alterations in IDH-wildtype CCC.
  • To determine if somatic VHL alterations contribute to CCC development.

Main Methods:

  • Comprehensive DNA/RNA next-generation sequencing was performed on a recurrent distal femoral CCC.
  • Matched germline testing was utilized to differentiate somatic from germline alterations.
  • Analysis included variant detection, tumor mutational burden, loss of heterozygosity, karyotyping, and gene expression profiling.

Main Results:

  • The recurrent tumor exhibited classic CCC morphology with no IDH1/2 mutations.
  • Pathogenic loss-of-function variants in COL2A1 and VHL were identified as somatic alterations.
  • Somatic VHL inactivation was confirmed, with decreased VHL mRNA expression and a complex karyotype.

Conclusions:

  • This is the first report of a molecularly profiled CCC with somatic VHL inactivation.
  • The findings expand the genomic understanding of CCC beyond its IDH-wildtype status.
  • VHL pathway dysregulation is suggested as a potential driver of tumorigenesis in a subset of CCC cases.