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| Status |
Public on Sep 29, 2024 |
| Title |
OncoScan™ CNV FFPE Assay data for desmoid tumors |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
SNP genotyping by SNP array
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| Summary |
Desmoid tumors are bland fibroblastic tumors with little histologic variation in different regions of the tumor. While desmoid tumors do not metastasize, they have a high rate of local recurrence after complete resection and no reliable predictors of clinical behavior exist. The presence of molecular intra- and inter-tumor heterogeneity has been well established in other, higher grade, sarcomas but little is known about molecular variability within histologically bland lesions. In this study, we sought to examine the extent of intra- and inter-tumoral clonal heterogeneity of desmoid tumors, which may contribute to their pathogenesis and possible relapse. We performed analysis of DNA methylation, DNA copy number alterations, point mutations and gene expression on 24 specimens from different areas from primary and recurrent desmoid tumors from 3 patients (7-9 specimens per patient). The studies showed a remarkable heterogeneity of DNA methylation, DNA copy number alterations, point mutations or gene expression in different regions in primary or recurrent tumors in each patient. We discovered the evidence for subclonal alterations in different areas of individual tumors. Among the four types of data, the transcriptomic profiles showed the highest degree of variability within tumors and between different tumors from the same patient. Gene expression signatures associated with favorable and unfavorable outcome were detected in different regions within the same tumor. This study shows an unexpected degree of intra- and inter-tumor heterogeneity in desmoid tumors. Our analysis indicates that even in this histologically monotonous lesion, molecular analysis of a single tumor biopsy may underestimate the magnitude of molecular alterations. We demonstrate that molecular intra- and inter-tumor heterogeneity is an important consideration in drug development and validation of prognostic and predictive biomarkers for these tumors.
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| Overall design |
OncoScan™ CNV FFPE Assay was performed according to the manufacturer's directions on DNA extracted from FFPE desmoid tumor specimens
Genomic DNA from 23 desmoid tumor specimens was used for genome-wide copy number and allelic ratio profiling with the OncoScan FFPE Assay (Affymetrix, Santa Clara, CA). Sample preparation and hybridization were performed by the Affymetrix Research Services Laboratory (Affymetrix, Santa Clara, CA). Results were visualized and analyzed with NexusExpress for OncoScan3 software (BioDiscovery, El Segundo, CA).
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| Contributor(s) |
Przybyl J |
| Citation missing |
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| Submission date |
Dec 13, 2023 |
| Last update date |
Sep 30, 2024 |
| Contact name |
Joanna Przybyl |
| E-mail(s) |
jprzybyl@stanford.edu
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| Organization name |
Stanford University
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| Department |
Department of Pathology
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| Street address |
300 Pasteur Drive
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| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL21558 |
[OncoScan_CNV] Affymetrix OncoScan CNV FFPE Assay |
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| Samples (23)
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| Relations |
| BioProject |
PRJNA1052113 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE250149_RAW.tar |
558.2 Mb |
(http)(custom) |
TAR (of CEL, OSCHP) |
| Raw data provided as supplementary file |
| Processed data provided as supplementary file |
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