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OncoScan™ CNV FFPE Assay data for desmoid tumors

ABSTRACT: OncoScan™ CNV FFPE Assay data for desmoid tumors

PROVIDER: PRJNA1052113 | ENA |

REPOSITORIES: ENA

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OncoScan™ CNV FFPE Assay data for desmoid tumors

Project description: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.

2024-09-29 | GSE250149 | GEO

Oncoscan™ Affymetrix array for pure LCIS, LCIS associated with ILC (invLCIS) and ILC

Project description:Oncoscan™ Affymetrix array was performed by Affymetrix using DNA extracted from macrodissected FFPE samples

2017-03-08 | GSE88909 | GEO

Affymetrix OncoScan FFPE Array array data from Li-Fraumeni Syndrome tumors

Project description:Loss of heterzygosity in TP53 Affymetrix OncoScan FFPE arrays were performed according to the manufacturer's directions on DNA extracted from tumors Copy number analysis of Affymetrix OncoScan FFPE array was performed for two osteosarcoma lung metastases, one lung adenocarcinoma, one meningioma, one pleomorphic sarcoma

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Affymetrix OncoScan FFPE Array array data from Li-Fraumeni Syndrome tumors

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OncoScan CNV array data for PNBX cohort

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Affymetrix OncoScan FFPE Microarray data for Malignant Pleural Mesothelioma Samples

Project description:For establishing a live-cell biobank of Malignant Pleural Mesothelioma (MPM) samples, cultures of two MPM patients were compared to the original tumor tissue using Affymetrix OncoScan Microarrays for genome-wide CNV and LOH detection.

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Cross-laboratory validation of the OncoScan FFPE Assay, a multiplex tool for whole genome tumour profiling

Project description:162 FFPE samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan¬ FFPE assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations.

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OncoScan CNV SNP array data for MNG/PTC samples

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Oncoscan for HER2 copy number assessment

Project description:Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues. Copy number analysis using Affymetrix Oncoscan arrays was performed for 29 primary breast cancers

2016-07-01 | E-GEOD-83916 | biostudies-arrayexpress

Oncoscan for HER2 copy number assessment

Project description:Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues.

2016-07-01 | GSE83916 | GEO

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