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Whole genome sequencing (bam files) of 5 samples of myxofibrosarcoma and 5 matched pairs

ABSTRACT: Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the whole genome sequence was performed.

PROVIDER: EGAS00001005444 | EGA |

REPOSITORIES: EGA

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Whole exome sequencing (bam files) of 55 samples of myxofibrosarcoma and 44 matched pairs

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Targeted-capture sequencing (bam files) of 81 samples of myxofibrosarcoma and 44 matched pairs

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Profiling DNA copy number alterations of myxofibrosarcomas with NimbleGen array CGH chips

Project description:Characterized by a wide histological spectrum, myxofibrosarcoma ranges from deceptively bland-appearing lesions to frankly pleomorphic sarcomas, representing a suitable model to elucidate the molecular aberrations in multistep disease progression. To explore cancer-associated genes of myxofibrosarcoma, ultrahigh-resolution array comparative genomic hybridization (aCGH) was used to profile DNA copy number alterations in myxofibrosarcoma tumor samples and cell lines. Along with normal reference DNA, 12 tumor samples and 2 cell lines (NMFH-1, OH931) of human myxofibrosarcoma were extracted for genomic DNAs, which were subjected to manufacturer’s (NimbleGen Inc) outsourcing service of DNA labeling, hybridization, and normalization of data obtained from 385K oligonucleotide array CGH chips.

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Project description:Global gene expression analysis of desmoplastic fibroblastoma (DF) and histologically similar tumors. FOSL1 is identified as a candidate target gene for the 11q12 rearrangments in DF. RNA was extracted from 3 frozen desmoplastic fibroblastoma (DF) biopsies and hybridized onto Affymetrix Human Gene 1.0 ST arrays. RNA from 6 myxofibrosarcoma (MFS), 6 desmoid fibromatosis (DFM), 5 solitary fibrous tumor (SFT) and 17 low-grade fibromyxoid sarcomas (LGFMS) were used as controls. The control dataset has been previously published and is available in the GEO database under Series accession GSE24369. The complete dataset representing: (1) the 3 desmoplastic fibroblastoma Samples and (2) the 34 control Samples from Series GSE24369 (re-processed using RMA), is linked below as a supplementary file.

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Project description:Hungarian BAM files

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