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Eval_GEMCODE DoubleMinuteBT WGS1 - samples

ABSTRACT: Whole Genome Sequencing files accompanying the paper titled "Structure and evolution of double minutes in diagnosis and relapse brain tumors". Please read the paper for more details.

PROVIDER: EGAD00001004337 | EGA |

REPOSITORIES: EGA

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Structure and evolution of double minutes in diagnosis and relapse brain tumors

Project description:Double minute chromosomes are extrachromosomal circular DNA fragments frequently found in brain tumors. To understand their evolution, we characterized the double minutes in paired diagnosis and relapse tumors from a pediatric high-grade glioma and four adult glioblastoma patients. We determined the full structures of the major double minutes using a novel approach combining multiple types of supporting genomic evidence. Among the double minutes identified in the pediatric tumor, only one carrying EGFR was maintained at high abundance in both samples, whereas two others were resent in only trace amounts at diagnosis but abundant at relapse, and the rest were found either in the relapse sample only or in the diagnosis sample only. For the EGFR-carrying double minutes, we found a secondary somatic deletion in all copies at relapse, after erlotinib treatment, but this was rare at diagnosis, suggesting potential resistance to the EGFR inhibitor. This mutation caused an in-frame RNA transcript to skip exon 16, a novel transcript absent in EST database and in about 700 brain tumors that we reviewed. We observed similar patterns involving longitudinal copy number shift of double minutes in another four pairs (diagnosis / relapse) of adult glioblastoma. Overall, in three of five paired tumor samples, we found that although the same oncogenes were amplified at diagnosis and relapse, they were amplified on different double minutes. Our results suggest that double minutes readily evolve, increasing tumor heterogeneity rapidly. Understanding patterns of double minute evolution can shed light on future therapeutic solutions to brain tumors carrying such variants.

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PCGP2 RMS WGBS - samples

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Project description:RNA-Seq files accompanying the paper titled "Somatic Histone H3 Mutations in Diffuse Intrinsic Pontine Gliomas and Non-Brainstem Paediatric Glioblastomas".

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Steroids-producing adrenocortical nodules (bulk RNA-seq)

Project description:This data was used in the analysis of the article titled ‘Steroids-producing adrenocortical nodules: a novel two-layered structure as a precursor lesion of cortisol-producing adenoma’.

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