Ce97e754-0a3b-4576-901b-61c4bb5ad99b - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001008278 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:We performed whole exome sequencing in DIPG and hemispheric HGG.
| EGAD00001008279 | EGA
Project description:Glioma study (gene expression and CGH): Brain tumours are the most common solid tumors in children and have the highest mortality rate of all solid pediatric tumours. Despite advances in multimodality therapy, children with high-grade gliomas invariably have an Overall Survival (OS) around 20% at 5 years. There is growing evidence that the biological knowledge and the histo-prognostic classifications used for the management of adult HGG may not fully apply to children. Interobserver variability and specificity of pediatric tumors with respect to the World Health Organization (WHO) classification have lead to a high rate of misclassification in multi-institutional studies. From 90 biopsies of children with HGG (High Grade Glioma), comprising 37 DIPG (Diffuse Infiltrating Pontine Glioma), 73 extracted RNA have been hybrized on Agilent 4x44K GE arrays and 71 extracted DNA have been hybrized on Agilent 44K and 4x44K CGH arrays. The dataset contains raw data files from Feature Extraction. Genomic data were jointly analysed with clinical and histological data comprising: date_of_diagnosis, date_of_last_news, WHO_grade, deceased_at_median_survival_time, deceased_at_2years, localization of the tumour in brain, gadolinium_T1_inf_T2. A specific analysis was performed on DIPG.
2012-02-22 | E-TABM-1107 | biostudies-arrayexpress
Project description:Overall paediatric high grade glioma (pHGG) has a poor prognosis, in part due to the lack of understanding of the underlying biology. We therefore used high resolution 244k oligo array comparative genomic hybridisation (oligo aCGH) (Agilent Technologies) to analyse DNA from 38 formalin-fixed paraffin embedded pHGG samples, including 13 DIPG (ten pre-treatment samples and three post-mortem). The pattern of gains and losses were distinct from those seen in HGG arising in adults. In particular we found 1q gain in 22% of our cohort compared to 9% in adults. Homozygous loss at 8p12 was seen in 6/38 (15%) of pHGG. This deletion has not been previously reported in adult or paediatric high grade gliomas. The minimal deleted region is of the gene ADAM3A and homozygous deletion of ADAM3A was confirmed by quantitative real time PCR (qPCR). This novel homozygous deletion of ADAM3A in pHGG merits further study. Loss of CDKN2A/CDKN2B was seen in 4/38 (10%) samples by oligo a CGH, confirmed by FISH on TMAs and was restricted to supratentorial tumours. Amplification of the 4q11-13 region was detected in 8% of cases and included PDGFRA and KIT, subsequent qPCR analysis was consistent with amplification of PDGFRA. MYCN amplification was seen in 2/38 samples (5%) and was shown to be significantly associated with anaplastic astrocytomas (p=0.03). Overall DIPG shared similar spectrum of changes to supratentorial HGG with some notable differences including high frequency of 17p loss and 14q loss and lack of CDKN2A/CDKN2B deletion. To our knowledge, this study examines the largest DIPG cohort to date using high-throughput genetic techniques. 38 high grade glioma samples including 13 DIPG (ten pre-treatment samples and three post-mortem) analysed by Agilent 244K array CGH. Samples BSG 1, 2, 3, 5, 6, 7, 8, 9, 10 and 11 are the ten pre-treatment DIPG samples. Samples BSG 4, 12 and 13 are the three post-treatment DIPG samples.
2010-12-01 | E-GEOD-21420 | biostudies-arrayexpress
Project description:This single cell RNA-seq experiment was performed to quantify DLL3 expression in tumor cells in small cell lung cancer patients.Tumors were rapidly dissociated after the surgical procedure using the Miltenyi Biotec Human Tumor Dissociation kit (cat# 130-095-929). Libraries were constructed using the VDJ NextGEM v1.1 10x Genomics Chromium kit according to the manufacturer's instructions. Samples were sequenced on a NextSeq 550 sequencer (Illumina). Corresponding EGA study number: EGAS50000001400, EGA dataset number: EGAD50000002034.
2025-12-11 | E-MTAB-16412 | biostudies-arrayexpress
Project description:To study the effect of ONC201 treatment on DIPG-VII, DIPG-IV, and DIPG-XIII cell lines, we treated cell lines and performed RNA-Seq analysis.
2023-12-31 | GSE239939 | GEO
Project description:This single cell RNA-seq experiment was performed to quantify DLL3 expression in circulating tumor cells in small cell lung cancer patients to predict response to tarlatamab treatment. CTCs enriched from the blood of three SCLC patients prior or post tarlatamab treatment using the CTC-iChip followed by magnetic depletion of RBCs were processed with the 10x Genomics Chromium platform (Chromium GEM-X Single Cell 3' Kit v4) and sequenced on a NextSeq 2000 system. Corresponding EGA study number: EGAS50000001401, EGA dataset number: EGAD50000002035
2025-12-11 | E-MTAB-16413 | biostudies-arrayexpress
Project description:In the past decades, the incidence of esophageal adenocarcinoma has increased dramatically in Western populations. Better understanding of disease etiology along with the identification of novel prognostic and predictive biomarkers are urgently needed to improve the dismal survival probabilities. Here, we performed comprehensive RNA (both coding and non-coding) profiling in various samples from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were included. In total, this comprehensive dataset consists of 102 RNA-seq libraries from 51 samples. The raw data for this study have been deposited to the controlled access archive EGA under submission EGAS00001004939.
2022-01-01 | E-MTAB-10002 | biostudies-arrayexpress
Project description:In the past decades, the incidence of esophageal adenocarcinoma has increased dramatically in Western populations. Better understanding of disease etiology along with the identification of novel prognostic and predictive biomarkers are urgently needed to improve the dismal survival probabilities. Here, we performed comprehensive RNA (both coding and non-coding) profiling in various samples from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were included. In total, this comprehensive dataset consists of 102 RNA-seq libraries from 51 samples. The raw data for this study have been deposited to the controlled access archive EGA under submission EGAS00001004939.
2022-01-01 | E-MTAB-10005 | biostudies-arrayexpress
Project description:In the past decades, the incidence of esophageal adenocarcinoma has increased dramatically in Western populations. Better understanding of disease etiology along with the identification of novel prognostic and predictive biomarkers are urgently needed to improve the dismal survival probabilities. Here, we performed comprehensive RNA (both coding and non-coding) profiling in various samples from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were included. In total, this comprehensive dataset consists of 102 RNA-seq libraries from 51 samples. The raw data for this study have been deposited to the controlled access archive EGA under submission EGAS00001004939.
2022-01-01 | E-MTAB-10004 | biostudies-arrayexpress
Project description:CTCF ChIP-seq of 39 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011059 (dataset).
2023-08-31 | E-MTAB-13117 | biostudies-arrayexpress