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• ChIP sequencing in Cancer Cell Lines

  The project is to evaluate the genomic binding sites of the histone demethylase JARID1C. This gene was recently identified in CGP as a novel recessive cancer gene in human renal cell carcinoma.

  Dataset EGAD00001001453

• RNA-seq study of longitudinal blood cell samples drawn from children at risk of type 1 diabetes

  The appearance of type 1 diabetes (T1D)-associated autoantibodies is the first and only measurable parameter to predict progression toward T1D in genetically susceptible individuals. However, autoantibodies indicate an active autoimmune reaction, wherein the immune tolerance is already broken. Therefore, there is a clear and urgent need for new biomarkers that predict the onset of the autoimmune reaction preceding auto-antibody positivity or reflect progressive b-cell destruction. Here we report the mRNA sequencing-based analysis of 306 samples including fractionated samples of CD4+ and CD8+ T cells as well as CD4, CD8 cell fractions and unfractionated PBMC samples longitudinally collected from seven children who developed beta-cell autoimmunity (case subjects) at a young age and matched control subjects.

  Dataset EGAD00001005767

• Somatic mutation and clonal evolution in the human bladder_WGS (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-genome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006113

• Somatic mutation and clonal evolution in the human bladder Novaseq (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-genome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006116

• Somatic mutation and clonal evolution in the human bladder_WES (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-exome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006115

• The Transcriptional Landscape of SHH Medulloblastoma

  To further understand the biology of Sonic hedgehog medulloblastoma and its molecular subtypes, we studied 250 human Shh-MB using strand-specific RNA sequencing. We identified novel alterations within the cAMP dependent pathway and found that 18% of tumors have genetic events that directly target the abundance and/or stability of MYCN. We also discovered an extensive network of fusions in focally amplified regions, and several loss-of-function fusions in tumor suppressor genes PTCH, SUFU and NCOR1. Molecular convergence on a core of specific genes by nucleotide variants, copy number aberrations, and gene fusions highlights key roles of specific pathways in the pathogenesis of Sonic hedgehog medulloblastoma.

  Dataset EGAD00001006305

• Paired WES and low coverage WGS of osteosarcoma

  Longitudinal genome-sequencing analysis of 12 patients with metastatic or refractory osteosarcoma. The study was approved at the University Hospital Basel, following the approval of the ethical committee for mutational analysis of anonymized samples (“Ethikkommission beider Basel” ref. 274/12). Informed consent was obtained from all 12 patients. All tumor samples were evaluated by an experienced bone pathologist to confirm the diagnosis. WES and low coverage WGS are aligned against the reference genome GRCh37. More details in the associated publication.

  Dataset EGAD00001007509

• RNA-sequencing of a representative cohort of 209 AML cases

  Sample libraries were prepped using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina) and aligned against the human genome (hg19) using STAR v2.5.4b2.

  Dataset EGAD00001007581

• Sequence Data from the phase 2 PrE0505 trial of Durvalumab with First Line Platinum-Pemetrexed for Unresectable Pleural Mesothelioma

  Dataset comprises of 84 bam files from exome sequencing data, including 40 tumor-normal pairs and 4 normal files. Each sample is numbered by the patient case ID such as 135, 156 and so on. The filenames are suffixed with "_tumor" and "_normal" to indicate tumor and normal bam files respectively.

  Dataset EGAD00001008016

• Deep targeted DNA sequencing dataset for the study "Molecular characteristics in Burkitt lymphoma over age groups"

  We performed deep targeted DNA sequencing with a panel of 134 selected cancer-related genes previously identified to be recurrently mutated in BL/B-AL. A Nextera rapid capture custom kit was designed using the Illumina DesignStudio. For every gene, all regions in which previous mutations had been described were covered. For 40 of these genes, the entire coding sequence was covered. Targeted deep sequencing was performed on a MiSeq-Sequencer using MiSeq Reagent Kit v2 (300 cycle) with 24 samples per run. There are 396 samples in this targetedDNAseq-dataset with 298 tumors (288 patients and 10 cell lines) and 98 normals. There are 132 female, 262 male, and 2 unknown gender samples in this dataset.

  Dataset EGAD00001007708