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• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MS-275 (20h), on genome GRCh38

  ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MS-275 (20h) sample(s). 5 run(s), 5 experiment(s), 5 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002493

• BLUEPRINT release August 2016, ChIP-Seq for CD38-negative naive B cell, on genome GRCh38

  ChIP-Seq data for 9 CD38-negative naive B cell sample(s). 48 run(s), 44 experiment(s), 44 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002524

• BLUEPRINT release August 2016, RNA-Seq for immature conventional dendritic cell - GM-CSF_IL4_T=6_days, on genome GRCh38

  RNA-Seq data for 3 immature conventional dendritic cell - GM-CSF_IL4_T=6_days sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002526

• Young Boost Trial for Breast Cancer patients

  The Young Boost Trial (YBT, YOUNG BOOST / BOOG 2004-01 (Borstkanker) | Kanker.nl investigated the optimal radiation dose for breast cancer patients aged 50 years or younger, treated with breast-conserving therapy (BCT). In this randomized study, participants were assigned to receive either a 26 Gy or a 16 Gy radiation boost, with the primary endpoint being local recurrence. To explore potential predictive biomarkers of treatment response in this patient group, whole exome sequencing (WES) was performed on tumor samples to identify genetic factors that could guide personalized treatment strategies and improve clinical outcomes for these young breast cancer patients.

  Study EGAS50000000797

• A Perioperative Study of Safusidenib in Patients with IDH1-Mutated Glioma

  10 participants with a radiological or pathological diagnosis of WHO Grade 2 lower-grade glioma (LGG) were recruited at a single center starting in December, 2022. Eligibility criteria permitted participants who had undergone prior surgery for WHO Grade 2 LGG, but excluded those with a history of prior radiation or chemotherapy.In Part A of the study, participants underwent an initial craniotomy with tumor biopsy and a lumbar puncture for cerebrospinal fluid (CSF) collection at study entry. Following sample collection, participants received safusidenib at the recommended phase 2 doses of 250 mg twice daily (b.i.d.) for a period of 22–36 days. This was followed by a second craniotomy for maximal safe tumor resection and a repeat lumbar puncture within 5 hours of the final pre-resection dose of safusidenib. Tumor, blood, and CSF samples were collected at both surgical time points for comprehensive translational research.Molecular analyses were performed on samples collected at both time points. These included pharmacokinetics (PK), targeted metabolomics, whole-genome sequencing (WGS) of tumor tissue, single-nucleus RNA sequencing (snRNA-seq), and DNA methylation profiling on all patients. Targeted metabolomics was conducted on samples from 9 participants, while spatial transcriptomics and spatial metabolomics were performed on tumor tissue from 3 participants each. Histone methylation profiling was conducted on samples from 8 participants.

  Study phs003976

• WES of 2 human osteosarcoma and corresponding cell lines

  Progress in the systemic control of osteosarcoma has been limited over the past decades thus indicating the urgent clinical need for the development of novel treatment strategies. Therefore, we have recently developed new preclinical models to study promising novel agents for the treatment of pediatric osteosarcoma. The checkpoint kinase (chk) inhibitor prexasertib (LY2606368) and its salt form (LSN2940930) have recently been shown to be active in adult and pediatric malignancies, including sarcoma. We have now tested the potency of prexasertib in clonogenic survival assays in two new lines of primary patient-derived osteosarcoma cells and in two established osteosarcoma cell lines as a single agent and in combination with cisplatin and the poly ADP-ribose polymerase (PARP) inhibitor talazoparib. Prexasertib alone results in strongly reduced clonogenic survival at low nanomolar concentrations and acts by affecting cell cycle progression, induction of apoptosis and induction of double-stranded DNA breakage at concentrations that are well below clinically tolerable and safe plasma concentrations. In combination with cisplatin and talazoparib, prexasertib acts in a synergistic fashion. Chk1 inhibition by prexasertib and its combination with the DNA damaging agent cisplatin and the PARP-inhibitor talazoparib thus emerges as a potential new treatment option for pediatric osteosarcoma which will now have to be tested in preclinical primary patient derived in vivo models and clinical studies.

  Study EGAS00001003923

• Analysis_of_genomic_integrity_of_disease_corrected_human_induced_pluripotent_stem_cells_by_exome_sequencing

  Induced pluripotent stem (iPS) cells hold great promise for autologous cell transplantation. In order to apply this therapy to monogenic disorder, disease-causing mutations must be corrected prior to transplantation. We generated iPS cells from patients with alpha-1 antitrypsin deficiency, which is caused by homozygous non-synonymous mutation in the SERPINA1 gene. In vitro differentiation of patient-derived iPS cells to hepatocytes showed recapitulation of the disease phenotype. We corrected the mutations by gene targeting using zinc finger nuclease (ZFN) and piggyBac transposon technologies. Our mutation correction is highly accurate. There is no exogenous sequence left behind at the targeted site. The corrected iPS cell-derived hepatocytes were indistinguishable from healthy hepatocyte, suggesting that the corrected gene was fully functional. The genomic integrity was also analyzed by CGH and SNP array, showing no genomic alterations. These are important points to ensure clinical safety as well as functional restoration of the corrected gene. One remaining question is if these corrected iPS cells are clinically safe at the single base-pair level. Recent publications suggested that cancer-related mutations are significantly accumulated during iPS cell propagation. We aim to assess the clinical safety of the corrected iPS cells by using exome sequencing. Outcome from this project would bring iPS cell technology one step closer to clinical applications.

  Study EGAS00001000055

• Inquiring the potential of donor derived CD19-CAR TSCM to treat B-cell malignancies.

  Relapse after allogeneic hematopoietic stem cell transplantation (alloHSCT) is associated with poor survival in advanced B-cell malignancies. Donor-derived CD19-CAR T cells offer the potential for durable remissions but are limited by poor engraftment, expansion, and persistence. We report results from a sequential Phase 1 study (NCT01087294) in which patients with B-cell malignancies relapsed after alloHSCT received either donor-derived standard or stem cell memory T (TSCM)-enriched CD19-CAR T cells without lymphodepletion preconditioning. CAR TSCM cells exhibited delayed but superior expansion and persistence, leading to higher complete remission rates (45% vs. 10%) for doses < 3×108 CAR T cells. Despite their potency, CAR TSCM cells induced milder cytokine-mediated toxicities, driven by IFN-γ rather than IL-6, as observed in standard CAR T cell recipients. While both T cell products differentiated into effectors, only CAR TSCM cells robustly reconstituted the stem-like compartment. Longitudinal clonal-tracking revealed CAR TSCM cells were maintained by clonal succession, whereas standard CAR T cells persisted through maintenance or attrition of early-expanded clones. Unlike standard CAR T cells, CAR TSCM treatment failure was primarily due to tumor- and host-related factors rather than intrinsic T cell defects. These findings establish TSCM cells as a safe and highly effective CAR T cell platform.

  Study EGAS00001008119

• BLUEPRINT September 2016, ChIP-Seq for class switched memory B cell from venous blood, on Genome GRCh38

  ChIP-Seq data for 1 sample(s) for class switched memory B cell from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001002951

• BLUEPRINT September 2016, ChIPmentation for effector memory CD8-positive, alpha-beta T cell, terminally differentiated from venous blood, on Genome GRCh38

  ChIPmentation data for 1 sample(s) for effector memory CD8-positive, alpha-beta T cell, terminally differentiated from venous blood, on Genome GRCh38. 5 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002943

• BLUEPRINT release August 2015, ChIP-Seq for effector memory CD8-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 2 effector memory CD8-positive, alpha-beta T cell sample(s). 10 run(s), 10 experiment(s), 10 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001472

• BLUEPRINT release August 2015, RNA-Seq for CD3-negative, CD4-positive, CD8-positive, double positive thymocyte, on genome GRCh38

  RNA-Seq data for 1 CD3-negative, CD4-positive, CD8-positive, double positive thymocyte sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001483

• BLUEPRINT release August 2015, ChIP-Seq for CD4-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 7 CD4-positive, alpha-beta T cell sample(s). 39 run(s), 39 experiment(s), 39 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001505

• BLUEPRINT release August 2015, RNA-Seq for endothelial cell of umbilical vein (resting), on genome GRCh38

  RNA-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001496

• BLUEPRINT release August 2015, ChIP-Seq for central memory CD4-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 1 central memory CD4-positive, alpha-beta T cell sample(s). 9 run(s), 7 experiment(s), 7 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001499

• BLUEPRINT release August 2015, ChIP-Seq for CD3-positive, CD4-positive, CD8-positive, double positive thymocyte, on genome GRCh38

  ChIP-Seq data for 1 CD3-positive, CD4-positive, CD8-positive, double positive thymocyte sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001503

• BLUEPRINT release August 2015, RNA-Seq for CD14-positive, CD16-negative classical monocyte, on genome GRCh38

  RNA-Seq data for 8 CD14-positive, CD16-negative classical monocyte sample(s). 8 run(s), 8 experiment(s), 8 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001506

• BLUEPRINT release August 2015, RNA-Seq for effector memory CD8-positive, alpha-beta T cell, on genome GRCh38

  RNA-Seq data for 1 effector memory CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001512

• BLUEPRINT release August 2015, ChIP-Seq for cytotoxic CD56-dim natural killer cell, on genome GRCh38

  ChIP-Seq data for 4 cytotoxic CD56-dim natural killer cell sample(s). 17 run(s), 17 experiment(s), 17 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001518

• BLUEPRINT release August 2015, RNA-Seq for mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs), on genome GRCh38

  RNA-Seq data for 3 mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs) sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001520

• BLUEPRINT release August 2015, RNA-Seq for cytotoxic CD56-dim natural killer cell, on genome GRCh38

  RNA-Seq data for 3 cytotoxic CD56-dim natural killer cell sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001521

• BLUEPRINT release August 2015, RNA-Seq for effector memory CD4-positive, alpha-beta T cell, on genome GRCh38

  RNA-Seq data for 1 effector memory CD4-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001526

• BLUEPRINT release August 2015, ChIP-Seq for mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs), on genome GRCh38

  ChIP-Seq data for 3 mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs) sample(s). 18 run(s), 18 experiment(s), 18 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001527

• BLUEPRINT release August 2015, ChIP-Seq for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell, on genome GRCh38

  ChIP-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 7 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001557

• BLUEPRINT release August 2015, RNA-Seq for endothelial cell of umbilical vein (proliferating), on genome GRCh38

  RNA-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001535