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• Whole genome sequencing of an individual's genomic DNA and that of its lymphoblastoid cell line.

  The genetic consequences of cellular transformation by Epstein-Barr-Virus were assessed by comparing whole genome sequences of the original genome (before transformation) and the genome after transformation.

  Dataset EGAD00001000693

• MCL Multiome

  This dataset contains the raw sequencing data (Runs) from the 10x Genomics single-cell Multiome Experiments which belong to the MCL group

  Dataset EGAD00001009819

• RNA-seq data from the tumor samples of head and neck cancer patients

  This dataset contains paired-end RNA sequencing data (2x50 bp) from the primary tumors and the recurrences/metastases of 6 head and neck cancer patients.

  Dataset EGAD00001011279

• PCNSL single cell dataset

  Mononuclear cells were isolated as cell suspensions by dissociation in a BD Horizon™ Dri Tumor & Tissue Dissociation Reagent (BD Biosciences) using a gentleMACS dissociator (Miltenyi Biotec). A totalseq-C antibody cocktail (Biolegend) was used, and the cell suspensions were diluted to a concentration of 1,000 cells/μL. Library sequencing was performed using the DNBSEQ-G400 (MGI Tech), Illumina HiSeq 2000, or Illumina NovaSeq 6000 5 (Illumina). The FASTQ files were aligned to the 10x provided reference genome using 10x Genomics Cell Ranger software v7.1.0 to create unique molecular identifier count tables of gene expression of the samples.

  Dataset EGAD50000000685

• RNA-seq data from 27 glioblastoma samples

  27 Fresh frozen tissue specimens were crushed by mortar and pestle, homogenized using the QIAShredder kit (Qiagen), and genomic DNA and total RNA were extracted using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer’s instructions. RNA libraries were synthesized using 200 ng of total RNA using the Ilumina TruSeq Stranded RNA LT Sample Prep Kit (Illumina), and subsequently sequenced on the NextSeq550 platform to a read depth of 80 million clusters and 160 million paired end reads (75 bp X 75 bp) using V2 chemistry.

  Dataset EGAD00001008362

• Oncogenic cooperation between the TCF7-SPI1 fusion and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia.

  In this study we investigate the role of TCF7-SPI1 fusions, more specifically in cooperation with RAS mutations. We make use of patients samples. This study contains paired-end RNA sequencing of the patients, Oxford Nanopore Technologies (ONT) sequencing, single cell RNA sequencing and RNA sequencing of treatment with inhibitors of these samples.

  Study EGAS00001005097

• A Comprehensive Genetic Study of Classical Hodgkin Lymphoma Using Circulating Tumour DNA

  This study on classical Hodgkin lymphoma (cHL) used advanced methods to analyse circulating tumour DNA (ctDNA) in 297 cases, offering insights into its genetic landscape and linking it to disease pathophysiology and clinical progression. Key findings include the identification of whole genome duplication as a predictor of poor chemotherapy response. Additionally, a highly recurrent somatic expression quantitative trait locus of the BCL6 gene was discovered, implicating regulatory mutations in cHL pathophysiology and highlighting BCL6 as both a vulnerability and therapeutic target. Consensus clustering identified two cHL subtypes distinguished by the underlying mechanisms of genetic instability, rather than by specific genetic mutations or EBV infection. The study also linked the number and clonality of neoantigens with tumour microenvironment and response to checkpoint blockade. Finally, our results suggested ctDNA analysis as a tool to distinguish ambiguous PET/CT-positive lesions persisting after treatment, aiming to reduce unnecessary medical interventions.

  Study EGAS50000000873

• Single-cell atlas of multiple myeloma and precursor diseases

  Single cell profiling of small cohorts of myeloma precursor disease patient samples including monoclonal gammopathy of unknown significance and smoldering multiple myeloma have shown diverse evolutionary patterns and immune changes that occur early in the disease process. Using scRNAseq and scBCRseq in a large cohort of fifty-three patients with myeloma precursor disease in comparison with myeloma and normal donors we describe the early genomic drivers of malignant transformation and describe their divergent clonal expansion in hyperdiploid compared to non-hyperdiploid samples. We describe intra-patient heterogeneity with potential therapeutic implications as well as the distinct evolution patterns (linear/branching) from myeloma precursor disease to myeloma. Finally, we describe the unique adaptations of the microenvironment as a response to distinct genomic changes in myeloma cells. These results further our knowledge to characterize myeloma precursor disease evolution, inform individual patient progression risk stratification and identify potential biomarkers that could be clinically exploited.

  Study EGAS00001006694

• Genomic insights into the population history of the Resande or Swedish Travellers

  Study EGAS00001006176

• Single-Cell Analysis of CD19-Specific CAR T Cell Treatment of Relapsed/Refractory CD19+ Acute Lymphoblastic Leukemia

  By leveraging single-cell transcriptome and T cell receptor (TCR) sequencing, we aimed to track the transcriptional signatures of chimeric antigen receptor (CAR) T cell clonotypes throughout the course of treatment and furthermore identify molecular patterns leading to potent CAR T cell cytotoxicity. The data presented in this study encompass blood and bone marrow samples from patients ≤ 21 years of age with relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) participating in the SJCAR19 phase I/II clinical trial (NCT03573700). In brief, patients enrolled in the clinical trial received either 1 x 10^6 (dose level 1) or 3 x 10^6 (dose level 2) per kilogram of body weight following successful generation of autologous CAR T cell products and lymphodepleting chemotherapy. Peripheral blood was drawn from each participant every week until week 4 post-infusion, at week 6 or 8, and month 3 or 6 if feasible. At week 4 post-infusion, blood marrow was also collected from participants. Total T cells (CD3+) were sorted from each post-infusion sample, as well as the pre-infusion CAR T cell products, and processed through 10x Genomics’ single-cell gene expression and V(D)J sequencing platform using the standard protocol. We identified a unique and unexpected transcriptional signature in a subset of pre-infusion CAR T cells that shared TCRs with post-infusion cytotoxic effector CAR T cells. Functional validation of cells with even a subset of these pre-effector markers demonstrated their immediate cytotoxic potential and resistance to exhaustion. The data deposited into dbGaP include all raw single-cell expression and V(D)J sequencing generated from samples obtained from 16 study participants.

  Study phs002966