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• RNA-seq data from primary AML samples with t(3;8)

  RNA-seq was generated to investigate differences in gene expression between t(3;8) AML and other primary AMLs. Briefly, sample libraries were prepared 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

  Dataset EGAD00001006819

• Whole Exome and Whole Genome Profiling as well Genome-Wide Methylation Profiling from Early to Advanced Chronic Lymphocytic leukemia (CLL), Genome-Wide Methylation Profiling in Monoclonal B Cell Lymphocytosis (MBL)

  Serial whole exome sequencing of samples collected from 21 patients at multiple time points during progression from early to late chronic lymphocytic leukemia (CLL) and one matching non-tumor tissue sample from each patient. Additional whole genome sequencing of samples from 3 selected patients. Genome-wide B cell methylation compared between 5 healthy donors from the same age group as patients, 20 patients with monoclonal B cell lymphocytosis and in serial CLL samples with matching whole exome sequencing. Moreover, genome-wide single-cell RRBS-profiling of B cells from one healthy donor and from one patient with CLL was performed using a protocol newly developed by the A. Meissner group.

  Study phs001431

• Neo-CheckRay

  Patients with oestrogen receptor-positive (ER+), HER2-negative, early breast cancer (BC) have low pathological complete response (pCR) rates following neoadjuvant chemotherapy (NACT). Phase 3 trials showed that adding an anti-PD-1 immune checkpoint inhibitor (ICI) improves pCR, but there was less benefit in the PD-L1 negative tumours, characterised by an immune “cold” tumour microenvironment (TME). We hypothesized that immune-modulating stereotactic body radiation therapy (iSBRT) could enhance treatment response by reprogramming the immune deprived TME in early ER+/HER2- BCA. We conducted a phase 2, randomized, multicentre trial evaluating NACT plus iSBRT, with or without durvalumab (anti-PD-L1) and with or without oleclumab (anti-CD73) in 147 patients with high-risk, early, ER+/HER2- breast cancer patients.

  Study EGAS50000001777

• Hematopoietic differentiation at single-cell resolution in NPM1-mutated AML

  To investigate the relationship between somatic mutations and phenotypic hematologic differentiation at the single-cell level, we used a droplet-based multi-omics single-cell platform on eleven NPM1-mutated AML diagnostic samples. We developed a bioinformatics framework to perform phylogeny-driven genotype correction, that allowed us to study 52 103 single cells. Intra-leukemic genetic heterogeneity was detectable in all patients, including a branched architecture in nine of them, always owing to co-occurring signaling mutations. We identified two groups of NPM1-mutated AML, one characterized by a progenitor immunophenotype and a second one with a predominant monocytic differentiation. We also identified various degrees of intra-leukemic immunophenotype heterogeneity, sometimes associated with strong genetic/phenotype correlations.

  Study EGAS00001006565

• Neuroblastoma tumor heterogeneity and cell plasticity (from patients)

  Two cell identities, noradrenergic and mesenchymal, have been characterized in neuroblastoma cell lines according to their epigenetic landscapes relying on specific core regulatory circuitries of transcription factors. Yet, their relationship and relative contribution in patient tumors remain to be defined. Here, we document a spontaneous plasticity between the noradrenergic and mesenchymal identities in a subset of cell lines. Strikingly, mesenchymal neuroblastoma cells revert to a noradrenergic phenotype in vivo. Consistently, tumor cells with a mesenchymal identity are detected in single-cell transcriptomic analyses of neuroblastoma tumors and PDX models. Our data also highlight neuroblastoma intra-tumor heterogeneity with the co-existence of distinct tumor populations, including sympathoblast-like and chromaffin-like cells suggesting that neuroblastoma cells arise from a common sympatho-adrenal progenitor.

  Study EGAS00001005322

• The University of Hong Kong Colon Cancer Organoids Genomics Study Data Access Committee

  Dac EGAC00001001405

• Data Access Committee of the Department of Molecular Neurology, UKEr

  Dac EGAC00001002455

• The Chinese University of Hong Kong (CUHK) Circulating Nucleic Acids Research Group (CNARG)

  Dac EGAC00001002648

• Tracking the evolution of esophageal squamous cell carcinoma under dynamic immune selection by multi-omics sequencing

  Dac EGAC00001002881

• DAC - Dept. of Pathology LUMC

  DAC of the Department of Pathology of Leiden University Medical Center

  Dac EGAC50000000376