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• Whole Exome Sequencing (WES) data of PERFECT trial

  Whole exome sequencing (WES) data of patients with resectable esophageal adenocarcinoma treated with neoadjuvant atezolizumab and chemoradiation (PERFECT). 78 matched samples (Tumor-Normal) from 39 patients with resectable esophageal adenocarcinoma of the PERFECT trial. Whole exome sequencing performed for mutation detection analysis.

  Dataset EGAD50000001153

• NKI-AvL OpACIN DNA-seq of stage III melanoma patients

  The dataset “NKI-AvL OpACIN DNA-seq of stage III melanoma patients" includes 2 x 18 normal and 2 x 18 tumor FASTQ files from paired-end whole exome sequencing on Illumina HiSeq2500 for 18 stage III melanoma patients.

  Dataset EGAD00001004217

• BLUEPRINT DNA methylation profiles of human hematopoietic progenitors

  DNA methylation was analyzed for stem/progenitor cell types and terminally differentiated cell types of the human blood lineage (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3, MK, CD4+ Tcell, CD8+ Tcell, Bcell, NK, Neut, Mono).

  Dataset EGAD00001002732

• Data set for pan.met study

  The dataset referenced by EGA Study ID EGAS00001004208 includes 20 human exome sequencing data and 11 human RNA sequencing data from tumor or normal tissues. Each sequencing data includes two pair-end short read files in fastq format.

  Dataset EGAD00001005957

• Transcription factor binding in human monocyte differentiation

  This dataset consists of ChIP-seq data data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to mRNA transfection for PU.1, IRF4, and EGR2. In total, it the data set includes 18 samples.

  Dataset EGAD00001006602

• PacBio HiFi sequencing of telobait-captured DNA from 48 patients

  PacBio HiFi sequencing was performed on 48 barcoded patients' genomic DNA after a telobait-capture protocol to enrich for telomeric regions. The sequencing reads of each patient were de-multiplexed and presented as patient-specific PacBio CCS BAM files.

  Dataset EGAD00001008626

• Dataset for LCPlus_WGS

  WES/WGS sequencing data of 56 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009275

• Bulk RNA from sorted CD8+ T cells after 48h co-culture with human Mito-DsRed MSCs.

  For human samples, total cellular RNA was isolated from post-sorted Mito+ and Mito CD8+ cells using the RNeasy Mini Kit (Qiagen). Stranded RNA libraries were created using SMARTSeq Stranded.

  Dataset EGAD00001011082

• HipSci whole exome sequencing for embryonic stem cell control lines

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we use commercially available embryonic stem cell lines as control samples against which to compare HipSci's iPS cell lines. We performed whole exome sequencing using Agilent whole exome pulldown method.

  Study EGAS00001001726

• Timing the Philadelphia chromosome and trajectory to chronic myeloid leukaemia

  We sequence >1000 whole genomes from 9 patients with CML, providing the largest sequencing dataset for this cancer. We reconstruct phylogenetic trees using somatic mutations and infer BCR::ABL1 timing and tumour growth rates. We correlate mutation landscapes and clonal trajectories with clinical features.

  Dataset EGAD00001015353

• DNA methylation of peripheral blood leukocytes from patients with Li-Fraumeni syndrome

  Genomic DNA (~ 1 μg) from LFS patients was treated using sodium bisulfite (Qiagen) converting unmethylated cytosine to uracil but leaving methylated cytosine intact. These samples were then hybridized to the HumanMethylation450 BeadChip or HumanMethylationEPIC BeadChip from Illumina at the Centre for Applied Genomics (TCAG) at the Hospital for Sick Children using the manufacturer’s recommended protocol.

  Study EGAS00001007075

• Dataset of 2485 CD8 T cells from non-muscle-invasive bladder cancer patients in context of BCG treatment

  FASTQ files from scRNAseq (smartseq2 protocol) from 2485 CD8 T cells from 4 non-muscle-invasive bladder cancer patients who received BCG treatment (induction treatment of 6 weekly instillations). Concerning the 'phenotype' column in metadata : pre-treatment samples include tumor samples ('Tumor') and normal adjacent bladder tissue ('Extratumor'). For post-treatment samples : no residual tumor was found in the bladder of the 4 patients after the BCG treatment . The post-treatment samples with 'Tumor' as phenotype denote samples from macroscopically suspect zones, but with microscopically no tumor detected.

  Dataset EGAD50000002007

• Aggregated panel-seq VCF for initial cohort screened for BoB

  Aggregated VCF file from cancer genes panel seq for the initial (n=500) cohort of solid tumors screened for the Basket of Baskets study

  Dataset EGAD00001008437

• CD8-targeted IL-2 unleashes tumor-specific immunity in human cancer tissue by reviving the dysfunctional T cell pool

  Tumor-specific CD8+ T cells are key effectors of antitumor immunity but are often rendered dysfunctional in the tumor microenvironment. Immune checkpoint blockade can restore antitumor T cell function in some patients, however most do not respond to this therapy, often despite T cell infiltration in their tumors. We here explored a CD8-targeted IL-2 fusion molecule (CD8-IL2) to selectively reactivate intratumoral CD8+ T cells in patient-derived tumor fragments. Treatment with CD8-IL2 broadly armed intratumoral CD8+ T cells with enhanced effector capacity, thereby specifically enabling reinvigoration of the dysfunctional T cell pool to elicit potent immune activity. Notably, the revival of dysfunctional T cells to mediate effector activity by CD8-IL2 depended on simultaneous antigen recognition and was quantitatively and qualitatively superior to that achieved by PD-1 blockade. Finally, CD8-IL2 was able to functionally reinvigorate T cells in tumors resistant to anti-PD-1, underscoring its potential as a novel treatment strategy for cancer patients.

  Study EGAS00001007712

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  To elucidate the regulation of B cell recptor repertoire in B cell subsets and its contribution to autoimmune diseases, B cell subsets from 36 Systemic Lupus Erythematosus(SLE), 90 Systemic Sclerosis(SSc), 85 Myositis(IIM), 21 Mixed Connective Tissue Disease(MCTD), 18 Sjogren's syndrome(SjS), 27 Rheumatoid Arthritis(RA), 23 Behcet's disease(BD), 18 Adult Onset Still���s Disease(AOSD), 24 ANCA-associated Vasculitis(AAV), 16 Takayasu���s Arteritis(TAK) and 137 healthy controls(HC) were collected (Naive_B, USM_B, SM_B, DN_B, Plasmablast. RNA-seq and BCR-mapping was performed with each B cell subset samples.

  Study JGAS000485

• Non-viral precision T cell receptor replacement for personalized cell therapy

  The T cell receptor (TCR) provides the fine specificity of T cells to recognize mutations in cancer cells 1-3. We developed a clinical-grade approach based on CRISPR/Cas9 non-viral precision genome editing to simultaneously knock-out the two endogenous TCR genes, TCRα (TRAC) and TCRβ (TRBC), and insert in the TRAC locus the two chains of a neoantigen-specific TCR (neoTCR), isolated from the patient’s own circulating T cells using a personalized library of soluble predicted neoantigen-HLA capture reagents. Sixteen patients with refractory solid cancers received up to three distinct neoTCR-transgenic cell products, each expressing a patient-specific neoTCR, in a cell dose-escalation, first-in-human phase 1 clinical trial (NCT03970382). One patient had grade 1 cytokine release syndrome, and one grade 3 encephalitis. All had the expected side effects from the lymphodepleting chemotherapy. Five patients had stable disease, and the other 11 had disease progression as best response on therapy. NeoTCR-transgenic T cells were detected in tumour biopsies post-infusion at frequencies higher than the native TCRs pre-infusion. This study demonstrates the feasibility of isolating and cloning multiple TCRs recognizing mutational neoantigens, the simultaneous knock-out of the endogenous TCR and knock-in of the neoTCRs using single-step, non-viral precision genome editing, the manufacturing of neoTCR engineered T cells at clinical grade, the safety of infusing up to three gene edited neoTCR T cell products, and the ability of the transgenic T cells to traffic to the patients’ tumours.

  Study EGAS00001006898

• RNA sequencing of Ewing sarcoma and CIC-DUX4 sarcoma

  RNA sequencing of a collection of 6 Ewing sarcoma and 3 CIC-DUX4 sarcoma tumoroids plus 3 matched patient tumors. Tumoroids were established from digested patient tumor material as 3D culture in Matrigel. After 2-3 month of growth, RNA was isolated from individual tumoroid models using the RNeasy Kit (Qiagen) and used for whole exome sequencing. RNA from corresponding patient tumors was tested in parallel, if available.

  Dataset EGAD50000000557

• Variant calling from CC220-MM-001 cohorts A,B,D

  These are genomic and transcriptomic high risk molecular segments for 167 samples collected at baseline from deidentified patients enrolled in cohorts A,B or D in the CC-220-MM-001 clinical study. Data are provided in a patient call table in csv format. Calls are generated from WGS data with mutations called by mutect2 best practices pipeline, CNV calls from Battenberg; and RNA-seq aligned with star aligner and quantified by Salmon.

  Dataset EGAD50000000388

• RRBS profiling for a cohort including 88 precancer specimens from 62 resected lung nodules from 39 patients including atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (ADC) and 39 matched normal lung tissues.

  To study the evolution of DNA methylation at genome level and methylation intra-tumor heterogeneity (ITH) during early lung carcinogenesis, we performed multiregional reduced representation bisulfite sequencing (RRBS) of 127 resected lung samples from 39 patients using single end library Hiseq3000.

  Dataset EGAD00001006367

• RNA sequencing of CAR-T cells with CD38-CD73-Tim-3-HLA-DR+ phenotype and others in infusion products of tisagenlecleucel for B-cell precursor acute lymphoblastic leukemia

  We enrolled 19 patients with BCP-ALL who took tisagenlecleucel, and infusion products and patient samples were obtained before and after CAR-T infusion. Single-cell analysis by CyTOF revealed that central memory CAR+ T cells increased in long-term responders, whereas PD-1highCD38highCXCR3+ effector CAR+ T cells were enriched in relapsed patients after CAR-T infusion. Furthermore, in long-term responders, CAR+ T cells obtained from infusion products were enriched with CD38-CD73-Tim-3-HLA-DR+ phenotype, and characterized by decreased ability to produce adenosine, and they showed more memory-like transcriptomic characteristics. We elucidated the characteristics of tisagenlecleucel related to a durable response, which could contribute to improving the clinical outcome.

  Study JGAS000760

• McGill Cord Blood Methylome Capture Sequencing Data

  The study includes methylC-capture sequencing (MCC-Seq) on 73 cord blood DNA samples from the result of natural pregnancies (control) and through the assisted reproductive technologies for infertile couples (ART/infertile). Samples were collected as a part of the Quebec-based 3D (Design, Develop, Discover) longitudinal pregnancy cohort study. All the data were generated with 100bp paired-end reads using the Illumina NovaSeq 6000 systems.

  Dataset EGAD00001009495

• Single cell RNA sequencing of co-culture of human organoids with polarized pro-inflammatory (M1) or anti-inflammatory (M2) macrophages

  In order to know if the mechanisms we identified in mice – demonstrating that macrophages are able to orchestrate the intestinal regenerative process – are conserved in humans we develop a co-culture system with human intestinal organoids and human polarized macrophages. We co-culture human organoids with pro-inflammatory or anti-inflammatory macrophages for 48h. On day 3 cells were collected to perform single cell RNA sequencing.

  Dac EGAC50000000270

• WGS of thymic epithelial tumors and paired normal

  Among the 20 newly sequenced cases, we conducted additional whole-genome sequencing (WGS) on five out of eight CN-type thymomas, excluding three with low tumor cell fractions (< 0.1). Libraries for WGS were prepared using the TrueSeq DNA PCR-free Prep Kit following standard Illumina protocols.

  Dataset EGAD50000001160

• scRNAseq of co-culture of human organoids with polarized pro-inflammatory or anti-inflammatory macrophages

  In order to know if the mechanisms we identified in mice – demonstrating that macrophages are able to orchestrate the intestinal regenerative process – are conserved in humans we develop a co-culture system with human intestinal organoids and human polarized macrophages. We co-culture human organoids with pro-inflammatory or anti-inflammatory macrophages for 48h. On day 3 cells were collected to perform single cell RNA sequencing.

  Dataset EGAD50000000675

• RNA-seq of multiple myeloma patient samples

  RNA from CD138+ plasma cells from patients with a plasma cell dyscrasia were sequenced using the TruSeq Stranded Total RNA Ribo-zero Gold kit (Illumina). Paired-end 75bp reads were generated on a NextSeq500 or HiSeq4000 (Illumina). The dataset consists of 1 MGUS sample, 5 SMM samples, 69 newly diagnosed myeloma samples, 1 relapsed myeloma sample, 1 previously treated myeloma samples, and 4 PCL samples. Matching whole genome sequencing data are available for these samples under study EGAS00001003164.

  Dataset EGAD00001004543

• Whole genome bisulfite sequencing data of human monocyte sample 43_Hm01_BIMo_Ct from healthy male donor.

  Human monocytes from a healthy male blood donor were obtained after written informed consent and anonymised. Library preparation was performed essentially as described in the “Whole‐genome Bisulfite Sequencing for Methylation Analysis (WGBS)” protocol as released by Illumina. The library was sequenced on an Illumina HiSeq2500 using 101 bp paired-end sequencing. Read mapping was done with BWA.

  Dataset EGAD00001001390

• IGPP Consortium GWSS Summary Results Data

  The data are the aggregate results from an IGPP Consortium genome-wide survival study, showing overall risk for Parkinson disease progression associated with each variant in a longitudinal cohort study. 11.2 million deeply imputed variants in 3,821 PD patients who were prospectively tracked with 36,123 visits over a median of 6.7 years from disease onset (inter-quartile range, 4.2 years) were analyzed. Data include hazard ratio, SNP ID, and P value.

  Dataset EGAD00001007060

• Strand-seq data of primary acute myeloid leukemia patient samples with complex karyotype

  In this study, we aimed to identify somatic structural variation of acute myeloid leukemia with complex karyotype (CK-AML) at the single-cell level and to investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from four CK-AML patients. We also performed strand-specific single-cell sequencing of two patient-derived xenografts (PDXs).

  Dataset EGAD00001011172

• NSCLC ctDNA multigenic panel

  We analyzed cfDNA plasma samples of subjects with non-small cell lung cancer: treatment naïve (n=24) and prior-treated (n=8). Driver variants for 11 genes was available with Oncomine Lung cfDNA Assay, were assessed by Next-Generation Sequecing. Sequencing data were pre-processed in Ion S5 Torrent Server and aligned to the hg19 human reference genome. Variant calls were performed by IonReporter 5.10 software.

  Dataset EGAD50000000908

• Dataset for desmoplastic small round cell tumor - RNA

  This dataset contains 32 RNA sequencing samples of patients with desmoplastic small round cell tumor. Sequencing was performed on Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina HiSeq X and NovaSeq 6000 using Illumina TruSeq RNA and TruSeq Stranded RNA Kit. The sequencing was always paired.

  Dataset EGAD50000000912

• H3Africa AWIGEN Pilot MetaboChip

  Pilot study on the interplay between genetic, epigenetic, and environmental risk factors for obesity and related cardiometabolic diseases with 973 samples from South Africa genotyped on Illumina Human MetaboChip array.

  Dataset EGAD00010001258

• Salivary Gland Cancer TSO500 dataset

  DNA was extracted from archival tissue of 119 patients with various SGC subtypes and sequenced using a targeted NGS panel encompassing 523 cancer related genes (TruSight Oncology 500, TSO500). This dataset belongs to the publication entitled: 'Identification of fusion genes and targets for genetically matched therapies in a large cohort of salivary gland cancer patients'.

  Dataset EGAD00001008759

• WGS - germline - oral squamous cell carcinoma

  We conducted a retrospective, single-center Canadian cohort study of patients who underwent primary surgery for OSCC between 2010 and 2024. Nucleic acid quality was assessed using the 4150 TapeStation System (Agilent) prior to library preparation. WGS was performed on germline DNA, following Genome Analysis Toolkit’s (GATK) Best Practices and procedures, with a target of 30X deduplicated coverage per sample, using an Illumina NovaSeq 6000 instrument.

  Dataset EGAD50000002608

• Transcriptome of memory B cells with autoproliferation in MS

  Transcriptional profile of resting/hi and autoproliferating/Dim memory B cells in Multiple sclerosis patients. In brief, non-proliferating (CFSEhi) and AP+ (CFSEdim) CD19+ CD27+ B cells from PBMCs of 5 natalizumab-treated female RRMS (NAT) patients were sorted following 7 days of autoproliferation. Transcriptome libraries were constructed from the same samples, except for one sample pair, which was excluded due to limited input material (5 donors as for Methylome, D1; D2, D3, D5, D6; samples from donor D4 unfortunately technically failed). SMARTer Total Stranded RNA-seq library construction with ribosomal depletion was performed and then sequenced on NovaSeq S4 lane.

  Dataset EGAD50000001270

• Comprehensive Genomic and Transcriptomic Analysis of Rare Cancers for Guiding of Therapy (H021)

  Here we analyzed the molecular profiles and clinical outcomes of 1,310 patients (proportion of rare cancers, 75%) enrolled in a prospective observational study by the German Cancer Consortium that applies whole-genome/exome and RNA sequencing to inform the care of adults with incurable cancers. Based on 472 single and six composite biomarkers, a cross-institutional molecular tumor board provided evidence-based management recommendations, including diagnostic reevaluation, genetic counseling, and experimental treatment, in 88% of cases. Recommended therapies were administered in 362 of 1,138 patients (31.8%) and resulted in significantly improved response and disease control rates (23.9% and 55.3%, respectively) compared to previous therapies, translating into a progression-free survival ratio &gt;1.3 in 35.7% of patients.

  Study EGAS00001004813

• A prognostic human brain network for diffuse midline glioma

  Diffuse midline glioma (DMG) are near-universally lethal tumours of the paediatric central nervous system. In animal models, DMG form brain-wide, integrated networks through neuron-to-glioma synapses and glioma-to-glioma gap junctional coupling. This extensive connectivity robustly promotes the growth and invasion of DMG and other glial malignancies through paracrine mechanisms and direct neuron-to-glioma synapses. The organisation and clinical implications of these connections in the living human brain, however, remain to be elucidated. Here, we develop tumour network mapping to compute the brain-wide connectivity profile of DMG: defining a conserved brain network across pontine and thalamic DMG associated with patient short-term survival (DMG network). Tumour functional connectivity with the DMG network was independently predictive of patient overall survival across two external validation cohorts. Tumour growth mapped to DMG network-specific trajectories and peak, in-network neurometabolic changes across development spatiotemporally aligned with the peak age incidence of DMG. Single-nucleus RNA-sequencing confirmed diverse synaptic gene enrichment in high-connectivity DMG. Strikingly, incidental surgical resection of high-connectivity thalamic DMG tissue conferred a significant survival advantage. Collectively, these data define a conserved and prognostically important brain network in children with DMG, consistent with the hypothesis that DMG exploit otherwise healthy brain circuits to promote tumour growth.

  Study EGAS50000001752

• scRNA-seq of LN and lymphoma stroma

  The activities of non-haematopoietic cells (NHCs), including mesenchymal stromal cells and endothelial cells, in lymphomas, reportedly underlie lymphomagenesis. However, understanding of lymphoma NHCs has been hampered by unexplained NHC heterogeneity, even in normal human lymph nodes (LNs). Here, we constructed a single-cell transcriptome atlas of &gt;100,000 NHCs collected from 27 human samples, including LNs and various nodal lymphomas, revealing 30 distinct subclusters, including some that were previously unrecognized. Notably, this atlas was highly useful for comparative analysis with lymphoma NHCs, which revealed an unanticipated landscape of subcluster-specific changes in gene expression and interaction with malignant cells in follicular lymphoma NHCs, facilitating our understanding of stromal remodelling in lymphoma and potentially suggesting novel biomarkers. Our study largely updates NHC taxonomy in human LNs and pertains to analysis of disease status, providing a rich resource and deeper insights into LN and lymphoma biology and offering to advance lymphoma management and therapy.

  Study EGAS00001005732

• single cell transcriptomic analysis of tumor samples collected from 5 patients with EMM

  Contains the raw single cell RNAseq data used for the study

  Study EGAS50000000034

• ATAC-seq data in normal colon mucosa

  This dataset includes ATAC-seq data generated in normal colon mucosa obtained in four healthy volunteers during colonoscopy indicated for colorectal cancer screening. Subjects had no lesions in the colon. Also includes one frozen sw480 colon adenocarcinoma cell line sample for piloting the protocol

  Study EGAS00001005281

• Deciphering Intratumoral Molecular Heterogeneity in Clear Cell Renal Cell Carcinoma with a Radiogenomics Platform

  We used 200 ccRCC samples from 51 tumors to simultaneously isolate DNA, RNA, and protein according to established protocol. RNA quality was assessed using an Agilent Bioanalyzer, and total RNA with RIN&gt;7 was used for further RNA sequencing. 184 ccRCC samples from 49 tumors passing initial quality control underwent RNA sequencing at Admera Health Inc. (Genohub Inc., Austin, TX). RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA high throughput (HT) sample preparation kit following the manufacturers’ protocol. Pair-end RNA Seq data was deposited in this cohort.

  Dataset EGAD00001005356

• Single MII oocyte mRNA expression from women

  This dataset contains 14 paired-end FASTQ sequences from mRNA-Seq on single human M-II stage oocytes that were collected from ovarian tissue from unstimulated patients undergoing fertility preservation treatments due to cancer diagnoses, which did not influence ovarian function. Cumulus-oocyte-complexes were matured in vitro according Gruhn et al (Science 365: 1466-1469) and short term flash frozen prior to lysis, RNA extraction, full length cDNA preparation and amplification using the Ultra-low-input SMART-Seq2 v4 kit from Takara Clonetech. Further, these cDNA were used to prepare libraries for sequencing according the Nextera XT DNA library preparation kit from Illumina

  Dataset EGAD00001005971

• Sequencing data for oesophageal and related samples - Black et al (WES)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WES OACs/BOs/normals)

  Dataset EGAD00001011188

• Genotype data from 'Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture.'

  Previous studies have highlighted how African genomes have been shaped by a complex series of historical events. Despite this, genome-wide data has only been obtained from a small proportion of present-day ethnolinguistic groups. By analysing new autosomal genetic variation data of 1333 individuals from over 150 ethnic groups from Cameroon, Republic of the Congo, Ghana, Nigeria and Sudan, we demonstrate a previously underappreciated fine-scale level of genetic structure within these countries, for example correlating with historical polities in western Cameroon. By comparing genetic variation patterns among populations, we infer that many northern Cameroonian and Sudanese groups share genetic links with multiple geographically disparate populations, likely resulting from long-distance migrations. In Ghana and Nigeria, we infer signatures of intermixing dated to over 2000 years ago, corresponding to reports of environmental transformations possibly related to climate change. We also infer recent intermixing signals in multiple African populations, including Congolese, that likely relates to the expansions of Bantu language-speaking peoples.

  Study EGAS00001006944

• ASPSCR1-TFE3 gene fusion panel deep amplicon sequencing data

  Dataset contains compressed, paired-end Fastq files of deep amplicon sequencing data from a custom ASPSCR1-TFE3 gene fusion panel for three alveolar soft part sarcoma cases described in "Development and first-in-human CAR T therapy targeting the pathognomonic MiT-fusion driven protein GPNMB".

  Dataset EGAD50000002438

• snRNA splicing signature RNA-Seq

  This dataset has RNA-Seq fastq files which were generated as part of the snRNA splicing signature study. Analysis can be performed to regenerate splicing signatures found for RNU4-2, RNU5B-1 and RNU5A-1 by comparing cases versus controls.

  Dataset EGAD50000001299

• Strand-seq data of six CK-AML patient samples and three matching PDXs

  We performed strand-specific single-cell sequencing of six primary leukemia samples from four CK-AML patients. We also performed strand-specific single-cell sequencing of three matching patient-derived xenografts (PDXs). The dataset contains BAM files for each cell.

  Dataset EGAD50000000634

• Dataset for desmoplastic small round cell tumor - WGS

  This dataset contains 25 WGS sequencing samples of patients with desmoplastic small round cell tumor. Sequencing was performed on Illumina HiSeq X and NovaSeq 6000 using Illumina TruSeq Nano DNA Kit. The sequencing was always paired.

  Dataset EGAD50000000911

• Clones derived from early passage tumoroids of colorectal cancer

  We obtained different clones from early passage CRC tumoroids to study mutational signatures specific for truncal or private somatic alterations. These whole genome sequences are part of a larger study on the heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer.

  Dataset EGAD50000000152

• DDD Phenotype Dataset

  Phenotype data for 1230 participants from both South Africa and The Democratic Republic of Congo

  Dataset EGAD00001015752

• WGS data of XPC-ko human small intestinal organoid cultures

  Whole genome sequencing (WGS) data of human small intestinal organoid cultures, which were deleted for the XPC gene using CRISPR-Cas9. Contains WGS data of 1 clone and 1 subclone.

  Dataset EGAD00001003779