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• Dataset of 10 WES from bladders tumors and PBMC of 4 non-muscle invasive bladder cancer patients

  WES (FASTQ files) of paired tumor and PBMC samples of non-muscle-invasive bladder cancer patients. All CTRL samples originate from PBMC. For patient UC2, DNA from 3 different synchronous tumors were extracted. DNA from tumors was extracted from fresh frozen tumors,except for patient UC4 (FFPE). NB : patients aliases are the following :ROXY : UC1, OMAD : UC2, MAKI : UC3, HAPE : UC4

  Dataset EGAD50000002008

• scRNA-seq of Patient-derived tumor fragments (PDTFs)

  scRNA-seq of Patient-derived tumor fragments (PDTFs) which were treated with either Isotype (DP47), Isotype-IL2v (DP47-IL2v), anti-PD1 (PembroPGLALA) or PD1-IL2v (PembroPGLALA-IL2v) for 48 hours. Dataset content: 10 samples from 3 donors File type: paired-end fastq files Protocol: Chromium Single Cell 3' Reagent Kits User Guide (Dual Index) with Feature Barcoding technology for Cell Surface Protein (CG000317) Technology: Illumina sequencing Experimentation: scRNA-seq using the 10X technology

  Dataset EGAD50000000584

• Fetal body map

  From 2nd trimester human foetuses we derived liver and intestinal stem cells. These were clonally expanded until enough material was available for whole genome sequencing. For each foetus, reference tissue (skin or bulk liver) was also sequenced to determine all germline variants. These were subtracted from the clones to determine all somatic mutations that had been acquired during embryonic and fetal development.

  Dataset EGAD00001003997

• Genomic Data for Integrative Profiling of T790M Negative EGFR Mutated NSCLC

  Contains WES and RNA-seq for the 59 patients with first- and second-generation EGFR TKI-resistant metastatic EGFR-mutated NSCLC.

  Dataset EGAD00001010272

• Sequencing data for oesophageal / related samples - Kazachenka et al (DNA)

  Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" WGS for 452 samples

  Dataset EGAD00001011095

• A Multifactorial Tumor and Immune Cell Profile Determines Response to Immune Checkpoint blockade in Melanoma

  The complex crosstalk between tumor and immune cells during immune checkpoint blockade mandates the development of integrated models that interpret the anti-tumor immune response and predict clinical outcome. We have integrated genome-wide sequence and structural alterations with pre and on-therapy transcriptomic and T cell repertoire features for a cohort of 64 immunotherapy-naïve melanomas treated with anti-PD1 monotherapy or combined anti-PD1 and anti-CTLA4 therapy. While tumor mutation burden (TMB) was associated with improved response to therapy, expressed mutation burden was superior to TMB in predicting outcome. An increased pre-existing T cell density differentiated responding from non-responding tumors independent of therapy. Importantly, T cell repertoire reshaping determined by T cell receptor (TCR) clonotypic regressions and expansions reflected response to therapy such that a more dynamic repertoire predicted improved clinical outcome. Through whole-transcriptome analyses, we discovered differential abundance of B cell subsets in responding tumors, which highlights the importance of the interplay between pre-existing T and B cell immunity in shaping therapeutic response. Tumor temporal trajectories during therapy revealed distinct patterns of molecular response related to expressed mutation elimination or retention that accurately interpreted clinical response. High-dimensional genomic, transcriptomic and immune repertoire data were integrated by both a machine learning and a censored regression approach, resulting in a harmonized multi-modal predictor of response to immune checkpoint blockade. B cell abundance, expressed mutation load and tumor aneuploidy were combined to identify patients at high risk for recurrence, such that high risk patients had a significantly shorter progression-free survival (HR=9.18, 95% CI: 3.14-26.85, p=3.4e-06) especially in the anti-PD1/anti-CTLA4 group (HR=20.34, 95% CI: 4.08-101.32, p=1.68e-06).

  Study EGAS00001004548

• PDAC organoid genomic heterogeneity

  The establishment of patient-derived pancreatic cancer organoid culture in recent years creates an exciting opportunity for researchers to perform a wide range of in vitro studies on a model that closely recapitulates the tumor. Among the outstanding questions in pancreatic cancer biology are the causes and consequences of genomic heterogeneity observed in the disease. However, to use pancreatic cancer organoids as a model to study genomic variations, we need to first understand the degree of genomic heterogeneity and its stability within organoids. Here, we used single-cell whole-genome sequencing to investigate the genomic heterogeneity of two independent pancreatic cancer organoids, as well as their genomic stability with extended culture. Clonal populations with similar copy number profiles were observed within the organoids, and the proportion of these clones was shifted with extended culture, suggesting the growth advantage of some clones. However, sub-clonal genomic heterogeneity was also observed within each clonal population, indicating the genomic instability of the pancreatic cancer cells themselves. Furthermore, our transcriptomic analysis also revealed a positive correlation between copy number alterations and gene expression regulation, suggesting the “gene dosage” effect of these copy number alterations that translates to gene expression regulation.

  Study EGAS00001006782

• CADD/GADD centers on Antisocial Drug Dependence

  CADD (Center for Antisocial Drug Dependence): Funded through NIDA 011015 to study genetic influences on, and treatment of, antisocial drug dependence, studying both clinical probands and their families, and community samples of matched controls, twins, and participants in an ongoing longitudinal adoption study. A collaboration between three organizations at two campuses of the University of Colorado. Longitudinal with three waves of data collection completed. GADD (Genetics of Adolescent Antisocial Drug Dependence): Funded originally through NIDA 012845, s multisite collaboration including adolescent subjects at high-risk for antisocial drug dependence and their siblings, recruited in Denver, CO and San Diego, CA. Longitudinal with two waves of data collection completed, one in progress as of May, 2018.

  Study phs001841

• Splicing signature analysis of RNU2-2 samples

  Dominant pathogenic variants in the snRNA RNU2-2 were recently reported as a cause of neurodevelopmental disorders. In our study we identified additional individuals with dominant variants (n.4G>A and n.35A>G) and we also identified biallelic variants as a novel frequent cause of neurodevelopmental disorder. We obtained blood samples and performed short-term lymhocytes cultures for 19 cases (5 n.4; 5 n.35; 9 biallelic). We generated exome-capture RNA-Seq for these cases that we compared to 49 controls (probands affected from a neurodevelopmental disorder but without RNU2-2 variants). We observed that RNU2-2 variants mainly disturb alternative exon skipping, although affecting different exons.

  Study EGAS50000001410

• CM067 WES - Clinical Outcomes by Tumor Mutational Burden and Inflammatory Gene Expression With Combined Nivolumab and Ipilimumab or Monotherapy in Advanced Melanoma

  Purpose Exploratory analyses of CheckMate 066 and 067 trials were conducted to investigate associations of tumor mutational burden (TMB), a 4-gene inflammatory gene expression signature, and BRAF mutation status with tumor response, progression-free survival (PFS), and overall survival (OS) in patients with advanced melanoma. Patients and Methods Patients with known programmed death ligand 1 (PD-L1) expression and BRAF mutation status received nivolumab (NIVO) or dacarbazine in CheckMate 066 and either NIVO, ipilimumab (IPI), or NIVO+IPI in CheckMate 067. Whole exome sequencing and RNA sequencing were used to determine TMB and inflammatory gene expression signature scores, respectively. These biomarkers were evaluated in terms of their association with PFS and OS. Results In the NIVO, NIVO+IPI, and IPI arms of CheckMate 067, longer survival was associated with high (> median) versus low (≤ median) TMB with hazard ratios (HRs) (95% confidence interval [CI]) for PFS of 0.45 (0.30–0.65), 0.55 (0.38–0.81), and 0.60 (0.43–0.82), and for OS of 0.46 (0.30–0.71), 0.53 (0.34–0.82), and 0.52 (0.36–0.74), respectively. For NIVO-treated patients, these results were confirmed in CheckMate 066. A survival benefit was observed with high TMB and absence of BRAF mutation. Survival was associated with high versus low inflammatory signature scores with HRs (95% CI) for PFS of 0.56 (0.34–0.94), 0.40 (0.23–0.72), and 0.43 (0.27–0.70), and for OS of 0.37 (0.20–0.66), 0.38 (0.19–0.74), and 0.46 (0.27–0.79), in the NIVO, NIVO+IPI, and IPI arms, respectively. Weak correlations were observed between PD-L1, TMB, and the inflammatory signature. Conclusions Combined assessment of TMB, inflammatory gene expression signature, and BRAF mutation status may be predictive for response to immunotherapy in advanced melanoma.

  Dataset EGAD00001007573

• Pre-neoplastic somatic mutations including MYD88L265P in lymphoplasmacytic lymphoma

  In this study, we sequenced multiple stages of the B-lineage in elderly individuals and patients with lymphoplasmacytic lymphoma to study whether mutations are accumulated in normal-cell counterparts prior to lymphoma

  Dataset EGAD00001008196

• WXS and RNA-seq for 22 patients treated with radiation + immunotherapy

  Over 500 active clinical trials are investigating combination radiation (RT) and immune checkpoint blockade (ICB) as a cancer treatment; however, the majority of trials have found no positive interaction. We performed a comprehensive molecular analysis of a randomized phase I clinical trial of patients with non-small cell lung cancer (NSCLC) treated with concurrent or sequential ablative RT and ICB. Concurrent treatment was superior to sequential treatment in augmenting local and distant tumor responses and improving overall survival in a subset of patients with highly aneuploid tumors, but not in those with less aneuploid tumors. Our analysis suggested that concurrent treatment eliminated immunologically cold aneuploid tumors better than sequential treatment and improved patient outcomes. In addition, we report that RT alone decreased intratumoral cytotoxic effector T cell and adaptive immune gene expression signatures, in contrast to upregulation of key immune pathways after concurrent administration of RT and ICB. Our findings distinguish the differential genomic and transcriptomic effects of RT versus RT and ICB and challenge the prevailing paradigm that local ablative RT beneficially stimulates the immune response. We propose the use of tumor aneuploidy as a novel biomarker and therapeutic target in personalizing treatment approaches for patients with NSCLC treated with RT and ICB.

  Study EGAS00001006212

• scRNAseq data of human innate lymphoid cells (ILCs) and natural killer (NK) cells from fresh umbilical cord blood

  scRNA-seq was performed on the BD Rhapsody platform. ILCs (ILC1, ILC2, ILC3) and NK cells were bulk sorted from fresh cord bloods of 3 donors. The 4 samples containing ILCs and NK cells from each donor were stained with Sampletag antibodies (12 samples in total) before Abseq staining with the BD Immune Discovery panel and 6 additional antibodies was performed to better classify immune cell subsets. The sorted population were pooled before loading onto the BD Rhapsody cartridge. The manufacturer's protocol was followed for library construction and samples were sequenced on a Illumina NovaSeq 6000.

  Dataset EGAD50000001713

• Colon Cancer Organoid Cultures and Tumors Whole Genome Sequencing Data

  Five hundred nanograms of genomic DNA was fragmented by Covaris S2, the fragmented DNAs were performed end-repair, A-tailing at the 3 prime end, adaptors ligation with an IDT dual-indexed UMI adaptor system at the terminal ends. The adapter ligated library with size range 300-750bp were selected by dual-SPRI method. Twenty percent of the size selected PCR-free libraries were enriched by 5 PCR cycles prior to library size assessment by Bioanalyzer Fragment Analyzer. The PCR-free libraries were quantified by qPCR.The PCR-free libraries were denatured and diluted to optimal concentration. Illumina NovaSeq 6000 was used for Pair-End 151bp sequencing.

  Dataset EGAD00001005759

• 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

• Genetics of Inherited Muscle Disease

  The samples are drawn from a collection of patients with a heterogeneous set of neuromuscular disorders, including congenital muscular dystrophy, congenital myopathy, limb-girdle muscular dystrophy, Emery-Dreifuss muscular dystrophy, and arthrogryposis, along with unaffected parents and siblings in some cases. The samples were collected by the following clinicians affiliated with the associated institutes: Kathryn North and Nigel Clarke (Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Australia) Hanns Lochmuller and Kate Bushby (The Newcastle Muscle Centre, Newcastle University, UK) Peter Kang (Boston Children's Hospital) Carsten Bonnemann (National Institutes of Health, Bethesda, MD, USA) Nigel Laing (University of Western Australia) All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 or Illumina's Rapid Capture Exome enrichment kit and sequencing was performed on an Illumina HiSeq 2000. In addition some samples were whole genome sequenced on Illumina HiSeq X Ten.

  Study phs000655

• Whole exome sequencing of long-term, never relapse exceptional responders of trastuzumab-treated HER2+ metastatic breast cancer

  Trastuzumab has significantly improved the overall survival of patients with HER2+ metastatic breast cancer (MBC). However, outcomes can vary, with patients progressing within 1-year of treatment or exceptional cases of complete response to trastuzumab for ≥ 10 years. Identification of the underlying genomic aberrations of “exceptional responders (ExRs)” compared to “rapid non-responders (NR)” increases our understanding of the mechanisms involved in MBC progression and identification of biomarkers of trastuzumab response and resistance. Whole exome sequencing was performed on six ExRs compared to five NR. The overall fraction of genome copy number alteration (CNA) burden was higher in NR patients (P=0.07), while more significantly pronounced in copy number gains (P=0.03) in NR compared to ExRs. Delineation of the distribution of CNA burden across the genome identified a greater degree of CNA burden in NR within chr8 (P=0.02) and in chr17 (P=0.06) and conferred a statistically significant benefit in overall survival.

  Study EGAS00001004486

• Spatial and Temporal Homogeneity of Driver Mutations in Diffuse Intrinsic Pointine Glioma

  Diffuse Intrinsic Pontine Gliomas (DIPG) are deadly pediatric brain tumors where needle biopsies help guide diagnosis and targeted therapies. To address spatial heterogeneity, we analyzed 134 specimens from various neuroanatomical structures of whole autopsy brains from nine DIPG patients. Evolutionary reconstruction indicates histone 3 (H3)K27M – including novel H3.2K27M - mutations potentially arise first and are invariably associated with specific, high-fidelity obligate partners throughout the tumor and its spread, from diagnosis to end-stage disease, suggesting mutual need for tumorigenesis. These H3K27M ubiquitously-associated mutations involve alterations in TP53 cell-cycle (TP53/PPM1D) or specific growth factor pathways (ACVR1/PIK3R1). Later oncogenic alterations arise in sub-clones and often affect the PI3K pathway. Our findings are consistent with early tumor spread outside the brainstem including the cerebrum. The spatial and temporal homogeneity of driver mutations in DIPG implies they will be captured by limited biopsies and emphasizes the need to develop therapies specifically targeting obligate oncohistone partnerships.

  Study EGAS00001001654

• Contribution of allelic imbalance to colorectal cancer

  Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge, and unbiased CRISPR-Cas9 knockout and activation screens identified altogether 79 genes within AI peaks regulating cell growth. Genetic and functional data implicates loss of TP53 as a sufficient driver of AI. The WGS highlights an influence of copy number aberrations on the rate of detected somatic point mutations. Importantly, the data reveal several associations between AI target genes, suggesting a role for a network of lineage-determining transcription factors in colorectal tumorigenesis. Overall, the results unravel the contribution of AI in colorectal cancer and provide a plausible explanation why so few genes are commonly affected by point mutations in cancers.

  Study EGAS00001002966

• Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring

  In many areas of oncology, we lack sensitive tools to track low burden disease. While cell-free DNA (cfDNA) shows promise in detecting cancer mutations, we found that the combination of low tumor fraction (TF) and limited number of DNA fragments restricts low disease burden monitoring through the prevailing deep targeted sequencing paradigm. We reasoned that breadth may supplant depth of sequencing to overcome the barrier of cfDNA abundance. Whole genome sequencing (WGS) of cfDNA allowed ultra-sensitive detection, capitalizing on the cumulative signal of thousands of somatic mutations observed in solid malignancies, with TF detection sensitivity as low as 10-5. The WGS approach enabled dynamic tumor burden tracking and post-operative residual disease detection, associated with adverse outcome. Thus, we present an orthogonal framework for cfDNA cancer monitoring via genome wide mutational integration, enabling ultra-sensitive detection, overcoming the limitation of cfDNA abundance, and empowering treatment optimization in low-disease burden oncology care

  Study EGAS00001004406

• Immune landscape of oncohistone-mutant gliomas reveals diverse myeloid populations and tumor-promoting behavior

  Histone H3-mutant gliomas are deadly brain tumors characterized by a dysregulated epigenome and stalled differentiation. In contrast to the extensive datasets available on tumor cells, limited information exists on their tumor microenvironment (TME), including the immune infiltrate. Here, we characterize the TME of H3.3K27M and G34R/V-mutant gliomas, and multiple H3.3K27M mouse models, using transcriptomic and proteomic, including spatial single-cell approaches. Resolution of immune lineages indicates uniform high-infiltration of H3-mutant gliomas with diverse myeloid populations, high-level expression of immune checkpoints, and scarce lymphoid cells, findings uniformly reproduced in all H3.3K27M models tested. We show these myeloid populations communicate with H3-mutant cells mediating immunosuppression and sustaining tumor formation and maintenance. Dual inhibition of myeloid cells and immune checkpoints showed significant therapeutic benefit in pre-clinical syngeneic models. Our findings provide valuable characterization of the TME of oncohistone-mutant gliomas, and insights into means to modulate the myeloid infiltrate for the benefit of patients.

  Study EGAS00001007510

• Investigating low frequency variants in CAD/MI cases, controls and pedigrees using whole exome sequencing and custom pulldowns

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Dataset EGAD00001000400

• Pilot study towards the development of a Companion/Complimentary Diagnosis platform using liquid biopsy with cfDNA for immune checkpoint inhibitor therapy in advanced urothelial cancer

  Preliminary analysis was conducted to develop a cfDNA-based platform capable of predicting gene mutation profiles, TMB, gene expression profiles (molecular subtype diagnosis), and immunohistochemical findings (PD-L1 expression) using the primary lesion tissue of bladder cancer and upper urinary tract epithelial cancer, verifying the feasibility of such development.

  Study JGAS000714

• 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

• ERDERA WES reanalysis - DPF1 Batch 1

  Processed data for 100 WES from the Data Processing Freeze 1

  Dataset EGAD50000002187

• Patient TSO500 VCF files

  Tumours from MMRd EC patients treated with 2 cycles neoadjuvant ICI. TruSight Oncology 500 (TSO 500) panel for all 10 tumour samples from patients included in the trial.

  Dataset EGAD50000000694

• PREGO

  Core set of the PREGO biobank containing experimental genotypes at 209,706 autosomal sites measured on Affymetrix PMRA Axiom array plates for a group of 3,234 individuals from Western France.

  Dataset EGAD00010002661

• Colorectal cancer methylation profiling

  4 AC samples, each with adenoma, carcinoma and normal colon tissue (12 samples in total) were analysed on the Infinium MethylationEPIC BeadChip for copy number alteration analyses.

  Dataset EGAD00010001691

• Angiopredict Whole genome Shallow Sequencing

  Shallow sequencing of metastatic colorectal cancer samples for the Angiopredict and Nobev cohorts described in: van Dijk et al., JCO, in revision

  Dataset EGAD00001003990

• SCNA-Seq of tumor DNA samples

  Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping of corresponding tumor material

  Dataset EGAD00001002150

• Endometriosis

  Whole exome sequencing data for matched normal and endometriosis samples. Samples were prepared using Agilent Sureselect capture kit, and sequenced on an Illumina HiSeq 2500. The submitted files are in BAM format.

  Dataset EGAD00001004964

• Single-cell RNA-sequencing of H3-K27M diffuse midline glioma.

  Fastq files are deposited for single-cell transcriptomes of patient H3-K27M diffuse midline gliomas, generated using the SMART-seq2 method.

  Dataset EGAD00001011339

• Exome sequencing of osteosarcoma, blood and saliva

  We profiled 31 osteosarcoma tumor patient samples, 18 blood and 1 saliva control samples by exome sequencing, for a total of 50 samples. The raw fastqs are provided.

  Dataset EGAD00001011370

• Identification of Recurrent SMO and BRAF Mutations in Ameloblastomas

  RNA-seq data from two cases of ameloblastoma was analyzed for candidate gene fusions and point mutations. Recurrent point mutations identified in the RNA-seq data, as well as mutations identified with limited panel targeted deep sequencing, were validated as somatic. Expanding to a larger cohort of 28, one of two activating mutations was found in 80% of cases. No recurrent gene fusions events were identified.

  Study phs000739

• RNASeq from PPGL-derived PC12 cell lines cultivated in normoxia and hypoxia conditions.

  PC12 cells derived from rat PPGL were then either continued cultivated in the same normoxia condition (37˚C, 5% CO2 and 21% O2 balanced with N2) or were placed in a hypoxic incubator, that maintained a constant hypoxic environment (37˚C, 5% CO2 and 1% O2 balanced with N2), for different short (12h, 24h, and 48h) or prolonged time (36 days, approximately 860h).

  Study EGAS50000000814

• Molecular profiles in early onset prostate cancer

  Paired germline (blood) and tumour samples were collected from prostate cancer cases <65 years at diagnosis to identify genetic changes in early onset prostate cancer.  Whole exome sequencing was performed on these samples. The aim was to determine if these changes are associated with more aggressive disease and to identify targets for treatment and screening by identifying associations with family history, DNA repair germline mutations, and clinical features.

  Study EGAS50000001467

• Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics

  We performed scRNA-seq of patient-derived glioblastoma cells alone or after co-culture with human iPSC-derived cerebral organoid cells. Transcriptional changes implicated in the invasion process that are coherent across patient samples indicate that GBM cells reactively upregulate genes required for their dispersion. Potential interactions between GBM and organoid cells identified by an in silico receptor-ligand pairing screen suggest functional therapeutic targets.

  Study EGAS00001003852

• RNAseq of Follicular Lymphoma

  RNAseq analysis of 28 Follicular Lymphoma (FL) criopreserved samples was performed using ribosomal-depleted total RNA to analyze long non-coding RNA and coding transcript expression profiles comparing two different histological groups of FL tumors (FL1-3A versus FL3B/DLBCL). These comparisons were performed either in a subset of tumor purified cell samples (N=12) as in unpurified tumor samples including normal cells for the lymph node microenvironment (N=16).

  Study EGAS00001002980

• Whole Exome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"

  Whole Exome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"

  Dataset EGAD00001003434

• SNP array files, IDAT files, from 34 members of a Family with a high prevalence of psychosis

  We investigated the genetic causes of major mental disorders (MMDs) including schizophrenia, bipolar disorder I, major depressive disorder, and attention deficit hyperactive disorder, in a large family pedigree from Alpujarras, South of Spain, a region with a high prevalence of psychotic disorders. We applied a systematic genomic approach based on karyotyping (N=4), genotyping by genome-wide SNP array (N=33), whole-exome sequencing (N=4), and whole-genome sequencing (N=12). We performed genome-wide linkage analysis, family-based association analysis, and polygenic risk score estimates. Significant linkage was obtained at chromosome 9 (9q33.1-33.2, LOD score= 4.11), a suggestive region that contains five candidate genes ASTN2, BRINP1, C5, TLR4, and TRIM32, previously associated to MMDs. Comprehensive analysis associated the MMD phenotype with genes of the immune system with dual brain functions. Moreover, the psychotic phenotype was enriched for genes involved in synapsis. These results should be considered once studying the genetics of psychiatric disorders in other families, especially the ones from the same region, since founder effects may be related to the high prevalence.

  Study EGAS00001004592

• Single Cell RNA-Sequencing of BCG Naive and Recurrent Non-Muscle Invasive Bladder Cancer Reveals a CD6/ALCAM-Mediated Immune-Suppressive Pathway

  Non-muscle invasive bladder cancer (NMIBC) represents 70&#8211;80% patients with newly diagnosed bladder cancer, and Bacillus Calmette-Guerin (BCG) remains a cornerstone treatment for intermediate- and high-risk NMIBC to prevent disease recurrence and progression. However, a significant number of patients experience recurrence after their first course of BCG, posing significant challenges in the management of the disease. We conducted single cell RNA sequencing (scRNA-Seq) on freshly collected NMIBC samples, distinguishing between those naive to BCG treatment and those that recurred post-BCG treatment. We observed a clear activation of inflammatory pathways across cell types during recurrence, but these were not associated with canonical immune checkpoint or T cell exhaustion phenotypes. Analysis of cell-to-cell communication revealed enhanced interactions between T cells and urothelial cells in BCG-recurrence, predominantly modulated by CD6 and activated leukocyte cell adhesion molecule (ALCAM). Furthermore, we found CD6hi T cells to be immunosuppressed and enriched in recurrent samples, suggesting a potential role for CD6 as an immune evasion signal in NMIBC.

  Study phs003742

• Single-nuclei gene-expression analysis of pheochromocytoma and paraganglioma links tumor subtypes with tumor microenvironment

  Pheochromocytomas and paragangliomas (PCPG) are rare neuroendocrine tumors associated with autonomic nerves. We used single nuclei-RNA-seq (snRNA-seq) for analysis of 30 PCPG representing 13 known driver genes, plus two normal adrenal medullas to dissect cell composition, refine PCPG subtypes and compare PCPG and normal tissue expression. Incorporating bulk-tissue and snRNA-seq data we identified seven PCPG gene-expression subtypes with genotype and cell type associations. The tumor microenvironment reflected HIF pathway activation and neovascularization by detection of abundant tip-like endothelial cells and pericytes concordant with VEGFA expression in neoplastic cells with mutations in VHL, genes encoding SDH subunits and MAML3-fusions. Macrophages were abundant in PCPG with distinct tumor-associated features. Schwann-cell-like cells were also enriched in some subtypes. The transcriptional profile of neoplastic PCPG cells resembled normal chromaffin cells but early chromaffin and neuroblast cell markers were expressed in some subtypes including GPR139, a putative therapeutic target for a subset of pseudohypoxic PCPG.

  Study EGAS00001005861

• Single cell data from TB patients

  The dataset comprises single-cell RNA sequencing (scRNA-seq) data derived from around 60,000 PBMCs collected from donors across different severity groups of extrapulmonary tuberculosis (EPTB) and healthy controls (3 healthy, 3 mild, 3 intermediate, 3 severe). The data include both transcriptomic and surface protein expression profiles obtained using the BD Rhapsody Single-Cell Multiomics System. Libraries were prepared for whole transcriptome analysis (WTA), AbSeq, and sample tagging, with sequencing performed on a NovaSeq 6000 system.

  Dataset EGAD50000001118

• Profiling of gene expression and epigenomics in the fetal brain

  scRNA-seq and Cut&Tag from a sample of the human fetal brain. To compare neurogenesis in the primary human brain with that in organoids, we profiled transcriptome and chromatin accessibility (10X multiome) as well as bulk Cut&Tag of histone modifications H3K27me3, H3K27ac and H3K4me3. We used a human brain sample from GW 19 for all experiments.

  Dataset EGAD50000000225

• RNA sequencing data of pediatric KMT2A-rearranged acute lymphoblastic leukemia (set 1)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of two KMT2A-r ALL patients (ALLT-325, ALLT-346). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Globin-Zero Gold rRNA Removal Kit (Illumina) was utilized for rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002582

• RNA sequencing data of pediatric hyperdiploid acute lymphoblastic leukemia (set 3)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of five hyperdiploid ALL patients (ALLT-364, ALLT-367, ALLT-368, ALLT-371, ALLT-377). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and TruSeq Stranded Total RNA Library Prep (Illumina) kit was utilized for rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002594

• RNA sequencing data of pediatric hyperdiploid acute lymphoblastic leukemia

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of four hyperdiploid ALL patients (ALLT-315, ALLT-320, ALLT-329, ALLT-347). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Globin-Zero Gold rRNA Removal Kit (Illumina) was utilized for rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002595

• Clonal expansion of mutated cell population in bladder urothelium

  1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference.

  Dataset EGAD00001003250

• Whole exome sequencing of an alveolar rhabdomyosarcoma patient with RET germline mutation

  Whole exome sequencing of an alveolar rhabdomyosarcoma patient with RET germline mutation and subsequent analysis of potential therapeutic mechanisms associated with the patient's rare germline mutation. Patient sampels were sequenced from an initial biopsy and from a relapse biopsy, in addition to normal blood as the matched normal DNA. RNA sequencing was performed on the relapse sample as initial sample was unable to produce usable RNA for analysis.

  Dataset EGAD00001006125

• The Xq22.3 contiguous gene deletion syndrome (ATS-ID): from genotype to further delineation of the phenotype

  Approximately 200 ng of high-quality of genomic DNA samples were used for library preparation. DNA libraries were prepared using the Human Core Exome Kit according to manufacturer’s recommendations (Twist Bioscience, San Francisco, CA, USA) and then sequenced on Illumina NovaSeq 6000 (Illumina, Inc., san Diego, CA, USA). Detailed protocol of WES data processing and variant analysis are available in Supplementary data.

  Dataset EGAD00001007740

• LSC RNA-Sequencing

  To infer the proteomic Mito signature in the LSC subcompartiment, myeloid blasts for 10 patients from the discovery cohort were FACS-sorted into CD34-GPR56+NKG2DLigands- (CD34-), alias 61dc5fb798e2520001702c03 CD34+GPR56+NKG2DLigands- (CD34+), alias 61dc5fb798e2520001702c03 Detailed gating strategy will be described in Donato, Correia, Andresen and Trumpp et al., (manuscript in preparation)

  Dataset EGAD00001008488

• DAC Wachten Laboratory and Toma Laboratory, University of Bonn/University Hospital Bonn

  DAC for collaborative projects of the Wachten Laboratory (Institute of Innate Immunity, University of Bonn, University Hospital Bonn) and the Toma Laboratory (Institute of Pathology, University Hospital Bonn). Contact: Prof. Dr. Dagmar Wachten dwachten@uni-bonn.de Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Germany Prof. Dr. Marieta I. Toma Marieta.Toma@ukbonn.de Institute of Pathology, University Hospital Bonn, Germany

  Dac EGAC50000000916

• Prospective Lynch Syndrome Database entries

  These data have been used to produce cancer incidence results for https://pubmed.ncbi.nlm.nih.gov/37181409/ , https://pubmed.ncbi.nlm.nih.gov/40231433/ and https://plsd.eu as available in March 2026. The tables contain demographic information at individual level, individual cancer events with given age, as well as prophylactic and therapeutic surgeries to remove organs. The data have been de-identified to ensure anonymity.

  Dataset EGAD50000002468

• Oxford Human Islet ATAC-seq data of 18 human pancreatic islet preparations

  18 human pancreatic islet preparations derived from 17 donors were processed for ATAC-seq. The data was generated on an Illumina Hiseq 2500 sequencing machine to generate 50bp paired end read data. The resulting fastq.gz and mapped bam files were deposited.

  Dataset EGAD00001003947

• ICR Exome Optimization series

  Exome sequencing of 142 samples with corresponding Sanger sequencing results for 416 variants and 288 negative sites. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads.

  Dataset EGAD00001001462

• Whole exome sequencing of long-term, never relapse exceptional responders of trastuzumab-treated HER2+ metastatic breast cancer

  The dataset contains Whole Exome Sequencing data (BAM files) of 22 samples from HER2+ metastatic breast patients. For 9 of the 13 tumours samples there are paired controls available from normal tissue. There are 8 tumours samples that are from treatment-responder patients and 5 tumours samples from non responder patients.

  Dataset EGAD00001006217

• Long read sequencing of 5 Intellectual Disability (ID) trios with PacBio Sequel. Dataset of samples: T2P, T2F and T2M

  5 trios were whole genome sequenced with PacBio Sequel to a depth of 15X (Trios 1-4) or 40X (Trio 5). For each trio the child was affected with severe ID, and the parents were unaffected. Dataset consists of Trio 2 samples: T2P, T2F and T2M

  Dataset EGAD00001006050

• HV31 - Bionano DLS optical mapping

  Bionano DLS optical mapping data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a molecule depth of ~153×. Optical mapping was performed at the Weatherall Institute of Molecular Medicine using the Bionano Saphyr platform.

  Dataset EGAD00001007049

• MPM patients

  - RNA-sequencing data: 5 normal pleurae and 40 malignant pleural mesotheliomas - Targeted DNA-sequencing of the 165 genes included in the “Solid and Haematological tumors” panel (BRIGHTCore, Brussels, Belgium): 6 MPM samples. 2 FASTQ files for each sample (paired).

  Dataset EGAD00001008740

• scRNAseq data of scrambled and siRNA-mediated knock-down of the minor spliceosome snRNA U6atac

  scRNAseq data of scrambled and siRNA-mediated knock-down (96h) of the minor spliceosome snRNA U6atac in androgen-sensitive LNCaP cells and in patient derived neuroendocrine organoids (PM154). Three replicates for each cell line.

  Dataset EGAD00001007996

• WGS and WTS data of patient diagnosed with HSTCL

  WGS and WTS data of a single patient diagnosed with HSTCL. Whole-genome sequencing (WGS) was performed for the tumor-normal sample. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 4000 2x151 bp read length. Whole-transcriptome sequencing (WTS): Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on Illumina HiSeq 2500 with 2x101 bp read length.

  Dataset EGAD00001005229

• GIS-LUNGTCR1-2016_SNP-ARRAY_CASE

  This dataset contains 61 tumors SNP-array dataset from 15 EGFR mutant lung adenocarcinoma patients.

  Dataset EGAD00010001177

• GIS-LUNGTCR1-2016_SNP-ARRAY_CONTROL

  This dataset contains 15 control SNP-array dataset from 15 EGFR mutant lung adenocarcinoma patients.

  Dataset EGAD00010001176

• 4 - transcriptome (.bam) files, 2 -called somatic mutations (.vcf) files and 2 coverage (.csv) files

  The dataset contains 4 .bam whole transcriptome files that were generated from 2 tumor samples (one .bam file per sample was created using exome-capture (hybrid capture) and the other .bam file was created using ribo-repletion (inverse mRNA selection) library preparation technology). The dataset also contains 2 somatic mutations (.vcf - sample) files (one per sample) which serve as input for Vardetector package (vardetector/vardetector at main · julijselb/vardetector) to produce somatic coverage over those mutations from the .bam file. Therefore, the dataset also contains 4- .csv files (number of reads per somatic mutation that contain the somatic mutation variant and the ones that do not contain the somatic mutation variant) that serve as outputs of the Vardetector package.

  Dataset EGAD50000002055

• Interval whole-genome sequence (WGS) data

  Whole-genome sequencing (WGS) genotype data generated as part of the Interval project. The data are reported, separately per chromosome, in variant call format (VCF). The genotypes are denoted in diploid format (for chrY the genotype 1 denoted as 1/1 and 0 denoted as 0/0). Note that multi-allelic variants are present in the data, but encoded to appear on separate, consecutive lines. The data are reported in following versions - unphased, phased, phased with imputation, sites only. Note: the unphased version has additional genotype information, while the phased versions only contain the genotypes.

  Dataset EGAD00001008661

• Prevalence and association of microsatellite instability and Lynch syndrome Pan-Cancer and development of a personalized cancer risk prediction tool for Lynch syndrome carriers in India

  The study aimed to systematically study MSI/ MMRd status in tumour DNA and germline mutations in mismatch repair (MMR) genes across a unique, large and heterogeneous group of commonly observed non-colorectal gastrointestinal and genitourinary tumours in the Indian population.

  Study EGAS50000001449

• scRNAseq of ALS patients

  The data set contains information from 9 individuals (5 ALS + 4 controls) using single cell RNA sequencing in combination with TCR V(D)J sequencing to study the immune profile of the central nervous compartment (CSF). Sequencing was done using 10x Genomics platform (5’ scRNAseq &amp; V(D)J Reagent Kits v1.1). 5P and TCR libraries were then pooled and for sequencing on the NovaSeq sequencer. Provided files are in .fastq.gz format and per individual four files are available (Read 1&amp;2 and Lane 1&amp;2).

  Dataset EGAD00001009623

• A Phase II Clinical Trial of the PARP Inhibitor Talazoparib in BRCA1 and BRCA2 Wild-Type Patients

  The Talazoparib Beyond BRCA (TBB), a phase II proof-of-concept clinical trial, was designed to test the efficacy of talazoparib, a potent, orally bioavailable PARP inhibitor, with an established Phase II recommended dose, in the treatment of advanced BRCA wildtype (WT), HER2-negative breast cancer and other solid tumors with homologous recombination (HR) deficiency. Eligible patients had advanced HER2-negative breast cancer or other solid tumors with a germline or somatic mutation in a gene linked to the HR pathway. Patients identified as harboring a deleterious or suspected deleterious germline or somatic mutation in the HR pathway were treated with single agent talazoparib until disease progression. Primary and metastatic tumor samples were sequenced with panel sequencing and exome sequencing to detect commonly mutated genes and those associated with DNA repair deficiency. In addition, ctDNA was sequenced at baseline and progression. Fastq files for tumor and ctDNA sequencing are deposited.&nbsp;

  Study phs002803

• The genomic landscape of cutaneous squamous cell carcinoma from immunosuppressed and immunocompetent patients reveals common drivers and a novel mutational signature associated with chronic azathioprine exposure

  Cutaneous squamous cell carcinoma (cSCC) has a high tumour mutational burden (50 mutations per megabase DNA pair). Combining whole exome analyses from 40 primary cSCC tumours, comprising 20 well differentiated and 20 moderately/poorly differentiated tumours, with accompanying clinical data from a longitudinal study of immunosuppressed and immunocompetent patients, coupled with integration of independent gene expression studies has allowed the identification of commonly mutated genes and altered pathways and processes. Mutational signature analysis revealed the presence of a novel signature (signature 32), which was found exclusively in the tumours from immunosuppressed patients who had been exposed to azathioprine. Characterisation of a panel of 15 keratinocyte cancer cell lines derived from tumours from immunocompetent and immunosuppressed patients reveals that they accurately reflect the mutational signatures and genomic alterations of primary tumours and provide a resource for the validation of tumour drivers and therapeutic targets.

  Study EGAS00001002612

• TRACERx: TRAcking non-small cell lung Cancer Evolution through therapy (Rx). Pilot Study. Multi-region sequencing of early-stage NSCLCs.

  Deciphering the complexity of non-small cell lung cancer (NSCLC) evolutionary histories may elucidate the basis for its dismal outcome. We performed multi-region sequencing of early-stage NSCLCs. Spatial dissection revealed branched tumor evolution, with driver mutations occurring before and after subclonal diversification. Intra-tumor heterogeneity in DNA copy number alterations, translocations and endogenous APOBEC mutational processes demonstrates that NSCLC may follow multiple distinct evolutionary trajectories simultaneously. In smokers, despite maintained carcinogen exposure, temporal dissection reveals a relative decrease in smoking-related mutations during tumor progression, accompanied by an increase in APOBEC-related mutations. In the tumors from ex-smokers, genome-doubling occurred before subclonal diversification, suggesting prolonged latency before clinical detection. Multi-region sequencing demonstrates the relentless and heterogeneous nature of genomic instability processes in early-stage NSCLCs.

  Study EGAS00001000809

• Whole genome characterisation of lung cancer organoids and tissue

  Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here we describe a method to establish long-term expanding human airway organoids from broncho-alveolar biopsies or lavage material. The pseudostratified airway organoid epithelium consists of basal cells, functional multi-ciliated cells, mucus-producing goblet cells, and CC10-secreting club cells. Airway organoids derived from cystic fibrosis (CF) patients allow assessment of CFTR function in an organoid swelling assay. Organoid culture conditions also allow gene editing as well as the derivation of various types of lung cancer organoids. Respiratory syncytial virus (RSV) infection recapitulated central disease features and dramatically increases organoid cell motility, found to be driven by the non-structural viral NS2 protein. We conclude that human airway organoids represent versatile models for the in vitro study of hereditary, malignant, and infectious pulmonary disease.

  Study EGAS00001002899

• Integrative sequencing reveals alterations in untreated and castration resistant prostate cancer

  We report the integrative sequencing of genomic, transcriptomic and DNA methylation changes in 28 untreated (PC) and 13 castration resistant prostate cancers (CRPC). AR, TGF-β and WNT signaling pathways were altered in CRPCs. We identified two new fusion genes, TMPRSS2-SKIL and DOT1L-HES6. Fusion analysis in an independent cohort validated SKIL as a recurrent 3’ fusion partner and oncogene in prostate cancer. The HES6 fusion was found in an AR-negative CRPC, and HES6 overexpression in vitro led to androgen independent growth. A distinct DNA methylation signature was found for CRPC. Transcriptome assembly uncovered 128 previously unannotated prostate cancer associated transcripts, including the ERG regulated transcript TPCAT-10-36067 whose knockdown had a dramatic effect on the growth, invasiveness, and rate of apoptosis of prostate cancer cells.

  Study EGAS00001000526

• ATAC-Seq of healthy and IBD blood samples

  PBMCs from blood samples of 9 age- and gender-matched healthy subjects and 25 IBD patients were isolated through a Ficoll density gradient and used to isolate live CD4 T cells through a magnetic cell isolation kit (Miltenyi Biotec). Twelve thousand live CD4 T cells were then used to prepare ATAC-Seq libraries. Briefly, crude nuclei of live CD4+ T cells were treated with Tagment DNA buffer and Tagment DNA Enzyme (Nextera DNA Library Prep Kit, Illumina), and then the DNA was purified by MinElute PCR Purification Kit (Qiagen). Transposed DNA fragments were amplified using specific adapters followed by purification with MinElute PCR Purification Kit (Qiagen). Fragments from 240-360pb were selected in the PippinHT system (Sage Science). The quality of the library and its DNA concentration were assessed by Bioanalyzer instruments (Agilent Technologies) and ultimately submitted for sequencing using Illumina HiSeq 2500 sequencer, V4 chemistry.

  Study EGAS00001007343

• Neoadjuvant nivolumab or nivolumab plus ipilimumab in early-stage triple negative breast cancer: phase 2 adaptive BELLINI trial. RNA-Seq

  The adaptive BELLINI trial explored whether short combination ICI induces immune activation (primary endpoint: two-fold increase in CD8+ T cells or IFNG), providing rationale for neoadjuvant ICI without chemotherapy. In window of opportunity cohorts A (4 weeks anti-PD1) and B (4 weeks anti-PD1 + anti-CTLA4), we observed immune activation in 53% (8/15) and 60% (9/15) of patients, respectively. High tumor-infiltrating lymphocytes (TILs) correlated with response. Based on these data, we opened cohort C for patients with high TILs (≥50%) who received 6 weeks neoadjuvant anti-PD1 + anti-CTLA4 followed by surgery (primary endpoint: pathological complete response, pCR). 53% (8/15) of patients had major pathological response (< 10% viable tumor) at resection, with 33% (5/15) having pCR. All cohorts met Simon’s two-stage threshold for expansion to stage II. In conclusion, neoadjuvant immunotherapy without chemotherapy demonstrates potential efficacy and warrants further investigation in patients with early TNBC.

  Study EGAS50000000567

• Neoadjuvant nivolumab or nivolumab plus ipilimumab in early-stage triple negative breast cancer: phase 2 adaptive BELLINI trial. WES

  The adaptive BELLINI trial explored whether short combination ICI induces immune activation (primary endpoint: two-fold increase in CD8+ T cells or IFNG), providing rationale for neoadjuvant ICI without chemotherapy. In window of opportunity cohorts A (4 weeks anti-PD1) and B (4 weeks anti-PD1 + anti-CTLA4), we observed immune activation in 53% (8/15) and 60% (9/15) of patients, respectively. High tumor-infiltrating lymphocytes (TILs) correlated with response. Based on these data, we opened cohort C for patients with high TILs (≥50%) who received 6 weeks neoadjuvant anti-PD1 + anti-CTLA4 followed by surgery (primary endpoint: pathological complete response, pCR). 53% (8/15) of patients had major pathological response (< 10% viable tumor) at resection, with 33% (5/15) having pCR. All cohorts met Simon’s two-stage threshold for expansion to stage II. In conclusion, neoadjuvant immunotherapy without chemotherapy demonstrates potential efficacy and warrants further investigation in patients with early TNBC.

  Study EGAS50000000568

• DAC Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma

  Data access requests for the raw data used in publication "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  Dac EGAC50000000016

• Dataset for whole exome sequencing of PTCLs

  The dataset consists of whole exome sequencing FASTQ files and analyzed data, including single nucleotide variants (SNVs) and short insertions and deletions (Indels) of candidate driver genes.

  Dataset EGAD50000001798

• DCC_R26.PRAD-CNSM-Array

  Raw Array data from the PRAD-CA for ICGC DCC Release26

  Dataset EGAD00010001414

• DCC_R26.2.PRAD-CNSM-Array

  Raw Array data from the PRAD-CA for ICGC DCC Release27

  Dataset EGAD00010001519

• NKI-AvL CRC-OVC scTCR RNA-seq

  The dataset “NKI-AvL CRC-OVC scTCR RNA-seq" includes 368 BAM files from paired-end RNA sequencing on Illumina MiSeq for 2 colorectal cancer and 2 ovarian cancer patients.

  Dataset EGAD00001004342

• Exome sequencing of tumor samples

  We utilized exome sequencing for DNA obtained from saliva (germline DNA) and the four spatially separated tumor foci and 3 corresponding lymph node metastases

  Dataset EGAD00001000762

• Rare coding variants in lupus risk genes

  Set of 133 bam files from patients affected with Lupus. BAM alignments for exonic variants present in 76 Lupus-related genes. VCF file describing the variants.

  Dataset EGAD00001004859

• 10X Genomics WGS data of de novo assembly individual EGYPT

  10x Genomics linked read data used in variant phasing and de novo assembly scaffolding for the EGYPT individual (mapped against GRCh38).

  Dataset EGAD00001006035

• NICHE - RNA-seq of MMR proficient and MMR deficient early stage colon cancers

  The dataset includes 77 FASTQ files from single-end total RNA sequencing on Illumina HiSeq2500 for 39 patients.

  Dataset EGAD00001006042

• WES of CTCL patients

  Paired end whole exome sequencing (WES) data of tumor/normal pairs (sorted malignant CD3+/Vb+ T-cells and CD19+ non-malignant B-cells) for the identification of somatic mutation.

  Dataset EGAD00001006895

• BAM-file spanning the breakpoint region +/- 100kb of Ewing sarcoma

  Extracted regions from WGS of Ewing sarcoma spanning fusion breakpoints +/- 100kb for ctDNA tracking in plasma

  Dataset EGAD00001009110

• Somatic L1 retrotransposition dynamics in high-grade serous ovarian cancer

  Somatic L1 retrotransposition was mapped in high-grade serous carcinoma (HGSC) tumors using LDI-PCR/Nanopore-seq method. This method identifies somatic L1 insertions originating from two active L1 loci at chr22q12.1 and chrXp22.2. Multiple tumors from same patient were utilised to understand L1-mediated intrapatient heterogeneity.

  Study EGAS50000001198

• Genomic and transcriptomic landscape of aggressive thyroid cancer

  Molecular characteristics of anaplastic thyroid cancer (ATC) and advanced differentiated thyroid cancers (DTCs) have not been fully elucidated. In this study, we applied various types of massively-parallel sequencing technology to 113 advanced TCs, including 27 ATCs and 86 advanced DTCs, to reveal their genomic and transcriptomic characteristics.

  Study EGAS00001003540

• Smart-seq3 scRNA-seq of cells from primary (OV2295) and metastatic (OV2295R2) high-grade serous ovarian cancer cell-line

  In this project, single cells extracted from two high-grade serous ovarian cancer cell-lines, one primary (OV2295) and one metastatic (OV2295R2), where split into two 384 well plates and libraries were prepared using Smart-seq3 single cell RNA sequencing (Hagemann-Jensen et al, 2020).

  Study EGAS00001006868

• Circulating Tumor DNA Analysis in ERBB2-Amplified Colorectal Cancer: Biomarker Analysis of the MyPathway Trial

  Combination of two HER2-directed antibodies, pertuzumab and trastuzumab (P+T), has antitumor activity in HER2-positive colorectal cancer (CRC). Although liquid biopsies are increasingly being used in clinical oncology, the association between tumor and circulating tumor DNA (ctDNA) ERBB2 status and ctDNA monitoring for early response and resistance are unknown. Eighty-five patients with ERBB2-amplified and/or overexpressed CRC were treated with P+T in the MyPathway trial; 42 had ctDNA testing at Cycle 1 Day 1 (C1D1), and 38 had longitudinal plasma tested for ctDNA. We analyzed the ctDNA vs tissue ERBB2 concordance, genomic co-alterations, and ctDNA dynamics and association with response. Forty-one (98%) of 42 patients had genomic alterations detected in ctDNA at C1D1, and 29 (69%) had ERBB2 amplification in ctDNA. There was a strong correlation between ERBB2 copy number on next-generation sequencing in tissue and C1D1 ERBB2 ctDNA copy number. Thirty-seven percent achieved a molecular response by C3D1 on P+T, which was associated with prolonged progression-free survival and overall survival (OS). CDKN2A and KRAS mutations were associated with shorter OS, and a trend was seen with PIK3CA mutations. Several emerging co-alterations were identified in ctDNA at progression, including in the MAPK and PI3K pathways and other tyrosine receptor kinases. ctDNA can detect ERBB2 amplification in many, but not all, patients with ERBB2 amplification detected in tumor samples. ctDNA molecular response was associated with better survival, and ctDNA co-alterations may offer insights into mechanisms of intrinsic and acquired resistance.

  Study EGAS50000000916

• LLNEXT Pilot MGS sequencing

  This dataset contains sequencing data from fecal microbiome from LLNEXT project

  Dataset EGAD00001011293

• Canadian prostate cancer samples (CPC-GENE) for PanProstate study

  CPC-GENE has sequenced the genomes of 350 intermediate risk prostate cancers to identify genetic signatures that differ in cancers that responded well to treatment compared with those that did not. CPC-GENE also has sequenced multiple regions of prostate cancer from the same gland to determine if and how the genetic make-up of prostate cancer varies within an individual man’s prostate

  Study EGAS00001003037

• Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

  Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n=17) and DNA methylation (whole-genome bisulphite sequencing, n=10) in human islets, generating high-resolution chromatin state maps through integration with established ChIP-seq marks. We found enrichment of GWAS signals for T2D and fasting glucose was concentrated in subsets of islet enhancers characterised by open chromatin and hypomethylation, with the former annotation predominant. At several loci (including CDC123, ADCY5, KLHDC5) the combination of fine-mapping genetic data and chromatin state enrichment maps, supplemented by allelic imbalance in chromatin accessibility pinpointed likely causal variants. The combination of increasingly-precise genetic and islet epigenomic information accelerates definition of causal mechanisms implicated in T2D pathogenesis.

  Study EGAS00001002592

• Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19

  In coronavirus disease 2019 (COVID-19), hypertension and cardiovascular diseases are major risk factors for critical disease progression. However, the underlying causes and the effects of the main anti-hypertensive therapies-angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs)-remain unclear. Combining clinical data (n = 144) and single-cell sequencing data of airway samples (n = 48) with in vitro experiments, we observed a distinct inflammatory predisposition of immune cells in patients with hypertension that correlated with critical COVID-19 progression. ACEI treatment was associated with dampened COVID-19-related hyperinflammation and with increased cell intrinsic antiviral responses, whereas ARB treatment related to enhanced epithelial-immune cell interactions. Macrophages and neutrophils of patients with hypertension, in particular under ARB treatment, exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1. Although the limited size of our cohort does not allow us to establish clinical efficacy, our data suggest that the clinical benefits of ACEI treatment in patients with COVID-19 who have hypertension warrant further investigation.

  Study EGAS00001004772

• A model for predicting response to PD-1 inhibitors in NSCLC

  Whole exome sequencing was used to examine the impact of human leukocyte antigen B44 in a non-small cell lung cancer cohort treated with single agent pembrolizumab with over five years of follow-up.

  Study phs002244

• Multidimensional Proteomics analysis of intractable cancers with prospective observational cohort for precision medicine

  Multi-omics project of Non small cell Lung Cancer. Exome and RNAseq datasets were generated from normal-tumor pairs of Non small cell Lung Cancer patients from the retrospective cohort.

  Study EGAS50000000592

• Liquid biopsy for molecular characterization of diffuse large B-cell lymphoma and early assessment of minimal residual disease

  Genomic data from Diffuse-large B-cell lymphomas at diagnosis and during the treatment. The processed samples were : -Circulating tumor DNA: at diagnosis and after2-cycles of treatment. -Tumour lymph node at diagnosis -Genomic DNA

  Dataset EGAD50000000310

• Whole-exome sequences of ovarian clear cell carcinomas and paired normal DNA

  Whole-exome sequencing dataset for the Australian Ovarian Cancer Study (AOCS) and The Jikei University School of Medicine (JIKEI) ovarian clear cell carcinoma (OCCC) clinical outliers project, representing 10 donors. Consists of 20 fastq files: one normal and one tumour from each patient.

  Dataset EGAD00001006004

• Feb2020 interim Genes and Health (28k) GSA imputed genotyped data

  Genotyped data for 28,022 British individuals with South Asian ancestry from the Genes and Health cohort (Feb2020), which were imputed with the GenomeAsia pilot reference panel.

  Dataset EGAD00001007815

• Molecular Characterization for Nasopharyngeal Carcinoma (NPC)

  Total RNA was isolated from 50 formalin-fixed paraffin-embedded nasopharyngeal cancer (NPC) specimens using the RecoverAll Total Nucleic Acid Isolation kit (Ambion). Tumor RNA libraries were prepared with 200ng RNA using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold, and sequenced with &gt;80 million 100 bp paired-end reads.

  Dataset EGAD00001009047