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• FIT interval CRCs versus Screen-detected CRCs

  Formalin-fixed, paraffin-embedded samples from 27 FIT interval CRC and 54 screen-detected CRCs collected in a pilot-program of FIT-based CRC screening in the southwest and northwest regions in the Netherlands, were used in this study. DNA was extracted for 1) Shallow Sequencing (copy number analysis) and 2) TSACP Amplicon Cancer Gene Panel (mutations) of 22 FIT Interval CRCs and 45 screen-detected CRCs.

  Dataset EGAD00001006409

• Genomic abnormalities of TP53 define distinct risk groups of paediatric B-cell non-Hodgkin lymphoma

  Whole exome sequencing data from 90 diagnostic lymphoma samples run and published as part of the Leukemia manuscript. 133 total exomes were sequenced including tumour and normal controls. Copy number array data was also generated for 95 patients.

  Dataset EGAD00001008162

• WGS data subfolder HF3J5CCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HF3J5CCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001008493

• sWGS of OV cell lines for ACN rascal study

  This dataset contains 60 .bam files of shallow WGS data (~0.1X) from ovarian cancer cell lines. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008118

• Unifying recovery dynamics in heterogeneous diseases exemplified by COVID-19

  To model recovery dynamics, using severe COVID-19 as the example, we align heterogeneous recovery trajectories via a novel computational scheme applied to longitudinally sampled blood transcriptomes. We thus generate pseudotime trajectories, which we then link to cellular and molecular mechanisms based on cell deconvolution analysis and molecular pathway prediction, thus presenting a unique framework for studying recovery processes over time.

  Dataset EGAD00001008331

• Whole exome and RNA sequencing data from the OXIRI phase 1b clinical trial in Asian pancreatic ductal adenocarcinoma (PDAC) patients

  This dataset contains 8 samples, each of which has paired-end WXS fastq files for Tumour and Normal samples, as well as RNA-Seq fastq file.

  Dataset EGAD00001008632

• cfMeDIP data for 22 WCDT samples

  We analyzed the cell free DNA methylomes using 22 plasma samples from patients with mCRPC prostate cancer in the WCDT project. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.

  Dataset EGAD00001008713

• Whole-genome and transcriptome sequencing files obtained in monozygotic twins discordant for Mayer-Rokitansky-Küster-Hauser syndrome

  Raw, unfiltered, paired-end fastq files obtained through whole-genome and RNA-sequencing, respectively. RNA-seq of affected individuals in three twin pairs. WGS of blood in five twin pairs as well as uterine rudiment tissue of selected affected individuals.

  Dataset EGAD00001008992

• Targeted DNA sequencing dataset for the study "Molecular profiling of EBV associated diffuse large B-cell lymphoma"

  We performed deep targeted DNA sequencing with a panel of 74 selected cancer-related genes previously identified to be recurrently mutated in EBV associated DLBCL. Sequencing was performed on a HiSeq platform (Illumina) with 250 bp paired-end reads. There are 68 FFPE samples in this targetedDNAseq-dataset with 46 unpaired tumors and 22 normals used as a panel of normals.

  Dataset EGAD00001009396

• The University of Hong Kong Colon Cancer Ganciclovir Study WGS Data

  Human clonal intestinal organoids were treated with 1µM MMF (Roche), 20 μM GCV (Hainan Poly Pharm Co Ltd), or in combinations (1 µM MMF + 20 μM GCV or 1 µM MMF + 40 μM GCV) continuously for 4-6 weeks. DNA was extracted after drug treatment. WGS was performed with 150 bp PE sequencing at 30X using an Illumina Novaseq sequencer.

  Dataset EGAD00001009667

• WGS of off-target analysis of base editing in organoids

  Seven clonal organoid lines and one bulk wild-type control sample were paired-end whole-genome sequenced using the Illumina Novaseq 6000 system. We sequenced four clonal intestinal organoid lines harbouring engineered TP53 and FBXW7 mutations as well as three lines targeted for oncogenic APC/TP53/PIK3CA/SMAD4 mutations. The reads were mapped to hg38 genome assembly and data is provided as BAM files.

  Dataset EGAD00001009827

• Tumor/Normal WXS and RNASeq from patients dosed with neoTCR T-cell therapy

  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). Included are the tumor and normal WXS and tumor RNAseq for dosed patients.

  Dataset EGAD00001009830

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (scRNA)

  Data supporting: “Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.” Nowicki-Osuch, Zhuang et al. scRNAseq (FASTQ files) 59 samples

  Dataset EGAD00001010074

• Papua New Guinean Genome Altitude Project Dataset 1

  The PGAP dataset 1 includes 81 whole genome sequences for Papua New Guinean individuals sampled in Daru (N=38) and Mount Wilhelm (N=43). DNA was extrated from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer. The PGAP dataset provides Fastq, mapped cram files (GRCh38) and phenotype measurements.

  Dataset EGAD00001010143

• WGS data from NEN patient derived tumor organoids (PDTOs) and matched parental tumors - MUMC

  The dataset includes cram files from WGS of 2 NEN tumors and matched PDTOs. For all tumors, cram files from WGS of matched normal tissue from the corresponding patients are included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.

  Dataset EGAD00001009988

• Gut microbiome from melanoma patients

  Metagenomics shotgun sequencing was conducted on fecal samples from the Australian patients enrolled in the OpACIN-neo clinical trial (n = 38). Metagenomic shotgun sequencing was performed utilizing the same DNA from the same preparations as for the 16S rRNA gene analysis. Individual libraries were prepared using Nextera XT, and sequencing was performed on the Illumina NovaSeq 6000 S1 (2 x 150bp; Xp workflow).

  Dataset EGAD00001010028

• BCG Molecular Subtyping

  Dataset for the paper: Non-muscle Invasive Bladder Cancer Molecular Subtypes Predict Differential Response to Intravesical Bacillus Calmette-Guérin

  Dataset EGAD00001010065

• RNAseq and ATACseq data

  RNAseq and ATACseq data for the FMF patients and healthy control. The RNAseq data was sequenced on a BGI MGI G400 machine, with PE100 reads. ATAC-seq libraries were prepared with Illumina Nextera primers and sequenced on NovaSeq 6000 platform with 50bp paired-end sequencing, where each sample was sequenced to approximate 60 million reads.

  Dataset EGAD00001010304

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0198_004A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_004A for Lymph node patient sample RLN_02_5Prime

  Dataset EGAD00001010237

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0198_005A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_005A for Lymph node patient sample RLN_03_5Prime

  Dataset EGAD00001010238

• DLP+ Single Cell Genomic Library 98211

  DLP+ Single Cell Genomic Library 98211 for Diffuse large B-cell lymphoma patient sample TFRIPAIR11_DLBCL

  Dataset EGAD00001010239

• DLP+ Single Cell Genomic Library A98180

  DLP+ Single Cell Genomic Library A98180 for Diffuse large B-cell lymphoma patient sample TFRI_Pair_13_DLBCL

  Dataset EGAD00001010240

• DLP+ Single Cell Genomic Library A98193

  DLP+ Single Cell Genomic Library A98193 for Follicular lymphoma patient sample TFRI_Pair_6_FL

  Dataset EGAD00001010241

• DLP+ Single Cell Genomic Library A98203

  DLP+ Single Cell Genomic Library A98203 for Diffuse large B-cell lymphoma patient sample TFRIPAIR8_DLBCL

  Dataset EGAD00001010242

• DLP+ Single Cell Genomic Library A98205

  DLP+ Single Cell Genomic Library A98205 for Follicular lymphoma patient sample TFRIPAIR9_FL

  Dataset EGAD00001010243

• DLP+ Single Cell Genomic Library A98208

  DLP+ Single Cell Genomic Library A98208 for Diffuse large B-cell lymphoma patient sample TFRIPAIR10_DLBCL

  Dataset EGAD00001010244

• DLP+ Single Cell Genomic Library A98221A

  DLP+ Single Cell Genomic Library A98221A for Follicular lymphoma patient sample TFRIPAIR5_FL

  Dataset EGAD00001010245

• DLP+ Single Cell Genomic Library A98225

  DLP+ Single Cell Genomic Library A98225 for Diffuse large B-cell lymphoma patient sample TFRIPAIR12_DLBCL_rel

  Dataset EGAD00001010246

• DLP+ Single Cell Genomic Library A98288

  DLP+ Single Cell Genomic Library A98288 for Follicular lymphoma patient sample TFRIPAIR2_FL

  Dataset EGAD00001010247

• DLP+ Single Cell Genomic Library A98297

  DLP+ Single Cell Genomic Library A98297 for Follicular lymphoma patient sample TFRIPAIR3_FL

  Dataset EGAD00001010248

• DLP+ Single Cell Genomic Library A98167

  DLP+ Single Cell Genomic Library A98167 for Diffuse large B-cell lymphoma patient sample TFRIPAIR4_DLBCL

  Dataset EGAD00001010249

• Paired RNA-Seq for Sarcoma tumors

  Paired RNA-Seq of 199 samples of Sarcoma tumors. The sequencing was done mostly on HiSeq 4000 with Illumina TruSeq Stranded mRNA, ist was also done on NovaSeq 6000 using the same kit. Very few samples were sequenced on HiSeq X Ten with Illumina TruSeq RNA or Illumina TruSeq Stranded mRNA.

  Dataset EGAD00001010256

• Single-cell ATAC-Seq (Chromium Next GEM Single Cell ATAC kit v1.1 from 10X Genomics )

  Human data for chromatin accessibility (scATAC-Seq) in CD34+ B cell precursors.

  Dataset EGAD00001010910

• 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

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0142_004

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0142_004 for Triple negative breast cancer sample SA1035X6XB03209

  Dataset EGAD00001011243

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0162_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0162_002 for Triple negative breast cancer sample SA1035X7XB03502

  Dataset EGAD00001011246

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0162_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0162_001 for Triple negative breast cancer sample SA1035X8XB03420

  Dataset EGAD00001011248

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0164_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0164_002 for Triple negative breast cancer sample SA530X3XB03295

  Dataset EGAD00001011250

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

  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 (WGS BOs/normals)

  Dataset EGAD00001011255

• scRNA-seq, WES, and bulk RNA-seq on longitudinal samples from 7 Lymphoma patients treated with CD20xCD3 bispecific antibodies

  We performed scRNA-seq on 15 fresh lymph node core biopsies from 7 Lymphoma patients treated with CD20xCD3 bispecific antibodies. We also performed whole-exome sequencing (WES) and bulk RNA-seq on formalin-fixed paraffin embedded (FFPE) tumor samples from these patients. WES was additionally performed on matched germline samples (blood) for each patient.

  Dataset EGAD00001011350

• WES raw data set for the study "Genomic profiling of localized (lFL) and systemic follicular lymphoma (sFL) reveals novel insights into FL pathogenesis"

  221 patient samples including 164 initial tumor (TI) samples (53/164 fresh frozen TI samples, and 111/164 formalin-fixed paraffin-embedded (FFPE) TI samples), 22 paired matched normal samples, and 35 unpaired normal samples from healthy donors; FASTQ file format, Agilent SureSelect Human All Exon V6 Kit (Agilent Technologies, Inc., Santa Clara, California, USA)

  Dataset EGAD00001011369

• RNA-sequencing and targeted DNA-sequecing of human thyroid tumors and normal samples

  RNA-sequencing data: 5 normal thyroid tissues, 14 papillary thyroid carcinomas, 2 lymph node metastases, 19 poorly differentiated thyroid carcinomas and 17 anaplastic thyroid carcinomas; Targeted DNA-sequencing of the 165 genes included in the “Solid and Haematological tumors” panel (BRIGHTCore, Brussels, Belgium): 2 normal thyroid tissues, 2 poorly differentiated thyroid carcinomas and 7 anaplastic thyroid carcinomas; 2 FASTQ files for each sample (paired).

  Dataset EGAD00001011678

• RNAseq Atlas in HCC tumors

  The atlas provides a comprehensive exploration of genetic and transcriptomic landscapes within HCC, offering insights into key genomic alterations and gene expression patterns. The integration of DNA sequencing and RNAseq data enhances our understanding of the molecular complexity underlying HCC, potentially paving the way for targeted therapeutic strategies and biomarker discovery in the context of hepatocellular carcinoma.

  Dataset EGAD00001015341

• RNA-seq dataset: Short-term fasting before living kidney donation has an immune-modulatory effect

  This dataset contains 13 RNA-seq samples in CRAM format, generated using the Illumina NovaSeq 6000 platform. The Roche_mRNA_UniversalAdapterUniquePrime protocol was used for library preparation. The aim of the study is to determine the effect of Short-Term Fasting on the abundance and phenotype of different immune cell populations.

  Dataset EGAD00001015472

• RNA-seq data of Metabolic profiling of patient-derived organoids reveals nucleotide synthesis as a metabolic vulnerability in malignant rhabdoid tumors

  Patient-matched normal kidney organoid (103H) and MRT tumoroid (103T2) models were treated for 24h with either DMSO (ctrl), 400nM MTX, or 50nM BAY to investigate the direct effects of drug treatment on the expression of key metabolic enzymes in the nucleotide biosynthesis pathways.

  Dataset EGAD00001015391

• AHA Uganda Study RNAseq Dataset

  This dataset was generated as part of the AHA Uganda Study, an Acute Rheumatic Fever case-control prospective study conducted in Uganda. This dataset consists of raw fastqs from RNA sequencing for 266 samples (226 cases, 40 controls) from 162 individuals over five timepoints. RNA was extracted from Paxgene blood samples using the Sureselect HS2 library preparation kit. Sequencing was performed on Illumina NovaSeq 6000, yielding ~30-40 million raw paired reads per sample.

  Dataset EGAD00001015810

• ERDERA WES reanalysis - DPF2 Batch 8

  This dataset comprises processed genomic data from 1001 samples, corresponding to 1001 whole-exome sequencing experiments from ERDERA Data Processing Freeze 2. Data files include CRAM, gVCF (containing short variants, copy number variants, and structural variants), RoH (BED), B-allele frequencies (BW), and variant IGV visualizations (XML). Associated phenotypic and pedigree information for all samples is also included.

  Dataset EGAD50000002635

• Immunogenomics of Malignant Brain Tumors

  We performed systematic and comprehensive multi-sector immunogenomic analyses on 93 samples from a cohort of 30 patients with primary or recurrent gliomas or metastatic brain tumors, representing the largest cohort of these brain cancers studied spatially to date. For each patient, we characterized multiple spatially distinct regions using whole-exome (WES), custom capture validation, RNA, and TCR-sequencing. Our findings underscore the significant differences in clonal architecture between gliomas and metastatic brain tumors which translates into distinct neoantigen landscapes and, in turn, tumor infiltrating T cell clonotypic diversity. These data therefore provide high resolution insights into the immunogenomic landscapes within malignant brain tumors which may inform tumor-specific therapeutic approaches.

  Study phs002612

• Phase I Clinical Trial Describing the Pharmacogenomics of Aspirin

  The study protocol for both cohorts has been previously described (Journal of Thrombosis and Thrombolysis 2012:1-12). HV1 cohort: Briefly 50 healthy volunteers were exposed to two weeks of 325mg/day aspirin after which whole blood RNA was collected in PAXgene tubes and profiled by microarray before and after aspirin exposure. The pre-aspirin samples were profiled on the U133A 2.0 array and the post-aspirin samples were profiled on the U1333plus 2.0 array. HV2 cohort: Briefly 53 healthy volunteers were exposed to four weeks of 325mg/day aspirin after which whole blood RNA was collected in PAXgene tubes and profiled by U133plus 2.0 array before and after aspirin exposure.

  Study phs000548

• Germline

  This study is part of the 'First 1,000 Days of Life and Beyond' study at the Inova Translational Medicine Institute. Whole-genome sequencing data from 1,291 parent-offspring trios was used to study the properties of clustered de novo mutations. The maternal clusters were found to be enriched in regions with accelerated maternal mutation rate and show distinct mutational signatures. For additional details, please refer to: "Germline de novo mutation clusters arise during oocyte aging in genomic regions with increased double-strand break incidence". Jakob M. Goldmann, Vladimir B. Seplyarskiy, Wendy S.W. Wong, Thierry Vilboux, Pieter B. Neerincx, Dale L. Bodian, Benjamin D. Solomon, Joris A. Veltman, John F. Deeken, Christian Gilissen, John E. Niederhuber. Nature Genetics.

  Study phs001522