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• Whole Genome Sequencing of Insulinomas

  Whole Genome Sequencing of Insulinomas and paired blood controls from the same patients.

  Study EGAS50000000321

• Tumor Profiler AML Study

  Multi-omics data generated from 22 samples from the Tumor Profiler AML cohort

  Study EGAS50000000577

• Targeted_sequencing_of_in_vitro_colonies___bulks

  In this study we will perform targeted sequencing on the bulk samples of in vitro colonies

  Study EGAS00001003175

• SCLC tumor sequencing

  In this study we have sequenced the tumor of 28 Small Cell Lung Cancer patients.

  Study EGAS00001003985

• Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients

  Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients

  Dataset EGAD00001001421

• Finnish - THL Psychiatric Family Collection Dataset

  The dataset encompasses 172 Runs from the WGSPD Project 3 - Genomic Strategies to Identify High-impact Psychiatric Risk Variants Project

  Dataset EGAD00001009315

• Single Nuclei RNA sequencing batch 1

  This dataset includes the first 9 PTC samples and 6 ATC samples profiled on the same sequencing flowcell.

  Dataset EGAD00001011366

• MSI_Cancer_Models___RNAseq

  The study will use RNAseq to aid in define determinants of WRN dependency in MSI Cell lines.

  Study EGAS00001004180

• Single cell RNAseq of PDAC organoids

  To study the role of WNT7B, three organoid lines were sequenced using SORT-Seq

  Study EGAS50000001544

• The landscape of cancer genes and mutational processes in breast cancer

  The landscape of cancer genes and mutational processes in breast cancer

  Dataset EGAD00001000133

• Epigenetic Intratumor Heterogeneity and Clonal Evolution in Aggressive Prostate Cancer

  Our study investigated the spatial epigenome variation within 5 aggressive prostate adenocarcinomas.

  Study EGAS00001000682

• Pilot_Fetal_Cell_Atlas_RNAseq

  As part of the Human Cell Atlas we will study fetal tissue.

  Study EGAS00001002553

• 15x_WGS_HELIC_MANOLIS_

  15x whole genome sequencing in samples from the Cretan Greek isolate collection HELIC MANOLIS

  Study EGAS00001001207

• H3K27me3-mediated epigenetic repression regulates neuroblastoma development and contributes to biological heterogeneity

  Characterization of the H3K27me3 repressive landscape in neuroblastoma tumor samples.

  Study EGAS00001008225

• Genetics of male infertility in India

  The study comprises of whole exome and genome files of infertile males of Indian origin.

  Study EGAS00001008171

• Targeted deep sequencing of somatic mutations

  We used targeted deep sequencing to accurately establish the allele frequencies of the mutations identified by exome sequencing

  Dataset EGAD00001000763

• WES from two human osteosarcoma with two samples each from the corresponding cell line

  WES from two human osteosarcoma with two samples each from the corresponding cell line, BAM files

  Dataset EGAD00001005370

• WGS data set used in the study, 2 samples

  WGS data set used in the study, 2 samples

  Dataset EGAD00001007966

• Targeted_EMSeq___Development

  Development of a targeted methylation assay to determine the cell-type composition of a sample.

  Study EGAS00001007202

• WGS data from both single-cell and bulk samples

  This dataset contains the raw BAM/CRAM files used in the manuscript "Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma" Steemers et al. (2026). This includes: - 332 PTA-based single-cell WGS samples (~15X depth) - 7 bulk tumour samples (~30X depth) with matched germline samples (~30X depth) - 14 bulk tumour samples seqeunced by the Princess Maxima Centre diagnostics department (~105X depth) with matched germline samples (~35X depth)

  Dataset EGAD50000002411

• RNASeq profiles from Indian HFrEF Cohort

  The dataset contains whole transcriptomics profiling from a cohort of 49 HFrEF patients. The myocardium samples were collected from these patients during heart transplant of LVAD implantation procedure. The RNA samples were collected in RNAlater. Total transcriptome libraries were prepared using TruSeq Stranded Total RNA Library Prep with Ribo-Zero Gold kit and sequenced on Illumina HiSeq4000.

  Dataset EGAD50000001196

• Whole Genome DNA Methylation MPI

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Catalog No. 30024), the EZ DNA Methylation-Gold Kit (Zymo, D5005) and DNA Clean & Concentrator-5 (Zymo, D4013), following the instruction manual Accel-NGS® Methyl-Seq DNA Library (Revision 160510). Paired-end libraries (2 × 150 bp) were sequenced on a NovaSeq 6000 instrument.

  Dataset EGAD50000001139

• Whole Genome DNA Methylation

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences 30024), the EZ DNA Methylation-Gold Kit (Zymo D5005), and DNA Clean & Concentrator-5 (Zymo D4013), following the instruction manual Accel-NGS Methyl-Seq DNA Library (Revision 160510). Paired-end (2 x 150 bp) libraries were sequenced on a DNBSEQ-T7 instrument (MGI) after library conversion.

  Dataset EGAD50000000766

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 12)

  The dataset contains whole genome sequencing data of 17 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 46 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.

  Dataset EGAD50000000441

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 13)

  The dataset contains whole genome sequencing data of 32 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 82 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.

  Dataset EGAD50000000442

• Overactivation of the IGF signalling pathway in osteosarcoma

  Tumour samples (low coverage WGS) from 35 patients with osteosarcoma were included. All samples were re-evaluated by an experienced bone pathologist who confirmed the diagnosis and a tumour content >50% per sample. All tumours represented conventional high-grade osteosarcomas.

  Study EGAS00001004767

• Longitudinal shotgun metagenomes of preterm infant fecal samples from the NutriBrain trial

  Metagenomic sequencing data generated from 438 fecal samples collected from preterm infants enrolled in the NutriBrain clinical trial, a study investigating the impact of early-life nutrition on gut microbiome development and neurodevelopmental outcomes.The dataset includes raw sequencing files generated on on Illumina NovaSeq 6000. Data files are provided in standard FASTQ format and support investigation of gut microbial composition and functional potential during early neonatal development.

  Dataset EGAD50000002667

• Detecting PKD1 variants in Polycystic Kidney Disease patients by single-molecule long-read sequencing

  Cohort of 19 ADPKD patients characterized using long-read sequencing. The variant identification provided high sensitivity in identifying PKD1 pathogenic variants, with a diagnostic yield of 94.7%. This dataset includes all sequencing data (BAM files) of the 19 patients, in addition to their raw variants (unfiltered) obtained from the long-read sequencing as well as Sanger sequencing (VCF file).

  Dataset EGAD00001003103

• GoNL release 5 raw SNV calls

  These files contain a total of 20.4M SNVs and the complete information output by the GATK UnifiedGenotyper v1.4 on all 767 GoNL samples. These calls are not trio-aware and all genotypes were reported regardless of their quality. Both filtered and passing calls are reported in these files. Filtered calls include (1) calls failing our VQSR threshold and (2) calls in the GoNL inaccessible genome.

  Dataset EGAD00001000743

• Methylation profiling by MCC-Seq of visceral fat (N=199) and whole-blood (N=206) derived from IUCPQ participants

  The study includes NGS-based methylC-capture sequencing (MCC-Seq) on 199 visceral adipose tissue and 206 whole-blood DNA samples derived from obese individuals (BMI >40 kg m-2) in the IUCPQ cohort. We generated 100bp paired-end reads using the Illumina HiSeq2000 or 2500 systems.

  Dataset EGAD00001004787

• low pass WGS of patient from the CN300 cohort

  We copy number profiled 688 tumor regions from 300 patients presenting with advanced prostate cancer and prospectively followed-up (median, 7 years) in the control group of the STAMPEDE trial. Patients were categorised into four metastatic states, namely high-risk non-metastatic (with or without local lymph node involvement) or metastatic (low or high volume).

  Dataset EGAD00001008800

• The BNT162b2 mRNA COVID-19 vaccine induces long-term effects on both adaptive and innate immune responses

  This dataset contains bulk RNA sequencing at different timepoints post-BNT162b2 mRNA COVID-19 vaccination. Stimulation experiments were performed at each of the timepoints (RPMI, Influenza, R848 and Influenza stimuli), resulting in 242 libraries distributed over 4 stimulations and 4 timepoints. Libraries were sequenced on the DBNSEQ platform.

  Dataset EGAD00001011042

• Landscape of Intratumoral NK Cell and ILC in Head and Neck Squamous Cell Carcinoma

  In this study, total innate lymphoid cells (ILCs), including natural killer (NK) cells, were FACS-sorted from eight dissociated primary head and neck squamous cell carcinoma (HNSCC) tumors. In addition, ILCs and NK cells were sorted from peripheral blood of tumor patients. The ILCs and NK cells were analyzed by single-cell RNA sequencing (scRNA-seq) using the Smart-seq2 approach.

  Study phs002002

• Single Cell Omics Resolves Transcriptional Alterations in Sjogren's Syndrome

  Single cell omics resolves transcriptional alterations in Sjogren's Syndrome. This data compares the single cell transcriptional profiles of the minor salivary glands between Sjogren’s Syndrome patients and non-Sjogren’s Syndrome subjects. Portions of this data were reported in two separate publications: Huang & Perez, et al., 2021 Nature Medicine and Yin, et al., 2021, Frontiers in Immunology . 

  Study phs002446

• EXPRESSION OF ANTIBODY-DRUG CONJUGATE TARGETS IN BREAST CANCER METASTASES AND NORMAL TISSUE

  Using bulk mRNA sequencing, we investigated the expression of 72 ADC targets, which are clinically approved or under investigation, in 909 samples (64 primary untreated, 749 metastatic, 96 normal) from 30 female patients from our post-mortem tissue donation program UPTIDER (NCT04531696). The study explores changes in target expression across multiple samples to identify novel targets of clinical interest and validation

  Study EGAS50000001334

• Nanopore Sequencing in adults with autism spectrum disorder (ASD) without intellectual disability

  This pilot study investigates the genetic and epigenetic underpinnings of late-diagnosed autism spectrum disorder (ASD) without intellectual disability or language impairment using long-read nanopore whole-genome sequencing. This approach allows the simultaneous analysis of complex structural variants (SVs) and DNA methylation patterns in genomic regions often missed by short-read methods, such as intronic, non-coding and repetitive regions.

  Study EGAS50000001736

• Renal Cancer Exome Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Dataset EGAD00001000014

• HipSci HumanExome BeadChip analysis - monogenic diabetes

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with monogenic diabetes.

  Study EGAS00001001273

• HipSci HumanExome BeadChip analysis - Macular Dystrophy

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Macular Dystrophy.

  Study EGAS00001002014

• HipSci HumanHT 12 Expression BeadChip analysis - Retinitis Pigmentosa

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Retinitis Pigmentosa.

  Study EGAS00001002030

• Familial_Thrombocytosis_germline_exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 3 relatives from a family with multiple affected familial thrombocytosis (FT) patients. Germline DNA from 2-4 patients affected with FT will be used to prepare libraries and sequenced in one lane of HiSeq sequencing, mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000088

• HipSci Illumina 450K Methylation analysis-Rare_BBS

  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 performed Methylation analysis using the Infinium HumanMethylation450 BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bardet-Biedl syndrome.

  Study EGAS00001001274

• HipSci HumanExome BeadChip analysis - Alport Syndrome

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Alport Syndrome.

  Study EGAS00001002009

• HipSci HumanExome BeadChip analysis - Retinitis Pigmentosa

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Retinitis Pigmentosa.

  Study EGAS00001002015

• HipSci HumanHT 12 Expression BeadChip analysis - Kabuki syndrome

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Kabuki syndrome.

  Study EGAS00001002022

• HipSci HumanHT 12 Expression BeadChip analysis - Congenital Hyperinsulinia

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Congenital Hyperinsulinia.

  Study EGAS00001002025

• HipSci Illumina 450K Methylation analysis - monogenic diabetes

  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 performed Methylation analysis using the Infinium HumanMethylation450 BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with monogenic diabetes.

  Study EGAS00001001275

• Whole-exome sequencing of PTC, benign nodule and normal tissues in 28 patients

  In order to comprehensively investigate the genetic relationship between PTC tumors and benign nodules, we totally collected 127 fresh-frozen biopsies samples from 28 patients with concurrent thyroid benign nodule and PTC (n=20) or simple benign nodule (n=8). We carried out whole-exome sequencing on all the 127 biopsies samples and RNA-sequencing in total of 40 samples.

  Study EGAS00001002312

• HipSci HumanExome BeadChip analysis - Hereditary Cerebellar Ataxias

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Cerebellar Ataxias.

  Study EGAS00001002005

• HipSci HumanExome BeadChip analysis - Kabuki syndrome

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Kabuki syndrome.

  Study EGAS00001002007

• HipSci HumanExome BeadChip analysis-Healthy volunteers

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies from healthy volunteers.

  Study EGAS00001000866

• HipSci HumanExome BeadChip analysis-Rare_BBS

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bardet-Biedl syndrome.

  Study EGAS00001001272

• HipSci HumanExome BeadChip analysis - Primary immune deficiency

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Primary immune deficiency.

  Study EGAS00001002012

• Analysis of transcriptomic profiles from affected and recovered muscle biopsies from children with reversible infantile respiratory chain deficiency.

  All patients carry mitochondrial mutation m.14674T>C but not must also carry mutations in related genes such as TRMU and EARS2. Analysis compares muslce biopsies of affected patients to controls, a patient after recovery to themselves during the the disease phase, and compared patients with additional EARS2 mutations to patients without pathogenic EARS2 mutations.

  Study EGAS00001004647

• HipSci HumanExome BeadChip analysis - Hereditary Spastic Paraplegia

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Spastic Paraplegia.

  Study EGAS00001002006

• HipSci HumanExome BeadChip analysis - Congenital Hyperinsulinia

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Congenital Hyperinsulinia.

  Study EGAS00001002010

• HipSci HumanExome BeadChip analysis - Hypertrophic Cardiomyopathy

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hypertrophic Cardiomyopathy.

  Study EGAS00001002011

• HipSci HumanExome BeadChip analysis - Battens disease

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Battens disease.

  Study EGAS00001002016

• HipSci HumanHT 12 Expression BeadChip analysis - Alport syndrome

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Alport syndrome.

  Study EGAS00001002024

• HipSci HumanHT 12 Expression BeadChip analysis - Hypertrophic Cardiomyopathy

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hypertrophic Cardiomyopathy.

  Study EGAS00001002026

• HipSci HumanHT 12 Expression BeadChip analysis - Macular Dystrophy

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Macular Dystrophy.

  Study EGAS00001002029

• HipSci HumanHT 12 Expression BeadChip analysis - Battens disease

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Battens disease.

  Study EGAS00001002031

• Leeds Melanoma Cohort (LMC) gene expression study

  Array-based profiling (whole genome DASL HT12.4, Illumina Inc) in over 700 FFPE tumour blocks from the population-based Leeds Melanoma cohort recruited in the North of England, with a long follow up. Data used in tumour immune micro-environment investigation (Nsengimana et al 2018, J Clin Invest doi: 10.1172/JCI95351).

  Study EGAS00001002922

• Somatic_mutation_in_skin_epidermis__SMS_

  We aim to assess the range and depth of mutations in genes linked with cancer in skin epidermis surrounding lesions which are undergoing surgical removal. Patient history will be collected to provide a detailed outline of tumour type (including histology), skin type, and sunlight exposure. We will perform ultra-deep targeted sequencing using genes implicated in cancer to try and understand the background of mutations surrounding these lesions

  Study EGAS00001002165

• Single-cell RNA sequencing on single CD45+ immune cells isolated from peripheral blood, lymphnode, ascites, tumour and adjacent normal tissues from six hepatocellular carcinoma patients.

  Single-cell RNA sequencing on single CD45+ immune cells isolated from peripheral blood, lymphnode, ascites, tumour and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional properties of these individual cells, were used to delineate the molecular subtypes, lineage, and functional properties of each cell group

  Study EGAS00001003449

• SDH_deficient_renal_tumours___WGS_

  Succinate dehydrogenase (SDH) deficient renal cancers are a rare and understudied subtype of renal cancer. As such they represent an unmet need in kidney cancer research. Here, we seek to describe the genomics and transcriptomics of SDH deficient renal cancers by sequencing five such tumours. We document their mutational burden, define driver mutations, demonstrate typical patterns of structural variants, and estimate the cell of origin and cellular composition.

  Study EGAS00001004102

• Whole-exome sequencing performed on a patient with chronic myelomonocytic leukemia and B cell acute lymphoblastic leukemia

  We studied the rare case of a patient who underwent transformation of myelodysplastic syndrome to chronic myelomonocytic leukemia and B cell acute lymphoblastic leukemia. We used fluorescence-activated cell sorting and whole-exome sequencing to identify driver mutations in the various clones. This allowed us to propose a model of branching clonal evolution with a possible germline predisposition to cancer.

  Study EGAS00001005117

• Role of cohesin/CTCF in human monocyte differentiation

  Here we study genome architecture in a postmitotic differentiation setting, the differentiation of human blood monocytes (MO). We profiled and compared epigenetic, transcriptome and 3D conformation landscapes during MO differentiation (either into dendritic cells or macrophages) across the genome, with and without siRNA-mediated depletion of RD21 or CTCF, and detected numerous architectural changes, ranging from higher level compartments

  Study EGAS00001005508

• Proteomic Characterization of Intrahepatic Cholangiocarcinoma Identifies Risk-Stratifying Subgroups, Proteins Associated with Time-To-Recurrence, and mTOR Effector Molecule EIF4A1 as a Druggable Therapeutic Target

  Using mass spectrometry-based proteomics, we analyzed two independent cohorts comprising 80 and 62 treatment-naive ICC tumors, 67 adjacent non-malignant tissues, and 9 patient-derived xenografts (PDX). In the first cohort, we identifed two subclusters with distinct times-to-recurrence (TTR). A 4-protein classifier trained on our data cohort accurately stratifies these ICC clusters in the Dong et al. dataset (2022) and in our independent second cohort, revealing similar associations between proteomic motifs and clinical outcomes. The Translation regulator EIF4A1 emerges as a therapeutic target, as its inhibition with novel drug eFT226 significantly reduces tumor growth in an ICC PDX model.

  Study EGAS50000001343

• Reference Epigenomes and Regulatory Landscape of CLL

  Analysis of the reference epigenomes and regulatory landscape of CLL as a whole and its major clinico-biological subtypes (with mutated and unmutated IGHV) in the light of the normal B-cell differentiation. We have extensively characterized the reference epigenomes of seven primary chronic lymphocytic leukemia samples (CLLs) with mutated (n=5) and unmutated IGHV (n=2) as well as several mature B-cell subpopulations (naive B cells from blood and tonsil, germinal center B cells, memory B cells and plasma cells from tonsil) using genome-wide maps of six histone marks (H3K4me3, H3K4me1, H3K27ac, H3K36me3, H3K9me3 and H3K27me3), DNA accessibility (ATAC-seq), DNA methylation (whole-genome bisulfite sequencing) and gene expression (RNA-seq). Furthermore, we have mapped the regulatory chromatin landscape of 100 additional CLL cases using chIP-seq of H3K27ac and ATAC-seq and linked these data to additional layers of information (whole-genome and/or whole-exome sequencing (WGS/WES), RNA-seq and DNA methylation microarrays) studied in the context of the International Cancer Genome Consortium (ICGC).

  Dataset EGAD00001004046

• Analysis of the co-occurrence of LOY and CHIP in Alzheimer's disease patients and control individuals using whole-exome sequencing (WES)

  We performed deep whole-exome sequencing of FACS-isolated CD4+ T lymphocytes, NK and myeloid cells from men with AD and controls exhibiting either LOY or retention of Y chromosome (ROY). We found 39 sequence variants in known (canonical) myeloid driver genes of clonal hematopoiesis (MD-CH) and known lymphoid driver genes (LD-CH), and maximally 14 (35%) of these could co-exist with LOY within the same clone. We further describe 192 unknown drivers of clonal hematopoiesis (UD-CH), which were markedly enriched in AD-LOY individuals (odds ratio=4.8, Benjamini-Hochberg-adjusted p=0.041), and over 20% of these variants were protein-truncating. In myeloid cells, the total burden of all detected drivers correlated with the percentage of LOY cells (Spearman ρ=0.52, adjusted p=0.00041).

  Study EGAS00001008234

• Clinical significance of novel subtypes of acute lymphoblastic leukemia in the context of minimal residual disease-directed therapy

  We evaluate clinical significance of recently identified subtypes of acute lymphoblastic leukemia (ALL) in 598 children treated with minimal residual disease (MRD)-directed therapy. Among the 16 B-ALL and 8 T-ALL subtypes identified by next generation sequencing, ETV6-RUNX1, high-hyperdiploid and DUX4-rearranged B-ALL had the best five-year event-free survival rates (95% to 98.4%); TCF3-PBX1, PAX5alt, T-cell, ETP, iAMP21, and hypodiploid ALL intermediate rates (80.0% to 88.2%); and BCR-ABL1, BCR-ABL1-like and ETV6-RUNX1-like and KMT2A-rearranged ALL the worst rates (64.1% to 76.2%). All but three of the 142 patients with day-8 blood MRD <0.01% remained in remission. Among new subtypes, intensified therapy based on day-15 MRD≥1% improved outcome of DUX4-rearranged, BCR-ABL1-like, and ZNF384-rearranged ALL, and achievement of day-42 MRD<0.01% did not preclude relapse of PAX5alt, MEF2D-rearranged and ETV6-RUNX1-like ALL. Thus, new subtypes including DUX4-rearranged, PAX5alt, BCR-ABL1-like, ETV6-RUNX1-like, MEF2D-rearranged and ZNF384-rearranged ALL have important prognostic and therapeutic implications.

  Study EGAS00001005084

• Solve-RD_EuroNMD_cohort-1_DF1+2_V1

  Solve-RD data submitted to the ERN-EuroNMD cohort for re-analysis (Data freeze 1+2) v1

  Dataset EGAD00001009768

• Pan-tumor genomic biomarkers for personalization of PD-1 checkpoint blockade based immunotherapy

  Tumor mutation burden (TMB) and a T-cell-inflamed gene expression profile (GEP) independently predict clinical outcome in pembrolizumab-treated patients in 22 indications and stratify distinct targets of resistance biology.

  Study phs001572

• Variant calling for UPST-SCCHN3 cohort

  Tumor versus Germline variant calling on UPST-SCCHN3 cohort

  Dataset EGAD50000002178

• NANOPORE_TALL_t_14_16_translocation

  Nanopore sequencing for patients with t(14;16) translocated T-ALL

  Dataset EGAD50000001785

• WXS_TALL_t_14_16_translocation

  Whole exome-sequencing for patients with t(14;16) translocated T-ALL.

  Dataset EGAD50000001783

• WGS_TALL_t_14_16_translocation

  WGS data for patients with t(14;16) translocated T-ALL.

  Dataset EGAD50000001782

• Targeting Heterochromatin Eliminates Malignant Stem Cells in Chronic Myelomonocytic Leukemia Through Reactivation of Retroelements and Innate Immune pathways

  RNA-sequencing, ATAC-sequencing, CUT&Tag-sequencing, data from CMML patient and aged-matched healthy donor CD34+ cells. RNA-sequencing data from patient CD34+ cells after treatment for 4 days with decitabine or UNC0638 inhibitors, alone or together, or left untreated

  Dataset EGAD50000000542

• Duplex sequencing of selected breast cancer patients

  Investigation of post-zygotic and germline variants using whole exome and ultra-deep duplex sequencing in paired uninvolved margin and primaty tumor samples from 126 breast cancer patients with differing survival outcomes, with skin or blood samples as reference. Pairs of uninvolved margin and blood samples were also collected for 15 reduction mammoplasty patients without personal or familial history of cancer, serving as controls.

  Dataset EGAD50000000769

• WES of breast cancer patients and controls

  Investigation of post-zygotic and germline variants using whole exome and ultra-deep duplex sequencing in paired uninvolved margin and primary tumor samples from 126 breast cancer patients with differing survival outcomes, with skin or blood samples as reference. Pairs of uninvolved margin and blood samples were also collected for 15 reduction mammoplasty patients without personal or familial history of cancer, serving as controls.

  Dataset EGAD50000000770

• 16SV4 ribosomal RNA gene sequencing data

  16SV4 ribosomal RNA gene sequencing data of GI samples and associated mixed community cultures collected from pediatric patients at risk for IBD.

  Dataset EGAD50000000485

• Tcells_CD_scRNAseq

  This set features unfiltered, aligned, UMI-based single cell RNA sequencing count data for 5290 Blood, intraepithelial ileum (IEL) and lamina propria ileum (LPL) T cells from Crohn's disease patients as published in Uniken Venema et al, Gastroenterology 2019

  Dataset EGAD00010001649

• Sequencing data for oesophageal and related samples - OACs release 1 (RNA)

  Dataset EGAD00001002259

• WGS data for medulloblastoma samples (MDT-AP)

  WGS data of medulloblastoma tumor/control pairs.

  Dataset EGAD00001003125

• GM18507 direct library preparation (DLP) single-cell genomes

  Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for near-diploid immortalized lymphoblastoid cell line GM18507.

  Dataset EGAD00001003148

• 184-hTERT-L2, SA501X3F, and SA501X4F bulk genomes

  Bulk whole-genome BAM files for 184-hTERT-L2, SA501X3F, and SA501X4F.

  Dataset EGAD00001003151

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - barretts_1

  Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357

  Dataset EGAD00001001394

• Single Cell RNA sequencing of Organoids from TSC2+/- patient IPSCs in H- and L-medium

  This dataset contains single cell RNA sequencing data from Organoids grown in high nutrient (H) and low nutrient (L) medium. Organoids were grown for 110 days. Organoids were grown from a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) and an isogenic control cell line (TSC2+/+).

  Dataset EGAD00001006332

• Single cell ATAC sequencing

  Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell ATAC sequencing following manufacturer's protocol (CG000168 User Guide RevB) for chemistry version 1.0 and targeting 10000 nuclei per sample. Libraries were sequenced using Illumina HiSeq4000 using recommended cycling parameters.

  Dataset EGAD00001007675

• Single cell TCR sequencing

  Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell TCR sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina NovaSeq 6000 using recommended cycling parameters.

  Dataset EGAD00001007674

• Single cell BCR sequencing

  Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell BCR sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina NovaSeq 6000 using recommended cycling parameters.

  Dataset EGAD00001007673

• 5' single cell RNA sequencing

  Pared-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics 5' single cell RNA sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina HiSeq 4000 using recommended cycling parameters.

  Dataset EGAD00001007672

• Cystic Fibrosis Varsity Project Multi-omics data

  This Dataset contains RNA-Seq, H3K27Ac ChIP-Seq, and ATAC-Seq data for 13 cystic fibrosis (CF) patients and 8 healthy volunteers (HV).

  Dataset EGAD00001009062

• Whole transcriptome sequencing of 38 follicular lymphoma tumours.

  This data set includes RNAseq from 38 follicular lymphoma tumours. All tumours were fresh frozen. Libraries were constructed by enriching for poly-A transcripts and sequenced as 75bp paired end reads on an Illumina HiSeq 2500 instrument.

  Dataset EGAD00001009650

• Paired RNA sequencing of 30 samples RRMM (multiple myeloma)

  Paired RNA sequencing of 30 samples RRMM using Illumina TruSeq stranded mRNA kit and either HiSeq2000 or HiSeq X Ten for sequencing.

  Dataset EGAD00001009680

• Whole transcriptome sequencing of 78 follicular lyphoma tumours

  This data set includes RNAseq from 77 follicular lymphoma tumours. All tumours were fresh frozen. Libraries were constructed by enriching for poly-A transcripts and sequenced as 75bp paired end reads on an Illumina HiSeq 2500 instrument.

  Dataset EGAD00001010894

• Telomere attrition becomes an instrument for clonal selection in aging hematopoiesis and leukemogenesis

  Whole genome sequencing of 288 single-cell-derived blood colonies from 3 individuals with splicing factor-mutated clonal hematopoiesis.

  Dataset EGAD00001015640

• Gene expression profiling by RNAseq of multiple cell types derived from patients with LSD1 mutations and healthy controls, and in isogenic cell lines with LSD1 mutation introduced by CRISPR-Cas9

  Cell lines (fibroblasts, reprogrammed from them hiPSCs and differentiated from hiPSCs endoderm, mesoderm and neuronal cells) derived from two male CPRF patients carrying distinct LSD1 mtuations and their healthy fathers as controls were subjected to gene expression analysis by bulk RNAseq to identify mis-regulated genes. Some cell lines were subject to treatment with HDAC inhibitor valproic acid (VPA) or DMSO as controls and also underwent RNAseq analysis. Two isogenic LSD1 mutant hiPSC lines with CRISPR-edited Family B LSD1 mutation were also used for RNAseq analysis (after endoderm differentiation, with or without VPA treatment).

  Study EGAS00001008240

• Clinical evaluation of long read sequencing-based episignature detection in developmental disorders

  Some developmental disorders (DD) are marked by specific genome-wide methylation changes, known as episignatures, which can support diagnosis and reveal underlying mechanisms. Current methods rely on indirect methylation profiling. Here, we assessed whether long-read whole genome sequencing with nanopore technology could directly detect both episignatures and genetic variants. We sequenced forty controls and twenty DD patients, using clustering and dimensional reduction to compare methylome patterns with microarray-based signatures. Our classifiers accurately identified episignatures in 17 of 19 patients with pathogenic variants, matching microarray results. This study shows nanopore sequencing enables comprehensive, haplotype-aware genomic and epigenomic analysis for DD diagnostics.

  Study EGAS50000000719