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• WTCCC3 case-control study for Primary Biliary Cirrhosis

  Genome-wide association scan was performed in 1,840 cases of primary biliary cirrhosis and 5,163 controls. Replication of new associations was tested in an independent set of 620 cases and 2,514 controls.

  Study EGAS00000000039

• 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

• FASTQ files of the cell-free RNA from the maternal blood

  cell-free RNA from the maternal plasma obtained at round the 12, 20, 28 and 36 week gestational age from the cases of preeclampsia combined with fetal growth restriction (n=39) and their matched controls (n=156). All samples are from the Pregnancy Outcome Prediction (POP) study.

  Dataset EGAD00001015416

• A Multimodal Atlas of Human Brain Cell Types 2021 Data

  Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This dataset consists of transcriptome samples collected during Patch-seq recordings from layer 5 pyramidal neurons in the human middle temporal gyrus.

  Study phs002697

• Efficacy of dual KRAS G12D–EGFR blockade versus triple combinations in patient-derived models of KRAS G12D-mutant colorectal cancer

  RNA sequencing was performed on patient-derived xenograft (PDX)-derived organoid models of metastatic colorectal cancer (mCRC). The aim of this study was to characterize the transcriptional landscape of KRAS-mutant mCRC cells in response to therapeutic strategies targeting the EGFR and KRAS signaling pathways. Transcriptomic profiling was conducted following drug treatments to investigate molecular changes associated with single and combination therapies. A total of 24 samples were analyzed.

  Study EGAS50000001700

• Possible DNA damage after paternal exposure to ionizing radiation in radar technicians

  Effects of accidental and prolonged radiation exposure on the human germline remain a topic of medical interest. Transgenerational signatures of ionizing radiation exposure are primarily implicated to be clustered de-novo mutations (cDNMs, multiple de-novo mutations within 20bp). We sequenced the whole genome of 110 children from 70 families (Radar cohort). The father in this cohort were exposed to 0-353mSv of ionizing radiation and serve as exposed samples.

  Study EGAS00001007321

• BRAF_and_MEK_resistant_cell_line_clones

  The Sanger Institute has the largest collection of genetically-characterised cancer cell lines world-wide (we have collected >1000 human cancer cell lines which are being screened against >400 cancer therapeutics (http://www.sanger.ac.uk/genetics/CGP/translation). These lines have been characterized to the level of gene copy number, gene expression and cancer gene mutation sequence data. This has enabled us to select melanoma lines with varying BRAF mutational status and that show sensitivity to a range of BRAF inhibitors. Sensitive lines are being used to generate resistant clones by serial exposure to increasing concentrations of BRAF and MEK inhibitors and these are being characterised by genome-wide copy number analysis as well as by whole exome sequencing.

  Study EGAS00001000172

• 3q-capture DNA sequencing of primary AMLs with 3q26 rearrangements

  This dataset contains DNA sequencing of the chromosome 3q region in 28 primary AML cases with 3q26 rearrangements (3q26-rearranged AML). Genomic DNA was fragmented using the Covaris shearing device (Covaris), and sample libraries were assembled following the TruSeq DNA Sample Preparation Guide (Illumina). After ligation of adapters and an amplification step, target sequences of chromosomal regions 3q21.1-q26.2 were captured using custom in-solution oligonucleotide baits (Nimblegen SeqCap EZ Choice XL). The design of target sequences was based on the human genome assembly hg19: chr3q21.1:126036241-130672290 - chr3q26.2:157712147-175694147. Amplified captured sample libraries were paired-end sequenced (2x100 bp) on the HiSeq 2500 platform (Illumina) and aligned against the hg19 reference genome using the Burrows-Wheeler Aligner (BWA).

  Dataset EGAD00001006820

• Cohesin Mutations in AML

  Cohesin shapes the nuclear chromatin architecture, including enhancer-promoter interactions, and its components, of which especially STAG2 and RAD21, are frequently mutated in myeloid malignancies. To elucidate mechanisms of leukemogenesis associated with cohesin mutations in humans, we comprehensively characterized genetic, epigenetic, transcriptional, and chromatin conformational changes in acute myeloid leukemia (AML). To corroborate our findings, we performed complementary siRNA-mediated depletion of STAG2, its paralogue STAG1 or RAD21 in cord blood-derived CD34+ primary human hematopoietic stem and progenitor cells (HSPCs). We show that STAG2 mutations consistently lead to the loss of STAG2 protein and are associated with a specific set of co-occurring mutations, while STAG1 was never mutated in AML. Loss of STAG2 was frequently compensated by STAG1. Still, specific loci displayed altered cohesin occupancy, gene expression and corresponding changes in local chromatin activation as measured by H3K27ac enrichment and chromatin accessibility. High-throughput chromosome conformation capture (in-situ Hi-C) revealed significantly altered chromatin looping in cohesin-mutated AMLs, including weakened enhancer-promoter contacts with reduced, cohesin-dependent promoter activity. In HSPCs, we detected transcriptomic and epigenetic effects overlapping STAG2-mutant AML-specific changes following STAG2 knockdown (KD), that were not invoked by the depletion of STAG1. We also found that STAG2 loss in cultured HSPCs impaired the differentiation capacity, especially erythroid colony formation which maintained HSPC-like gene expression. This work establishes STAG2 as a key regulator of cohesin-associated chromatin architecture, gene expression and differentiation in the human hematopoietic system and identifies candidate target genes that may be implicated in leukemogenesis.

  Study EGAS00001007405

• CUT&RUN in G3-MB

  Aligned BAM files from CCUT&RUN sequencing for BRD4 and H3K27ac in Group 3 Medulloblastoma cell models.

  Dataset EGAD50000002301

• CNS and systemic relapse in DLBCL

  Microarray data for 230 DLBCL patients

  Dataset EGAD00010001909

• RNA-seq from melanoma biopsies

  RNA-seq data for melanoma biopsies at baseline and after treatment

  Dataset EGAD00001009059

• Antibody Repertoires in CVID

  The data consist of the DNA sequences of antibody gene rearrangements from peripheral blood human B cells of subjects with Common Variable Immune Deficiency (CVID) and healthy controls subjects.

  Study phs000934

• BipEx_Landen_SWEBIC

  BipEx: Bipolar Exome Sequencing Broad & Karolinska Institutet. EGAS00001005860. "This research project was a collaboration between the Karolinska Institute and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of X SWEBIC Bipolar case samples from collaborators in Sweden. Genomic DNA from each samples was sequenced to a mean depth of 20x"

  Dac EGAC50000000142

• BipEx_Pedersen_Karolinska

  "BipEx: Bipolar Exome Sequencing Broad & Karolinska Institutet. EGAS00001005856. ""This research project was a collaboration between the Karolinska Institute BioBank and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 4,765 control samples from collaborators in Sweden. Genomic DNA from each samples was sequenced to a mean depth of 20x."" "

  Dac EGAC50000000141

• Multiomic Dissection of Movement and Neurocognitive Toxicity Following BCMA-Targeting CAR T Cell Therapy

  Raw sequencing data (GEX, TCR, adn CSP libraries) for longitudinal cerebrospinal fluid and PBMC samples from a multiple myeloma patient treated with cilta-cel who developed MNT.

  Dataset EGAD50000002339

• Long-read whole-genome sequencing dataset of aplastic anemia

  This dataset contains long-read whole-genome sequencing data generated from patients with aplastic anemia and RCC. Genomic DNA was prepared for long-read sequencing and sequenced using single-molecule real-time technology on a PacBio platform.

  Dataset EGAD50000002257

• BCR repertoir sequences from human buffy coat purified B-Cells with DIS3 and control ASO

  This dataset contains BCR sequences of buffy coat purified B-cells from 5 healthy donors. For each sample, sequences were obtained in two conditions : with control Aso and Dis Aso treatment.

  Dataset EGAD50000001601

• CRC Patient-derived-organoids Whole Genome Sequencing

  Whole Genome Sequencing raw paired-ends reads for 20 matched colorectal patient-derived-organoids (normal and tumor). Tumor samples were obtained from patients treated at Niguarda Cancer Center, (Milano, Italy) and Candiolo Cancer Institute (Candiolo, Turin, Italy).

  Dataset EGAD50000000617

• H3Africa ACEGID H3Africa Array Genotype

  SNP Genotyping for Lassa Fever cases and population controls from Nigeria and Sierra Leone using Illumina H3Africa array version 1

  Dataset EGAD00010002510

• Whole exome sequencing for primary lung adenocarcinoma samples

  We performed whole exome sequencing (WES) of 11 formalin-fixed paraffin-embedded lung tumour tissues and paired blood samples.

  Study EGAS00001003680

• 133 CRC RNA-seq fastq

  This dataset contain 133 pairs of colorectal tumor and adjacent normal tissue. For each sample paired RNA-seq fastq were generated using an Illuma Myseq-2000. Those colorectal cancer comprise 101 MSI and 32 MSS tumors.

  Dataset EGAD00001006667

• SCA1 and control cerebral organoids

  3' RNA-sequencing data of cerebral organoids from controls and individuals with SCA1 was performed at day 31 and day 60 of organoid formation. Matched case-control cerebral organoids were used (Ctrl A+SCA1 A and Ctrl B+SCA1 B) as well as isogenic cerebral organoids, CRISPR/Cas9 gene-edited from Ctrl A (SCA1-/CAG and SCA1CAG/CAG). Biological triplicates were assessed for all lines at both time points.

  Dataset EGAD50000002473

• HSP90 inhibitor resistant cells

  K562 cells were treated with different HSP90 inhibitors (PuH71 and Coumermycin A1) and the CNV profil was compared to the parental K562 (untreated). In addition, the CNV profile of HSP90AB1 knockout K562 cells was analyzed.

  Dataset EGAD00010002336

• Settlement of Polynesia

  Genotypes used to reconstruct the settlement timings and paths of Polynesia.

  Study EGAS00001005362

• Developmental Dynamics of Translation in the Human Brain

  We performed ribosome profiling and RNA sequencing from a total of 43 adult brain and 30 prenatal brain samples. The age of adult brain donors ranged from 18 to 82 years (average 39.5 years), with an average post-mortem interval of 9.9 hours. The gestational age of prenatal cortex samples ranged from 12 to 23 weeks, with a mean of 19.9 weeks. 

  Study phs002489

• RCC Infiltrated Macrophages and Monocytes

  Tumor infiltrated Macrophages and Monocytes were sorted on Aria II (Becton Dickinson) into TRIzol LS and flash frozen. RNA was extracted with chloroform. Isopropanol and linear acrylamide were added, and the RNA was precipitated with 75% ethanol. Total RNA (0.649–1 ng) with RNA integrity numbers 6.8 to 10 underwent amplification using the SMART-Seq v4. Ultra Low Input RNA Kit (Clontech; cat. #63488). Amplified cDNA (15 ng) was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems, KK8504) using 8 cycles of PCR.

  Dataset EGAD00001009393

• RNAseq of MCL cell lines

  This study profiles the transcriptomic response of the Mino-VEN-R and Jeko-BTK-R mantle cell lymphoma (MCL) cell lines to pirtobrutinib (PBN) treatment using bulk RNA sequencing. Mino-VEN-R models drug-tolerant persister (DTP) cells that arise during exposure to non-covalent BTK inhibitors. Building on our recent findings that DTP cells undergo metabolic and phenotypic state transitions governed by TCA cycle reprogramming, this dataset aims to capture gene expression changes associated with treatment-induced plasticity. The results contribute to a broader multi-omic framework exploring mechanisms of resistance and therapeutic vulnerability in MCL.

  Study EGAS50000001087

• Oncogene activated human breast luminal progenitors contribute basally located myoepithelial cells

  Basal-like breast cancer originates in luminal progenitors, frequently with an altered PI3K pathway, and focally in close association with genetically altered myoepithelial cells at the site of tumor initiation. The exact trajectory behind this bi-lineage phenomenon remains poorly understood. Here we used a breast cancer relevant transduction protocol including hTERT, shp16, shp53, and PIK3CA(H1047R) to immortalize FACS isolated luminal cells, and we identified a candidate multipotent progenitor. We found that the apparent luminal phenotype of these oncogene transduced progenitors was metastable giving rise to basal-like cells dependent on culture conditions.

  Study EGAS50000000505

• 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

• Infant Spindle Tumour Study (2019-04-11)

  We aim to describe the transcriptomic landscape of infant spindle cell tumours. . This dataset contains all the data available for this study on 2019-04-11.

  Dataset EGAD00001004954

• Converging and evolving immuno-genomic routes towards immune escape in breast cancer

  This study explores the evolution of tumor and blood immune microenvironment and related mechanisms that shape breast cancer progression, culminating in a heterogeneous lethal cancer.

  Study EGAS00001004956

• Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and alterations in 3D genome organization to boost oncogene expression

  Understand whether and how ERα can drive endometrial tumorigenesis. Study the mechanisms that lead to endometrial tumor progression and metastasis formation.

  Study EGAS00001007240

• Phenotypic characterization and prognostic impact of CD103+ tissue-resident memory T cells in diffuse large B cell lymphoma

  Tissue-resident memory T (TRM) cells are a population of memory T cells that stably occupy tissues and play a key role in immunosurveillance, having been linked to favorable survival outcomes in various solid tumors. While TRM cells have been identified in lymph nodes, their phenotype and prognostic significance in B-cell non-Hodgkin lymphoma (B-NHL), including diffuse large B-cell lymphoma (DLBCL), remains poorly characterized. The frequency of CD103 expressing T cells in patient samples with DLCBL was quantified by immunofluorescence (IF) staining of tissue biopsies (n=306) and flow cytometry (n=252) of cell disaggregates, and linked with clinical outcome. The phenotype of TRM cells was characterized by spectral flow cytometry (n=10 DLBCL and 2 reactive lymph node (rLN) samples) and single-cell RNA sequencing (scRNAseq) (n=12 aggressive B cell lymphomas and 4 rLN samples). An additional 51 samples from an external dataset were included to verify the single cell transcriptome findings. The flow cytometry and scRNAseq findings in DLBCL were extrapolated to additional B-NHL entities. Through analysis of these datasets we were able to characterize CD103+ TRM-like cells in DLBCL and other B-NHL entities and identified them to represent a prognostically favorable population with an activated/cytotoxic T cell phenotype.

  Study EGAS50000000943

• Sequenced IDH wildtype, untreated, human glioblastoma samples (GB-UK cohort)

  BAM files for 42 IDH wildtype, untreated, human glioblastoma samples from the GB-UK cohort, published in Noorani & Haughey et al. Cancer Discovery (2025).

  Dataset EGAD50000001649

• WGBS dataset for lymphnode metastasis samples from prostate cancer

  This dataset contains WGBS sequencing data of lymphnode metastasis samples from prostate cancer. Sequencing was performed on Illumina HiSeq X Ten. The sequencing was always paired.

  Dataset EGAD50000001183

• Dataset for RNA sequencing glioblastoma data

  This dataset contains RNA sequencing data of 36 glioblastoma samples. Sequencing was performed on Illumina NovaSeq 6000 using TruSeq Stranded RNA Kit. The sequencing was always paired.

  Dataset EGAD50000000688

• Germline loss-of-function P2RY8 variants in SLE

  Set of 8 bam files from patients affected with Lupus. BAM alignments for exonic variants present in P2RY8 gene. VCF file describing the variants.

  Dataset EGAD00001008330

• in silico drug target prediction for melanoma

  31 samples transcriptomics to simulate the knock-out of all targets of a drug on an objective function such as growth or energy balance.

  Dataset EGAD00001009089

• New Caledonia low-coverage whole-genome sequencing data

  Mapped sequence reads in BAM format for 64 individuals reporting Kanak ancestry recruited in New Caledonia sequenced at four times target coverage using the Illumina HiSeq 4000 platform.

  Dataset EGAD00001002665

• Glioblastoma stem cell lines RNA-seq data

  RNA-seq data for 54 Glioblastoma stem cell (GSC) lines. Fastq files of the strand-specific paired-end RNA-seq data are available.

  Dataset EGAD00001006195

• Ribo-Seq dataset of Targeting the dark proteome to expand the lineage-retained antigen landscape in neuroblastoma

  This dataset contains ribosome profiling (Ribo-seq) data generated to map actively translated open reading frames, including non-canonical ORFs from the "dark proteome", in neuroblastoma, supporting the identification of translation-validated tumor antigens. Ribosome-protected mRNA fragments (~28–30 nt) were isolated from 47 neuroblastoma samples comprising cell lines, patient-derived tumoroids, and primary patient tumors spanning the adrenergic (ADRN) and mesenchymal (MES) lineage states. Libraries were prepared following a modified version of the McGlincy & Ingolia 2017 protocol and sequenced single-end (1x50 bp) on the Illumina NextSeq 2000 platform. Raw data are provided as single-end fastq.gz

  Dataset EGAD00001016123

• DO NOT USE - Whole genome sequencing of SI-NETs from six patients

  Small intestine neuroendocrine tumor (SI-NET), the most common cancer of the small bowel, often displays a curious multifocal phenotype with several intestinal tumors centered around a regional lymph node metastasis, yet the typical path of evolution of these lesions remains unclear. Here, we determined the complete genome sequences of 24 tumor and 3 adjacent normal tissue samples with their paired normal blood samples (totally 33 whole genomes) from 6 patients with multifocal SI-NETs, allowing elucidation of phylogenetic relationships between multiple intestinal tumors and metastases in individual patients.

  Study EGAS00001005009

• AI

  Allelic imbalance (AI) region calls: start and end positions and the measured mBAF and LRR mean of each region after the BAF segmentation algorithm. Software: Illumina GenomeStudio;PennCNV v. 1.0.4;BAF segmentation v1.2.0.

  Dataset EGAD00010001926

• Ex vivo modeling of precision immuno-oncology responses in lung cancer

  Single-cell RNA-sequencing (scRNA-seq) data from paired lung cancer organoids and immune cells. The experiment was performed using the Single Cell 5' solution of 10X Genomics. The dataset includes 15 samples from 4 multiplexed experiments. The multiplexing was performed using the Feature Barcoding technology of 10X Genomics.

  Study EGAS50000000593

• WGS_11pcw_fetus_hdbr_15951_DNA

  Mutations act as molecular barcodes detailing the origins of the cells that compose a tissue. To generate a high resolution map of the clonal origins and migration of cells during early human development, we will perform whole genome sequencing across the extensively sampled tissues of fetuses. Furthermore, the somatic mutations will reveal in utero mutational processes.

  Study EGAS00001005756

• Presence of rare potential pathogenic variants in subjects under 65 years old with very severe or fatal COVID‑19

  Rare variants affecting host defense against pathogens could be involved in COVID‑19 severity and may help explain fatal outcomes in young and middle‑aged patients. Our aim was to report the presence of rare genetic variants in certain genes, by using whole exome sequencing, in a selected group of COVID‑19 patients under 65 years who required intubation or resulting in death (n = 44). To this end, different etiopathogenic mechanisms were explored using gene prioritization‑based analysis in which genes involved in immune response, immunodeficiencies or blood coagulation were studied. We detected 44 different variants of interest, in 29 different patients (66%). Some of these variants were previously described as pathogenic and were located in genes mainly involved in immune response. A network analysis, including the 42 genes with candidate variants, showed three main components, consisting of 25 highly interconnected genes related to immune response and two additional networks composed by genes enriched in carbohydrate metabolism and in DNA metabolism and repair processes. In conclusion, we have detected candidate variants that may potentially influence COVID‑19 outcome in our cohort of patients. Further studies are needed to confirm the ultimate role of the genetic variants described in the present study on COVID‑19 severity.

  Study EGAS00001006372

• Analysis of Treg gene expression patterns by RNA-Seq in patients with rheumatoid arthritis (RA) and healthy controls (HCs) : Comparison between young and elderly individuals

  We compared the gene expression of CD4+CD45RA-CD25hiCD127lo Treg cells from PBMCs between young and elderly RA patients and HCs by RNA-seq

  Study JGAS000693

• Combination Therapies for Personalised Cancer Medicine in drug resistant EGFR mutant lung cancer (2019-06-10)

  This study involves mutagenizing a range of different cell lines with ENU to identify those mutations which engender resistance to targeted treatment. . This dataset contains all the data available for this study on 2019-06-10.

  Dataset EGAD00001005080

• MutWP1: CRUK Grand Challenge Mutographs of Cancer: pancreas_LCM (2020-01-15)

  Samples prepared by LCM - 5 cases for pilot study. Bulk DNA not available. . This dataset contains all the data available for this study on 2020-01-15.

  Dataset EGAD00001005789