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• Accelerated clonal evolution in refractory versus relapsed chronic lymphocytic leukemia upon treatment

  Identify and track clonal evolution of clones in consecutive human chronic lymphocytic leukemia samples identified by whole exome sequencing.

  Study EGAS00001003652

• Whole exome sequencing of peripheral T-cell lymphoma (PTCL)

  Somatic mutations in 3 AITL and 3 PTCL, not otherwise specified (PTCL-NOS) specimens were explored using whole-exome sequencing.

  Study EGAS00001000557

• Breast_cancer_topographs

  Breast cancer topography will be explored using a combination of multi-region whole geome sequencing and in-situ RNA sequencing of fixed tissue specimens.

  Study EGAS00001003698

• RNA-seq analysis of human skin

  RNA sequencing analysis comparing epidermal subpopulations in normal and inflamed skin.

  Study EGAS00001002927

• Genome and transcriptome sequence data from a pre-B all (2nd relapse in CNS) tumor patient

  Genome and transcriptome sequence data from a pre-B all (2nd relapse in CNS) patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015291

• WXS dataset of Ewing and Ewing-like-sarcoma tumoroid biobank reveals distinct drug sensitivities: translocation makes the difference

  Creation of living organoid biobank for ewing and ewing-like sarcomas

  Dataset EGAD00001015417

• BIOCLOCK Phenotype Information Dataset

  This dataset contains phenotypic metadata from participants in the BIOCLOCK endurance exercise intervention and epigenetic aging study. It includes intervention status, cardiorespiratory fitness (VO2 max), body composition, estimated leukocyte proportions, and other relevant traits linked to epigenetic aging outcomes.

  Dataset EGAD00001015799

• Functional Significance of Prostate Cancer Risk-SNPs

  Prostate Cancer (PrCa), the most frequently diagnosed solid tumor in men in the U.S., results in ~192,000 new cases and ~27,000 deaths per year. Although the variation of PrCa incidence is likely to be the result of several factors, there is a large body of literature that strongly implicates a genetic etiology. Genome-wide association studies (GWAS) have emerged as the most widely used contemporary approach to identify genetic variants (in particular SNPs) that are associated with increased risk of human disease. For PrCa, at least five GWAS have now been performed yielding a substantial number of well-validated SNPs that are associated with an increased risk of PrCa, and that number continues to grow. A significant problem for many of the PrCa risk-SNPs identified so far, however, is that they do not lie within or near a known gene and they have no obvious functional properties. These findings suggest that many (if not most) of these risk-SNPs will be located in regulatory regions that control gene expression rather than in coding regions that may directly affect protein function. Therefore, in order to define the functional role of currently known risk-SNPs, the target genes must first be identified. A promising strategy to address this problem involves the use of expression quantitative trait loci (eQTL) analysis. Unfortunately, most of the publically available SNP-Transcript eQTL datasets utilize lymphoblastoid cells with only a handful using tissue from target organs. Although useful, these datasets alone are unlikely to be sufficient. Recent studies have demonstrated that gene expression and gene regulation occur in both a tissue-specific and tissue independent fashion and suggest that a complete repertoire of regulatory SNPs can only be uncovered in the context of cell type specificity. To date, such a tissue-specific dataset for normal prostate tissue does not exist. In this study, we have constructed a normal prostate tissue specific eQTL data set.

  Study phs000985

• The Effects of Long-Term Heavy Metal Exposure on Transcriptome Landscape in Human Peripheral Blood Cells

  The present study investigates the impact of long-term residence in a mining area on transcriptome changes induced by heavy metal exposure in human peripheral blood mononuclear cells (PBMCs) from 65 healthy subjects selected from the general population. This study includes the same participants which were recruited in our previous investigation on heavy metal long-term environmental exposure-related gene-specific methylation changes (phs003392.v1.p1). We performed a differential expression analysis to compare the mRNA transcriptome of 31 residents from the mining region (MRR) - individuals living in the Kapan mining area with reported environmental exposures to heavy metals - with that of 34 residents from non-mining regions (NMR) - individuals residing at a considerable distance from mining locations. We also evaluated the potential association of gene expression profiles with the blood metallome, including levels of Ca, Mg, Co, Fe, Mn, Cu, Mo, Se, Zn, As, Sb, Tl, Be, V, Ni. Poly-A selected strand-specific mRNA library was prepared with Illumina Stranded mRNA Prep kit. The sequencing was performed on the Illumina NovaSeq-6000 platform with 38.5 million single-end 100 bp reads on average generated per sample. Quality checking of the sequencing data was performed using Illumina Basespace reports and the program FastQC (V0.10.1). Reads were aligned against the Human Genome Hg38 using STAR (version 2.7.1a). According to our findings, long-term residence in a mining area is correlated with alterations in the blood transcriptome, with responses varying by sex. Pathway analysis revealed upregulation of immune response related pathways, and downregulation of translation and ribosome biogenesis in the PBMCs of the MRR. Pathways related to metal ion transmembrane transport, epigenetic modifications (histone deacetylases (HDACs) and DNA methylation) were upregulated in males, while in females mostly transcripts involved in inflammation and cytokine mediated signaling were upregulated. Additionally, among the dysregulated pathways, the TNF-α signaling via NF-κB showed opposite changes in females and males.

  Study phs003657

• mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel and secondary fusion transcripts in formalin-fixed paraffin-embedded tissue: a sarcoma showcase

  RNA sequencing is widely used to study gene abundance patterns, but less frequently to assess structural alterations such as fusion transcripts. In this study, we assess the performance of messenger RNA (mRNA) capture sequencing to identify fusion transcripts in formalin-fixed paraffin-embedded (FFPE) tissue of different types of sarcoma, followed by orthogonal confirmation using RT-qPCR. To validate our workflow, we used the TruSight RNA Pan-Cancer Panel to analyze a first cohort of 6 positive control tumors for which the diagnostic workup demonstrated the presence of a specific chromosomal rearrangement. Fusion transcript calling by FusionCatcher confirmed all known aberrations and enabled the identification of both fusion gene partners and breakpoints. Next, whole transcriptome TruSeq RNA Exome sequencing was applied to a second cohort of 17 patients, diagnosed with fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated round cell sarcoma (URCS), for whom fluorescence in situ hybridization (FISH) did not identify the classical pathognomonic rearrangements. Remarkably, for 6 out of 17 patients, mRNA capture sequencing readily detected a pathognomonic fusion transcript, i.e. PAX3-FOXO1 in 2 ARMS patients, and EWSR1-FLI1, EWSR1-ERG or EWSR1-NFATC2 in 4 URCS patients. These data show that RNA capture sequencing may enhance the detection rate of pathognomonic fusion genes in sarcoma. For the 11 patients with no known pathognomonic fusion transcript, 11 newly identified fusion transcripts were confirmed by RT-qPCR, including COPS3-TOM1L2, NCOA1-DTNB, WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2 and BRD4-LEUTX fusion transcripts in ARMS patients. Additionally, recurrently detected secondary fusion transcripts in two patients diagnosed with EWSR1-NFATC2-positive sarcoma were confirmed (COPS4-TBC1D9, PICALM-SYTL2, SMG6-VPS53 and UBE2F-ALS2). Our results provide new insights into the underlying genetic causes of these malignancies.

  Study EGAS00001005202

• ApoA-1 and Atherosclerosis in Psoriasis

  Apolipoprotein A-1 is a protein localized to high-density lipoprotein that functions to remove cholesterol from tissues for transport back to the liver. Psoriasis is a systemic inflammatory disease associated with poor high-density lipoprotein function and accelerated non-calcified burden by coronary computed tomographic angiography. In this study, 310 psoriasis patients from The Psoriasis, Atherosclerosis, and Cardiometabolic Disease Initiative (PACI) were studied at baseline to determine if levels of circulating apolipoprotein A-1 predict early onset coronary artery disease in inflammatory conditions. Of the 310 participants, 124 were followed for four years to determine if apolipoprotein A-1 predicts non-calcified coronary burden over time. The primary outcome of this study was non-calcified coronary burden by coronary computed tomography angiography. To assess non-calcified coronary burden, participants underwent coronary computed tomography angiography using the same scanner (320-detector row Aquilion ONE ViSION, Toshiba, Japan). For ApoA-1 quantification, fasting blood draw was performed the same day as the coronary computed tomography angiography. The 400MHz proton Vantera Clinical Analyzer was used to quantify Plasma apolipoprotein A-1. The study determined that low levels of apolipoprotein A-1 are associated with increased coronary artery burden and that this relationship persists over time. The data are available through dbGaP and the dataset includes all variables reported in the manuscript.

  Study phs003231

• Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis

  Despite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two-thirds will relapse with fatal disease within five years. AML is organized as a cellular hierarchy sustained by leukemia stem cells (LSC) at the apex, with LSC properties directly linked to tumor progression, therapy failure, and disease relapse 1–5. Despite the central role of LSC in poor patient outcomes, little is known about the genetic determinants driving their stemness properties. As LSCs share many functional and molecular properties with normal hematopoietic stem cells (HSC) 6, we investigated accessible chromatin unique across normal hematopoietic and cancer cell states and identified transposable elements (TEs) as genetic determinants of both primitive populations in comparison with their downstream mature progeny. A clinically-relevant TE chromatin accessibility-based LSCTE121 signature was developed that enabled patient classification based on survival outcomes. Through functional assays, primitive cell specific-TE subfamilies were found to serve as docking sites for stem cell-associated regulators of genome topology or lineage-specific transcription factors, including LYL1 in LSCs. Finally, using chromatin editing tools, we establish that chromatin accessibility at LTR12C elements in LSCs are necessary to maintain stemness properties. Our work identifies TEs as genetic drivers of primitive versus mature cell states, where distinct TE subfamilies account for stemness properties in normal versus leukemic hematopoietic stem cells.

  Study EGAS50000001141

• Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis

  Despite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two-thirds will relapse with fatal disease within five years. AML is organized as a cellular hierarchy sustained by leukemia stem cells (LSC) at the apex, with LSC properties directly linked to tumor progression, therapy failure, and disease relapse 1–5. Despite the central role of LSC in poor patient outcomes, little is known about the genetic determinants driving their stemness properties. As LSCs share many functional and molecular properties with normal hematopoietic stem cells (HSC) 6, we investigated accessible chromatin unique across normal hematopoietic and cancer cell states and identified transposable elements (TEs) as genetic determinants of both primitive populations in comparison with their downstream mature progeny. A clinically-relevant TE chromatin accessibility-based LSCTE121 signature was developed that enabled patient classification based on survival outcomes. Through functional assays, primitive cell specific-TE subfamilies were found to serve as docking sites for stem cell-associated regulators of genome topology or lineage-specific transcription factors, including LYL1 in LSCs. Finally, using chromatin editing tools, we establish that chromatin accessibility at LTR12C elements in LSCs are necessary to maintain stemness properties. Our work identifies TEs as genetic drivers of primitive versus mature cell states, where distinct TE subfamilies account for stemness properties in normal versus leukemic hematopoietic stem cells.

  Study EGAS50000001147

• Transcriptomic analysis of peripheral blood dendritic cells and monocytes from patients with familial chilblain lupus and hetereozygous mutations in TREX1

  Study EGAS00001006215

• Professors Colin Palmer and Ewan Pearson, from University of Dundee, are both members of the Access Group panel for the GoDARTS bioresource, which provided the data for the current study. The current Study used genotypes (EGAD00010000282) generated by the WTCCC2 (EGAS00000000121), on which both Colin and Ewan are also DAC panel members.

  Dac EGAC00001000504

• Identification of SPEN as a novel cancer gene and FGFR2 as a potential therapeutic target in adenoid cystic carcinoma

  Identification of SPEN as a novel cancer gene and FGFR2 as a potential therapeutic target in adenoid cystic carcinoma

  Dataset EGAD00001000175

• SNPArray_Thai

  The compressed file contains plink format file for the Affymetrix Human Origins SNP array data of 452 individuals generated and analyzed in Kutanan, Liu et al 2021 study of 33 ethnolinguistic groups in Thailand and Laos.

  Dataset EGAD00010002285

• A neoadjuvant, phase II trial demonstrates efficacy and tolerability of Talimogene laherparepvec in cutaneous basal cell carcinoma (NeoBCC trial)

  This dataset is related to the NeoBCC trial and includes 12 human tissue samples

  Dataset EGAD50000000371

• Mutational Landscape Determines Sensitivity to PD-1 Blockade in Non-Small Cell Lung Cancer

  Patients with non-small cell lung cancer were treated with pembrolizumab. Their tumors and matched normal blood were sequenced.

  Study phs000980

• Single Cell RNA Sequencing of Human Hematopoiesis

  This study includes single cell RNA sequencing of human CD34+ hematopoietic stem and progenitor cells throughout human life spanning midgestation into mature adulthood.

  Study phs002750

• Peripheral blood DNA methylation data from CD patients prior to and during ustekinumab treatment from AmsterdamUMC

  Longitudinal DNA methylation discovery data as obtained using the Illumina HumanMethylation EPIC BeadChip array (V1) on peripheral blood from CD patients at the AmsterdamUMC prior to and during ustekinumab treatment

  Dataset EGAD00010002649

• Peripheral blood DNA methylation data from CD patients prior to and during vedolizumab treatment from AmsterdamUMC

  Longitudinal DNA methylation discovery data as obtained using the Illumina HumanMethylation EPIC BeadChip array (V1) on peripheral blood from CD patients at the AmsterdamUMC prior to and during vedolizumab treatment

  Dataset EGAD00010002651

• DupiAERD

  Dataset contains bulk RNA sequencing reads from 44 NERD patients under dupilumab therapy before and after aspirin provocation at baseline and after 24 weeks of treatment. Dataset is a multiplexed .bam file containing all sequencing reads with tagged identifiers.

  Dataset EGAD50000000565

• CRC cell line MPRA

  Massively Parallel Reporter Assays (MPRA) of colorectal cell lines HCEC-1CT (normal colon) and HT29 and SW403 (MSS cancer). Probes identified using the CRC GWAS.

  Dataset EGAD50000000596

• TOTHER3

  Patritumab deruxtecan in HER2-negative breast cancer: part B results of the window-of-opportunity SOLTI TOT-HER3 trial and biological determinants of early response

  Study EGAS50000000385

• 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

• MATCH-molecular driver

  Patients were biopsied at progression on molecular targeted agents and WES and/or WTS were performed to identify resistance mechanisms. 271 underwent one or sequential tissue biopsies.

  Dataset EGAD50000000697

• WES patients with colorectal polyposis

  Twenty-seven patients were included and subjected to germline WES using NovaSeq 6000 platform. After filtering out variants for sequencing quality, variant allele fraction frequency, and population frequency, variants were manually prioritized by the ACMG criteria.

  Dataset EGAD50000000842

• CSF and PBMC scRNAseq RRMS patients at diagnostic n=5

  To get insights about immune cells infiltrating cells the CSF of RRMS patients (n=5), we proceed to 10X scRNAseq of paired CSF and blood circulating cells (about 20000 cells each) sampled at diagnostic.

  Dataset EGAD50000000445

• NanoSeq

  We performed NanoSeq on buccal mucosal samples. We used 28 mm^2 swab DNA as samples and 254 mm^2 swab DNA as controls.

  Study EGAS50000000718

• Duplex sequencing of 26 genes

  Buccal samples and paired esophageal epithelium were obtained using the three sizes of swabs and endoscopic biopsy, respectively. Forty samples from 10 subjects were analyzed via duplex sequencing. This dataset contains bam files that were mapped to the GRCh37 reference genome.

  Dataset EGAD50000000998

• BipEx_Timpson_Bristol

  "BipEx_EGAS00001006274_Timpson_Bristol Controls Exomes. This research project was a collaboration between University of Bristol, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 2,981 Control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x."

  Dac EGAC50000000144

• Short-read RNA-seq of doxycycline-inducible DUX4 human myoblast cell lines

  The dataset includes the short-read RNA sequencing data of DUX4i myoblasts (Clone-5 and Clone-7) with and without 16-hour DOX-treatment (n=1 in each condition).

  Dataset EGAD50000000719

• TRIGR collaboration between University of Helsinkin and Children's Mercy Research Institute

  DAC for collaborations between by the University of Helsinki and Children's Mercy Hospital, such as the Trial to Reduce IDDM in the Genetically at Risk (TRIGR), used to study the evolving epigenomics of immune cells in type 1 diabetes at single nuclei resolution

  Dac EGAC50000000543

• The Dynamic Immune Behavior of Primary and Metastatic Ovarian Carcinoma

  Single-cell RNA-seq data of prospectively collected normal ovarian tissue sample from 1 healthy individual and tumor tissue samples with or without chemotherapy from 19 HGSOC patients.

  Dataset EGAD50000000057

• miRNA

  miRNA Sequencing of olfactory mucosa (OM) cells derived from cognitively healthy and individuals with AD exposed to traffic-related ultrafine particles (UFPs) for 72h in submerged cultures. The UFPs used for exposures were: A0 and A20. Exposures were compared to the corresponding blank samples.

  Dataset EGAD50000001532

• 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

• SDR-seq_06_BCL

  SDR-seq_BCL data access. Two follicular lymphoma (FL) primary patient samples and one germinal center subtype diffuse large B-cell lymphoma (GCB) primary patient sample. FL1 and GCB1 are sequenced in Run1. FL2 is sequenced in Run2.

  Dataset EGAD50000000551

• RNA-seq in endometrial healthy and tumor tissues

  RNA has been extracted by Rneasy mini kit from around 30mg of flash frozen tissue derived from 3 healthy and 3 tumor endometrial tissues of post-menopausal patients. Raw paired-end fastq.gz files are provided.

  Dataset EGAD50000000200

• Whole-exome-sequencing in Motor neuron disease (MND)

  To identify the genetic cause and modifiers of Motor neuron disease (MND), we performed Whole-exome-sequencing of Motor neuron disease (MND) patients.

  Study JGAS000422

• Whole-exome-sequencing in Charcot-Marie-Tooth disease (CMT)

  To identify the genetic cause and modifiers of Charcot-Marie-Tooth disease (CMT), we performed Whole-exome-sequencing of CMT patients.

  Study JGAS000337

• DAC Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  DAC for Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  Dac EGAC50000000694

• Microarray CDX or EDX from primary tumor and metastasis

  expression analysis of FACS sorted human cells from primary tumors and distant organs micrometastases in xenografts. Patient Derived xenografts were generated transplanting tumor cells from metastatic breast cancer patients into mammary fat pad of immunocompromised mice

  Dataset EGAD00010002711

• Two scRNA-seq datasets from control and irradiated organoids.

  Dataset includes two scRNA-seq samples from control and irradiated organoids. Files included in the dataset are Fastq files. Sample libraries produced with Chromium X were sequenced on an Illumina NovaSeq 6000 sequencer.

  Dataset EGAD50000001933

• Spatial transcriptomics prostate cancer

  Spatial transcriptomic characterization of human fresh frozen prostate cancer and non-malignant regions from the same patient. 100 micron thick sections were made from the biopsies, adjacent to snRNA sequencing, and subjected to 10x Genomics Visium ST analysis.

  Dataset EGAD50000001634

• CFTR Gene Variant Detection in Moroccan Individuals via Nanopore Long-Read Sequencing

  This study consists of sequencing the whole CFTR gene (coding and non-coding regions) using Oxford Nanopore on Moroccan CF patients

  Study EGAS50000001423

• Phenytoin_case-control

  Genotype dataset from individuals diagnosed with phenytoin-induced Stevens-Johnson syndrome (SJS) or toxic epidermal necrolysis (TEN) and control individuals from the Thai population. DNA was extracted from whole blood, and SNP genotyping was performed using the Illumina HumanOmniExpressExome-8 v1.2 array.

  Dataset EGAD00010002790

• Single cell transcriptome analysis of breast invasive carcinoma

  We performed single-cell RNA-seq of breast invasive ductal carcinoma to identify the expressional heterogeneity in Luminal subtype and HER2-positive subtype.

  Study JGAS000309

• Semibulk RNA-seq analysis as a convenient method for measuring gene expression statuses in a local cellular environment

  For two cases of breast cancers, semibulk RNA-seq and single cell RNA-seq were performed.

  Study JGAS000387

• Elucidation of molecular mechanism of NAFLD-HCC

  We aimed to elucidate the interaction between cancer cells and immune cells in the tumor immune microenvironment of non-viral hepatocellular carcinoma.

  Study JGAS000311