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• Assessing the suitability of formalin-fixed paraffin-embedded (FFPE) tissue for genome-wide association studies (GWAS)

  This study evaluates the feasibility of conducting genome-wide association studies (GWAS) using DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue. Genotyping results from paired FFPE and blood samples were compared using both microarray technology and low-coverage whole-genome sequencing (lcWGS). The analysis demonstrated high concordance between FFPE- and blood-derived genotypes. Although both platforms performed well, microarrays achieved significantly higher recall and precision and currently offer greater cost-effectiveness and computational efficiency. These findings support the suitability of FFPE-derived DNA for GWAS, with microarrays representing the preferred approach at present. However, the broader variant detection enabled by lcWGS may represent an additional advantage to be explored in future studies, particularly in diverse populations.

  Study EGAS00001008103

• Exome Sequencing of a family with thrombocytopenia, red cell macrocytosis, and lymphoblastic leukemia predisposition

  A family with a history of bleeding, variable thrombocytopenia, red cell macrocytosis and two cases of pre B-cell acute lymphoblastic leukemia was studied in a single visit. The family was assessed for bleeding history using a bleeding questionnaire. Additionally, complete blood counts were measured and whole blood was collected from five affected individuals and three unaffected individuals for DNA extraction and whole exome sequencing. The goal of this study is to determine the genetic cause of thrombocytopenia, red cell macrocytosis, and predisposition to leukemia in a family. It is hoped that the information obtained from this study will help researchers understand the genetic and molecular basis of platelet and red cell production, as well as leukemia predisposition.

  Study phs000873

• The Cancer Dependency Map (DepMap)

  The Cancer Dependency Map (DepMap) aims to accelerate precision cancer medicine by creating a comprehensive map of tumor vulnerabilities. The DepMap project genomically profiles a wide range of cancer models and characterizes them for their sensitivity to genetic and compound perturbations. The data is computationally analyzed to create a systematic overview of the genetic dependencies and compound sensitivities of cancer types and the predictive biomarkers that point to patient populations most likely to benefit from targeting of these vulnerabilities. The DepMap public portal has become a comprehensive resource to identify cancer vulnerabilities by providing datasets at scale, cutting-edge computational tools, and sophisticated visualization tools that together have accelerated the discovery of novel targets and biomarkers. Please visit Depmap.org to access the public portal.

  Study phs003444

• WGS datasets of pediatric glioblastoma

  WGS with linked reads of pediatric glioblastoma. For each patient, blood and tumor tissue were sequenced. For two patients, we also provide sequencing data for the blood of their parents.

  Dataset EGAD00001005212

• DIPG WES and RNA-Seq

  We characterised H3K27M-mutant diffuse intrinsic pontine glioma (DIPG, n=21) and RNA-Seq (n=26 DIPG, 12 normal brain)

  Dataset EGAD00001006450

• Pomalidomide for the Treatment of Bleeding in HHT (PATH-HHT)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To determine efficacy (reduction in severity of epistaxis), tolerability, and improvement in quality of life of pomalidomide compared to placebo after 24 weeks of treatment.Background: This study addresses the efficacy of pomalidomide in the treatment of epistaxis in patients with Hereditary Hemorrhagic Telangiectasia (HHT) who have anemia and/or require blood transfusion or iron infusion for treatment of bleeding-induced anemia and iron deficiency. HHT (also known as Osler-Weber-Rendu disease) is an inherited bleeding disorder. Over 95% of patients develop recurrent epistaxis, which may be severe and result in chronic anemia, need for iron infusions and blood transfusions, substantial psychiatric comorbidity (including depression and post-traumatic stress disorder) and reduction in health-related quality of life (HRQoL). HHT is clinically diagnosed using the Curacao criteria, which consists of 1) spontaneous and recurrent epistaxis, 2) telangiectasias at characteristic sites, 3) visceral arteriovenous malformations (AVMs) or telangiectasias, and 4) a first degree relative with HHT (inheritance is usually autosomal dominant). Patients with three criteria are considered to have definite HHT, and those with 2 criteria probable HHT. HHT affects approximately 1 in 3,800 individuals. Significant manifestations of HHT often do not appear until the third or fourth decades, sometimes later.Participants: 144 patients from 11 clinical centers were enrolled.Design: This is a multi-center, double blind, randomized placebo-controlled trial that investigated the efficacy and safety of pomalidomide in patients with HHT and chronic epistaxis leading to iron-deficiency anemia or requiring intravenous iron infusions or blood transfusion.Screening evaluation included the Epistaxis Severity Score (ESS) with three-month recall, which reflected the patient's history of epistaxis and bleeding over the prior three months, as well as detailed review of iron infusion and red cell transfusion over the preceding six months. Eligible patients were provided a diary to record the duration of each epistaxis event that occurred during the 4 weeks prior to the baseline visit, and then returned for the baseline randomization visit, at which time patients underwent genetic testing, if this had not been previously performed, and completed an ESS with 4-week recall and quality of life assessments. Patients were randomized 2:1, stratified by study site, to either pomalidomide 4 mg/day or matching placebo during each of six 28 day cycles (24 weeks). Patients were seen every four weeks during treatment, and at a 4-week post-treatment follow-up visit to measure the ESS (with 4-week recall), laboratory assessments including iron stores and need for iron infusion, CBC, and metabolic profile. Patients were assessed for adverse events (AE) throughout the study. Treatment dosage could be reduced, or temporarily or permanently discontinued following AE-specific guidelines related to fatigue, cytopenias or other toxicities.Quality of life assessments were completed at baseline, and the 12- and 24-week visits, and the 4-week post-treatment follow-up visit using validated NIH instruments of 1) Neuro-QOL satisfaction with social roles and activities, 2) PROMIS emotional distress – depression, and 3) PROMIS fatigue, and the HHT-specific quality of life instrument developed specifically for this study. The effect of pomalidomide on duration of epistaxis was assessed via diary between weeks 8-12, 20-24 and the 4-week post-treatment period.Conclusions: Among patients with HHT, pomalidomide treatment resulted in a significant, clinically relevant reduction in epistaxis severity. No unexpected safety signals were identified (Al-Samkari et al., 2024; PMID: 39292928)

  Study phs003948

• RNA-seq and scRNA/TCR-seq data for publication: "Pharmacological inhibition of nonsense-mediated mRNA decay enhances anti-tumour immunity"

  PDFs RNA-seq and scRNA/TCR-seq data for Pharmacologic inhibition of nonsense-mediated mRNA decay enhances anti-tumour immunity

  Dataset EGAD50000001720

• WES of melanoma tumours prior to combined immune checkpoint blockade treatment.

  Paired melanoma tumor and normal (PBMC) WES data from a cohort of 26 patients subsequently treated with combined immune checkpoint blockade.

  Dataset EGAD00001005941

• In Vivo Cytokine eQTL Interactions from a Lupus Clinical Trial

  The purpose of this study is to discover in vivo cytokine expression quantitative trait locus (eQTL) interactions from a cohort of patients with systemic lupus erythematosus. 157 lupus patients were enrolled in a clinical trial to test the efficacy and safety of an anti-IL-6 monoclonal antibody. At three time points, we measured interferon (IFN) status, anti-IL-6 drug exposure and genome-wide gen expression. We identified 4,818 cis-eQTLs and then observed a statistically significant enrichment of in vivo eQTL interactions with IFN status and anti-IL-6 exposure.

  Study phs001702

• Acquired Cross-Resistance in Small Cell Lung Cancer Patient-Derived Xenografts

  Here we present whole genome sequencing and RNA sequencing of patient-derived xenograft (PDX) models of small cell lung cancer (SCLC). These models were derived at a variety of clinical time points from either biopsy/resection samples, malignant effusions, or circulating tumor cells (CTCs), and grown in the subcutaneous flank of NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl /SzJ) mice. The first analysis published with these data was to determine the genomic and transcriptomic features of PDX models derived after relapse that demonstrated in vivo resistance to multiple chemotherapy regimens (cross-resistance).

  Study phs003486

• ImmunoAgeing_Longitudinal

  The objective is to establish whether immunosenescence is associated with the development of clonal haematopoiesis in a healthy ageing population. This will be addressed in collaboration with the European consortium running the ImmunoAgeing project (www.immunoageing.eu). Genomic DNA derived from the peripheral blood of 394 individuals at 3-5 time-points over a 20-year period will be analysed. RNA bait pulldown (Agilent) will be used to perform targeted sequencing of genes known to be recurrently mutated in myeloid malignancies The presence, size and nature of clonal haematopoiesis will be correlated with quantitative measures of immunosenescence.

  Study EGAS00001003183

• PROMETEO

  The SOLTI-1503 PROMETEO trial was a single-arm, preoperative, window-of-opportunity phase II study conducted at four sites in Spain between December 2018 and February 2022. It enrolled female patients with operable HER2-negative breast cancer (triple-negative or Luminal B-like) and residual disease after neoadjuvant chemotherapy. Tumor biopsies were collected at five time points (baseline, post-NAC screening, C2D1, C3D1, and surgery) for translational research. This dataset includes raw paired-end RNA sequencing data (~110M reads per library) generated from the 113 biopy samples, archived in FASTQ format.

  Study EGAS50000001499

• 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

• WGS

  Whole Genome Sequencing

  Dataset EGAD00001001120

• Somatic mutations in twin breast cancers (2019-04-03)

  The aim of this study is to investigate the somatic mutations in twins with BRCA1/2 negative breast cancer with no strong family history. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004890

• L1 Retrotransposon sequencing in Cocaine Use Disorder - Study 1

  Cocaine Use Disorder (CUD) is a global public health problem, with no effective pharmacotherapies. While CUD is marked by high heritability, discovery of variants associated with risk for CUD has proven difficult. We used Restriction Enzyme Based Enriched L1 sequencing (REBELseq) to amplify L1 retrotransposons in gDNA isolated from medial prefrontal cortex NeuN+ neuronal nuclei from 25 CUD cases and 26 controls. Amplified libraries were sequenced on the Illumina HiSeq 4000 platform, and sequencing data was analyzed with the REBELseq bioinformatics pipeline.

  Study phs001966

• Small‑scale mutations are infrequent as mechanisms of resistance in post‑PARP inhibitor tumour samples in high grade serous ovarian cancer

  Targeted DNA sequencing of high-grade serous ovarian cancer (HGSC) tumour and normal samples from 26 patients. Following target hybrid capture of 63 genes involved in DNA repair and response to treatment with an Agilent SureSelect XT panel, sequencing libraries were generated using the SureSelect XT Low Input Target Enrichment System (Agilent) as per the manufacturer's protocol. Libraries were sequenced on an Illumina NextSeq 500 at the Peter MacCallum Cancer Centre (Melbourne, Australia).

  Study EGAS50000000146

• Tumor-associated preferred end coordinates and somatic variants as signatures of circulating tumor DNA

  Cell-free DNA fragmentation is a nonrandom process. We showed that cell-free DNA fragments with ends at certain genomic coordinates had higher likelihoods of being derived from hepatocellular carcinoma. Other coordinates were associated with cell-free DNA molecules originating from the liver. Quantitative assessment of cell-free DNA molecules bearing these respective groups of end signatures correlated with the amounts of tumor-derived or liver-derived DNA in plasma. There were millions of tumor-associated plasma DNA end coordinates across the genome. Due to their high prevalence, they were more readily detectable than somatic mutations as a cancer signature in plasma. Hence, detection of tumor-associated plasma DNA ends may offer a cost-effective means of capturing evidence for the presence of cancer through liquid biopsy assessment.

  Study EGAS00001003160

• Heart Failure Network: Diuretic Optimization Strategies Evaluation in Acute Heart Failure (HFN DOSE-BioLINCC)

  ObjectivesThe DOSE study sought to evaluate the most effective dosing (high vs. low) and administration (continuous infusion vs. intermittent boluses) combination of the diuretic Furosemide in the treatment of patients with acute decompensated heart failure.BackgroundAcute decompensated heart failure is the most common cause of hospital admissions among patients older than 65 years of age and is responsible for more than 1 million hospitalizations annually in the United States. Intravenous loop diuretics are an essential component of current treatment and are administered to approximately 90% of patients who are hospitalized with heart failure. Despite decades of clinical experience with these agents, prospective data to guide the use of loop diuretics are sparse, and current guidelines are based primarily on expert opinion. As a result, clinical practice varies widely with regard to both the mode of administration and the dosing.SubjectsA total of 308 patients were enrolled between March 2008 and November 2009 at 26 clinical sites in the United States and Canada. DesignThe DOSE study was a prospective, randomized, double-blind, controlled trial with a 2-by-2 factorial design. Patients were randomly assigned to either a low-dose strategy (total intravenous furosemide dose equal to their total daily oral loop diuretic dose in furosemide equivalents) or a high-dose strategy (total daily intravenous furosemide dose 2.5 times their total daily oral loop diuretic dose in furosemide equivalents) and to administration of furosemide either by intravenous bolus every 12 hours or by continuous intravenous infusion.The study treatment, with group assignments concealed, was continued for up to 72 hours. At 48 hours, the treating physician had the option of adjusting the diuretic strategy on the basis of the clinical response. An assessment of biomarkers, including creatinine, cystatin C, and N-terminal pro-brain natriuretic peptide, was performed at a central core laboratory at baseline, 72 hours, and 60 days. Patients were followed for clinical events to day 60. The coprimary end points were patients' global assessment of symptoms, quantified as the area under the curve (AUC) of the score on a visual-analogue scale over the course of 72 hours, and the change in the serum creatinine level from baseline to 72 hours.ConclusionsAmong patients with acute decompensated heart failure, there were no significant differences in patients' global assessment of symptoms or in the change in renal function when diuretic therapy was administered by bolus as compared with continuous infusion or at a high dose as compared with a low dose. (Felker et. al., 2011, PMID: 21366472)

  Study phs003524

• scRNAseq dataset of circulating T cells in FL patient before and after Lenalidomide treatment

  scRNAseq dataset of circulating T cells from 3 FL patients (P011, P014 and P020) included in the GALEN clinical trial. There is two time points for each patient : One before treatment (D0) and one at day 7 of Lenalidomide treatment (D7).

  Dataset EGAD50000001529

• Cord blood progenitor CITE-seq dataset

  Sequencing results of single-cell transcriptome and antibody libraries from two biological experiments of cord blood progenitor cells. Four samples from different time points were processed using 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Gene expression and antibody-derived libraries were sequenced separately.

  Dataset EGAD50000000405

• Delineate genomic and epigenomic changes in esophageal squamous cell carcinoma following radiotherapy

  We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  Dataset EGAD00001003799

• A Perioperative Study of Safusidenib in Patients with IDH1-Mutated Glioma

  10 participants with a radiological or pathological diagnosis of WHO Grade 2 lower-grade glioma (LGG) were recruited at a single center starting in December, 2022. Eligibility criteria permitted participants who had undergone prior surgery for WHO Grade 2 LGG, but excluded those with a history of prior radiation or chemotherapy.In Part A of the study, participants underwent an initial craniotomy with tumor biopsy and a lumbar puncture for cerebrospinal fluid (CSF) collection at study entry. Following sample collection, participants received safusidenib at the recommended phase 2 doses of 250 mg twice daily (b.i.d.) for a period of 22–36 days. This was followed by a second craniotomy for maximal safe tumor resection and a repeat lumbar puncture within 5 hours of the final pre-resection dose of safusidenib. Tumor, blood, and CSF samples were collected at both surgical time points for comprehensive translational research.Molecular analyses were performed on samples collected at both time points. These included pharmacokinetics (PK), targeted metabolomics, whole-genome sequencing (WGS) of tumor tissue, single-nucleus RNA sequencing (snRNA-seq), and DNA methylation profiling on all patients. Targeted metabolomics was conducted on samples from 9 participants, while spatial transcriptomics and spatial metabolomics were performed on tumor tissue from 3 participants each. Histone methylation profiling was conducted on samples from 8 participants.

  Study phs003976

• Chromatin accessibility in human monocyte differentiation

  This dataset consists of ATAC-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting TET2, IRF4 and EGR2. In total, it includes 26 samples.

  Dataset EGAD00001006601

• Detection of cancers three years prior to diagnosis using plasma cell-free DNA

  A major goal of early cancer detection is to identify subclinical disease when the tumor burden is low, so that treatments are more effective. But how early can cancers be detected prior to clinical signs or symptoms? This question can be answered only through the evaluation of participants whose clinical course has not been altered by the study itself. We here describe such an evaluation, performed on prospectively collected plasma samples from the Atherosclerosis Risk in Communities (ARIC) study, including 26 participants diagnosed with cancer and 26 matched controls. At the index time point, eight of these 52 participants scored positively with a multicancer early detection (MCED) blood test. All eight of these participants were diagnosed with cancer within 4 months after blood collection. In six of these 8 participants, we were able to assess an earlier plasma sample collected 3.1 to 3.5 years prior to clinical diagnosis. In four of these six participants, the same mutations detected by the MCED test could be identified, but at 8.6 to 79-fold lower levels. These results demonstrate that it is possible to detect circulating tumor DNA (ctDNA) more than three years prior to clinical diagnosis, and provide benchmark sensitivities required for the success of ctDNA-based tests for this purpose.

  Study EGAS00001008068