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• Kutanan and Liu et al 2021 Thai study DAC

  Dac EGAC00001002553

• Mutations in GNAI2 Cause Developmental and Immune Dysregulation

  To define a genetic syndrome of dysmorphism, brain malformations, skeletal defects, endocrine and immune dysfunction, 11 patients from 11 unrelated families who had similar features were studied. Whole exome sequencing was performed to identify disease-causing mutations. A disease segregated with de-novo or autosomal dominant mutations in a single gene, GNAI2, encoding the Gαi2 protein. We define a new Congenital Disorder associated with Gαi2 mutations and downstream functional effects.

  Study phs002817

• Exome_sequencing_in_patients_with_cardiac_arrhythmias

  The institut du thorax in Nantes (FR), the Academic Medical Center in Amsterdam (NL) and the University Hospital of Muenster (DE) have recruited 20 large families comprising at least 3 patients with cardiac arrhythmias and showing history of sudden cardiac death. For each family, the exome of one affected individual has been sequenced at the Wellcome Trust Sanger Institute (UK), in order to identify new genes associated with high risk of sudden cardiac death.

  Study EGAS00001000063

• Novel de novo pathogenic variant in the GNAI1 as a cause of severe disorders of intellectual development with autistic features

  Our probands A and B are boys-monozygotic twins with the clinical diagnosis of severe intellectual impairment, developmental stagnation, and dysphasia. They were diagnosed at the Department of Medical Genetics and Genomics (University Hospital Brno). Parents provided written informed consent, which was approved by the Research Ethics Committee of Masaryk University and Ethics Committee of University Hospital Brno. Peripheral blood samples were collected in sterile heparinized tubes for cytogenetic analysis. Genomic DNA samples were obtained from 1 ml peripheral blood in EDTA, according to the standard DNA isolation process using the MagNaPure system (Roche Diagnostics, Basel, Switzerland). Quality and quantity were checked using a DeNovix DS-11 Spectrophotometer (DeNovix Inc., Wilmington, DE, USA) and Qubit® 2.0 (Thermo Fisher Scientific, Inc., Waltham, MA, USA).

  Dataset EGAD00001007736

• Gut metagenome/FINRISK 2002 (Salosensaari et al. Nature Comms 2021)

  The main goal of the project is the study the associations between the gut metagenome and human health. The dataset contains data for n=7211 FINRISK 2002 participants who underwent fecal sampling. Demultiplexed shallow shotgun metagenomic sequences were quality filtered and adapter trimmed using Atropos (Didion et al., 2017), and human filtered using Bowtie2 (Langmead and Salzberg, 2012).

  Study EGAS00001005020

• Dopaminergic neuron differentiation of human embryonic stem cells

  2 replicates of dopaminergic neuron differentiation of human embryonic stem cells from timepoints day 17 and day 28, performed with 10X Genomics single cell RNA-seq. Part of the Ásgrimsdottir et al. (Arenas Lab).

  Study EGAS50000001099

• RNA-Seq data from 34 CAF-S3 subset in human breast and ovarian cancers

  This dataset is related to publications Costa et al. Cancer Cell 2018 and Givel et al. Nat. Commun. 2018 which describe the identification of 4 Cancer Associated Fibroblasts (CAF) in breast and ovarian cancer. This dataset contains transcriptomic profiles obtained by RNA-Seq of 34 CAF-S3 samples from breast and ovarian Tumors.

  Dataset EGAD00001004810

• RNA seq of MPNST tumour samples

  RNA sequencing of 10 MPNST tumour samples as part of a larger study of MPNST. Article: Lyskjær et al, 2020, J Pathol, "H3K27me3 expression and methylation status in histological variants of malignant peripheral nerve sheath tumours".

  Study EGAS00001004528

• Healthy Never Smokers

  Bronchial brushing dataset from healthy never-smokers after exposure to diesel exhaust. Include 18 samples from 9 research participants who underwent bronchoscopy after controlled exposure to diesel exhaust. Main study design described in detail in Ryu et al 2022 AJRCCM (PMID: 35202552). This dataset was used in Hill et al Nature 2023.

  Dataset EGAD00001010024

• RNA-seq data of breast cancer HCI011 model from Ros et al (2020)

  RNA-seq data of the HCI011 and HCI011R models, GDC032 treated and control (total of 21 samples), from the paper: FOXM1 is a biomarker of resistance to PI3Kα inhibition in ER+ breast cancer that is detectable using metabolic imaging (Ros et al, 2020)

  Dataset EGAD00001006245

• Liu et al Taiwan genome-wide data DAC

  Dac EGAC00001003038

• Thirant, Peltier et al Data Access Commitee

  Dac EGAC00001001789

• Long-Term Oxygen Treatment Trial (LOTT-BioLINCC)

  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 evaluate the efficacy of long-term treatment with supplemental oxygen in people with stable chronic obstructive pulmonary disease (COPD) and resting or exercise-induced moderate desaturation. Background: COPD is the fourth leading cause of death in the United States, with more than twelve million people currently diagnosed with the disease. In 2011, Medicare reimbursements for oxygen-related costs for people with COPD exceeded two billion dollars. The quality of life of a person with COPD decreases as the disease progresses, making treating and managing COPD in the moderate stages important. The benefits of oxygen supplementation were studied in the 1970s, but these benefits were specific to people with COPD who have severe resting hypoxemia. The LOTT trial was designed to address the effectiveness of supplemental oxygen therapy in treating people with COPD who have moderately low blood oxygen levels at rest or who have normal blood oxygen levels at rest, but have low or very low blood oxygen levels during exercise. Participants: There were a total of 1759 people screened for eligibility for the LOTT trial. Of the 1759 screened, 738 people with COPD were selected for randomization with 368 randomly assigned to the supplemental-oxygen group and 370 to the no-supplemental-oxygen group. Of the 738 people with COPD who underwent randomization, 133 (18%) had resting desaturation only, 319 (43%) had exercise-induced desaturation only, and 286 (39%) had both types of desaturation. Furthermore, in the supplemental-oxygen group, 220 people were prescribed 24-hour oxygen and 148 were prescribed oxygen during exercise and sleep only. Design: The LOTT trial was originally designed to test whether the use of supplemental oxygen would result in a longer time to death for people with COPD and moderate resting desaturation. After seven months, the trial design was judged to be infeasible; therefore, the trial was redesigned to include people with exercise-induced desaturation with a primary composite outcome of death or first hospitalization for any cause, whichever occurs first. Other outcomes measured included: death, health care utilization, COPD exacerbation, quality of life measurements, anxiety, depression, and measures of functional status. Potential participants were screened using questionnaires, a breathing test, a brief physical exam, a blood draw, and measurements of resting and walking blood oxygen levels. Based on those results, eligible participants returned for a second screening visit for further evaluations. At the end of the second visit, eligible participants were assigned randomly to supplemental oxygen therapy or no oxygen therapy. Participants assigned to supplemental oxygen therapy received stationary and/or portable oxygen systems. Participants were required to return for a one hour visit to determine how much oxygen to use while walking and to learn how to use the equipment. Participants who had low blood oxygen levels during rest were instructed to use supplemental oxygen 24 hours per day. Participants with normal resting blood oxygen levels, but low or very low blood oxygen levels during exercise were instructed to use it during physical activity and sleep. Throughout the treatment period, participants were asked to keep records of the number of oxygen tanks emptied or pounds of oxygen delivered, meter readings, and changes in equipment. Study officials contacted participants weekly for the first month, monthly for the next five months, and then every two months until the Year 1 study visit. Participants assigned to receive no oxygen treatment were contacted one week after assignment for a check-up. All participants returned for study visits once a year for up to seven years. At each of these visits, participants completed some of the same tests and questionnaires from the screening visit. Participants underwent a blood draw during the one year study visit. Participants in both treatment groups received two phone calls each year to check on status and use of oxygen. In addition, participants in both groups were asked to complete a quality of life questionnaire by mail at four months and sixteen months. Medicare claims were collected for the duration of each participant's enrollment in the study. Conclusions: In participants with stable COPD and resting or exercise-induced moderate desaturation, the prescription of long-term supplemental oxygen did not result in a longer time to death or first hospitalization than no long-term supplemental oxygen, nor did it provide sustained benefit with regard to any of the other measured outcomes. Long-Term Oxygen Treatment Trial Research Group, Albert RK, Au DH, Blackford AL, Casaburi R, Cooper JA Jr, Criner GJ, Diaz P, Fuhlbrigge AL, Gay SE, Kanner RE, MacIntyre N, Martinez FJ, Panos RJ, Piantadosi S, Sciurba F, Shade D, Stibolt T, Stoller JK, Wise R, Yusen RD, Tonascia J, Sternberg AL, Bailey W. A Randomized Trial of Long-Term Oxygen for COPD with Moderate Desaturation. N Engl J Med. 2016 Oct 27;375(17):1617-1627.

  Study phs003933

• Whole genome sequencing data of pediatric B-other subtype acute lymphoblastic leukemia

  For a long time, approximately 70% of childhood B-ALL cases could be classified routinely, and the remaining 30% were classified into the “B-other” group lacking the known genetic features. However, more recently, new genomic tools have uncovered new subtypes among the B-other groups. Approximately 10% of B-ALL cases lack the recurrent genetic abnormalities, and are referred as "B-other". They are typically more heterogeneous than other subtypes of B-ALL, and their prognoses are more variable. In a more recent update of the B-ALL classification, 27 subtypes were identified (Arber et al., 2022). The identification of some of these subtypes is dependent on NGS methods, such as RNA sequencing, which are not routinely used in all clinical laboratories. For example, ETV6::RUNX1-like and DUX4-rearranged subtypes have been identified using RNA sequencing. For this study, subtype predictions for some of the cases is acquired from ALLIUM (Krali et al., NPJ Precis Oncol., 2023) and ALLCatchR (Beder et al., Blood, 2022) based on the RNA-seq profiles.

  Study EGAS50000001497

• Breast Cancer PDTX Encyclopaedia

  Molecular data from the collection of PDTX breast cancer models described in Bruna et al, 2016. Cell. It includes whole exome sequencing, shallow whole genome sequencing, expression arrays and reduced bisulfite representation sequencing (RRBS).

  Study EGAS00001001913

• ChIP-seq data of Hodgkin lymphoma cell line L-428

  ChIP-seq data (H3K4Me3, H3K27Ac histone modifications) of Hodgkin lymphoma cell line L-428. Samples were processed as previously described (Sud et al., 2018). The files are in bam format, aligned to build 37.

  Study EGAS00001003033

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

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WGS BOs/normals)

  Dataset EGAD00001011255

• Coloured Project - Lankheet et al

  The data is for non-commercial use only.

  Dac EGAC50000000240

• Servicio Hematología_Hospital Universitario de Salamanca_Spain

  Data obtained from Diffuse large B-cell Lymphoma cases from the Haematology Service at the University Hospital of Salamanca. The study was approved by the local Institutional Review Board, and written informed consent, following the Declaration of Helsinki, was obtained from all patients before sample collection.

  Dac EGAC50000000155

• ICGC PCAWG Dataset: MALY-DE_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MALY-DE.

  Dataset EGAD00001002123

• ICGC PCAWG Dataset: PBCA-DE_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PBCA-DE.

  Dataset EGAD00001002127

• ICGC PCAWG Dataset: EOPC-DE_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: EOPC-DE.

  Dataset EGAD00001002124

• HIPO016 - glioblastoma tumour methylation microarray profiling

  Methylation microarray profiling (Illumina Human Methylation 450k and EPIC platforms) of 60 adult glioblastomas. Tumours were subtyped using the approach from Sturm et al. (https://doi.org/10.1016/j.ccr.2012.08.024): 12 IDH, 18 MES, 12 RTK I, 18 RTK II. DNA was prepared, assayed on the microarrays, and raw data computationally processed as described in Capper et al., "DNA methylation-based classification of central nervous system tumours": https://www.nature.com/articles/nature26000

  Dataset EGAD00010001797

• Large B cell lymphomas with CCND1 rearrangement have different immunoglobulin gene breakpoints and genomic profile than mantle cell lymphoma

  Next-generation sequencig data including whole-genome sequencing, whole-exome sequencing, and capture-based gene panels of large B cell lymphomas with CCND1 rearrangementas described in Özoğul,Montaner, Pol et al 2024.

  Study EGAS50000000564

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

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. Single cell metadata and analysis 38 Barrett's and normals

  Dataset EGAD00001005455