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• Uncovering tumor intrinsic and extrinsic factors that regulate hepatocellular carcinoma growth using patient derived xenograft assays

  Exome Sequencing and RNA Sequencing Data for PDX Samples

  Dataset EGAD00001005734

• H3Africa SIREN Phenotype

  Phenotype data for 3421 Samples from Nigeria and Ghana, genotyped with the Illumina NestSeq 500.

  Dataset EGAD00001011075

• Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY)

  The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) of the National Institutes of Health (NIH) has sponsored a consortium of investigators to conduct a clinical treatment trial, Treatment Options for type 2 Diabetes in Adolescents and Youth (TODAY). The primary objective of the TODAY trial is to compare the efficacy of three treatment arms on time to treatment failure based on glycemic control. The secondary aims are to:compare and evaluate the safety of the three treatment arms;compare the effects of the three treatments on the pathophysiology of type 2 diabetes (T2D) with regards to beta cell function and insulin resistance, body composition, nutrition, physical activity and aerobic fitness, cardiovascular risk factors, microvascular complications, quality of life, and psychological outcomes;evaluate the influence of individual and family behaviors on treatment response; andcompare the relative cost effectiveness of the three treatment arms.The three treatment regimens are: (1) metformin alone, (2) metformin plus rosiglitazone, and (3) metformin plus an intensive lifestyle intervention called the TODAY Lifestyle Program (TLP). The study recruits patients over a three-year period and follows patients for a minimum of two years. Patients are randomized within two years of the diagnosis of T2D.

  Study phs002447

• Identification of Host Genetic Factors That Are Determinant for the Development of Severe Forms of COVID-19

  We conducted whole exome sequencing (WXS) on 21 cases of Multisystem Inflammatory Syndrome in Children (MIS-C) related to COVID-19 from Brazil. All patients who were hospitalized underwent serum (ELISA) and molecular (RT-PCR) testing for SARS-CoV-2, and the main clinical symptoms associated with SARS-CoV-2 infection were collected. During hospitalization, data on complications, medical interventions, and laboratory findings were also collected. Our results revealed in an unprecedented way the occurrence of several rare loss-of-function variants in the NLRP12 gene among the affected children, and three other SNVs, predicted to be highly pathogenic, were identified in the IL17RC gene. An additional nonsense variant, in the IFNA10 gene, was identified in a single patient. Through in vitro functional analysis, we unequivocally demonstrated that these mutations impact NF-kB activation. These findings are similar to those observed in NLRP12-associated systemic autoinflammatory disorders, characterized by altered innate immune response, with increased NF-κB activation and excessive production of inflammatory cytokines. To our knowledge, our study is the first to provide a plausible molecular mechanism for MIS-C involving inborn errors in NLRP12. We suggest that some patients with MIS-C may benefit from Interleukin (IL)-1 pathway blockade treatments.

  Study phs003512

• Exploring the Microbiome-Gut-Brain Axis with Respect to Psychoneurological Symptoms for Children with Solid Tumors

  The human body hosts tens of trillions of microbes, a number 10 times greater than the number of human body cells. The collection of these human-associated microbes and their genomes is called the “human microbiome”. More than 90% of these microbes live in the gastrointestinal (GI) tract, representing 500 species on average. With the development of high-throughput sequencing technology and bioinformatics tools (e.g., 16S ribosomal RNA or 16S rRNA sequencing and shotgun metagenomics analysis), recent progress has been made to elaborate the critical role that the gut microbiome plays in human health and disease. A significant disruption (dysbiosis) of the composition and function of the gut microbiome is associated with carcinogenesis, chemotherapeutic metabolism, and treatment-related symptom toxicities. The current state of science on the gut microbiome in cancer has only recently started in animal models and adults, and has not been well investigated in children diagnosed and treated for cancer, nor with respect to associations with cancer treatment-related toxicities. This proposed study will explore the hypothesis that dysbiosis of the gut microbiome is associated with cancer treatment-related GI and psychoneurological symptoms. We will collect both stool samples (for the gut microbiome) and patient-reported outcomes across chemotherapy.

  Study phs002960

• using-ega-account

  Using your EGA account The purpose of this page is to help you access and download the data you have been granted permission to view through your EGA account. To obtain an EGA account please register here. Once your account is created, you can find details on how to manage your EGA account here. EGA access policy (New account holders please read) Access to EGA services are only provided to EGA account holders. EGA accounts are created, updated and closed upon direct instruction from the relevant DAC contact, using the EGA account management tools or through EGA Helpdesk. As part of the EGA account creation process, the EGA account holder must reset their password when instructed. Password resets are checked and verified usually within 24 business hours, during which time the EGA account is inaccessible. EGA accounts are assigned on an individual basis for the exclusive use of the registered EGA account holder; log-in details must remain private and only be used by the EGA account holder. Controlled access data files are only provided, in accordance to the permissions set by the DAC, to EGA account holders. EGA controlled access data files are encrypted prior to download and must be decrypted on the EGA account holders side. EGA account holders are provided access to the EGA download streamer to download access approved datasets and files therein. The EGA download streamer represents the primary means for the EGA account holder to download access approved datasets and files therein. EGA account holders may be provided with an EGA download account for accessing approved datasets and files therein, using FTP or Aspera in response to clearly defined technical reasons, which may restrict the use of the EGA download streamer. It is the sole responsibility of the EGA account holder to ensure full compliance to all terms and conditions of the Data Access Agreement are met once data is downloaded from the EGA. Should you move institute you must contact all Data Access Committee's contacts to update your details and, if necessary, re-apply for data access. The Data Access Agreement (DAA) is a contract made between the DAC and the EGA account holder; the EGA is not responsible for enforcing the DAA. EGA reserves the right to place EGA accounts 'onhold', pending DAC approval to re-activate, should EGA account 'misuse' be suspected. Further information Introduction to the EGA Frequently Asked Questions Subscribe to the EGA mailing list

  Documentation using-ega-account

• Using your EGA account

  Using your EGA account The purpose of this page is to help you access and download the data you have been granted permission to view through your EGA account. To obtain an EGA account please register here. Once your account is created, you can find details on how to manage your EGA account here. EGA access policy (New account holders please read) Access to EGA services are only provided to EGA account holders. EGA accounts are created, updated and closed upon direct instruction from the relevant DAC contact, using the EGA account management tools or through EGA Helpdesk. As part of the EGA account creation process, the EGA account holder must reset their password when instructed. Password resets are checked and verified usually within 24 business hours, during which time the EGA account is inaccessible. EGA accounts are assigned on an individual basis for the exclusive use of the registered EGA account holder; log-in details must remain private and only be used by the EGA account holder. Controlled access data files are only provided, in accordance to the permissions set by the DAC, to EGA account holders. EGA controlled access data files are encrypted prior to download and must be decrypted on the EGA account holders side. EGA account holders are provided access to the EGA download streamer to download access approved datasets and files therein. The EGA download streamer represents the primary means for the EGA account holder to download access approved datasets and files therein. EGA account holders may be provided with an EGA download account for accessing approved datasets and files therein, using FTP or Aspera in response to clearly defined technical reasons, which may restrict the use of the EGA download streamer. It is the sole responsibility of the EGA account holder to ensure full compliance to all terms and conditions of the Data Access Agreement are met once data is downloaded from the EGA. Should you move institute you must contact all Data Access Committee's contacts to update your details and, if necessary, re-apply for data access. The Data Access Agreement (DAA) is a contract made between the DAC and the EGA account holder; the EGA is not responsible for enforcing the DAA. EGA reserves the right to place EGA accounts 'onhold', pending DAC approval to re-activate, should EGA account 'misuse' be suspected. Further information Introduction to the EGA Frequently Asked Questions Subscribe to the EGA mailing list

  Documentation download/using_ega_account

• A somatic reference standard for cancer genome sequencing with COLO829

  Identification of somatic alterations in cancer has become feasible with the massive adoption of next generation sequencing. However, due to variability in sequencing and informatics pipelines, a common somatic reference is needed. We thus performed paired whole genome sequencing of a metastatic melanoma cell line (COLO829) and a matched lymphoblastoid line (COLO829BL) across three institutions (TGen, Illumina, Genome Sciences Centre at the British Columbia Cancer Agency). We performed a meta-analysis of all data, in combination with the originally reported analysis of these cell lines by Pleasance et al (PMID: 20016485), and report a somatic reference standard based on consensus events. DNA extractions, library preparation, sequencing, and analysis were separately performed at each site. Results were compiled with sequence data previously generated for the cell lines to identify true positive variants, collectively representing a somatic reference standard. Overall, common somatic events include point mutations, small insertion/deletions, and genes affected by concurrent copy number changes. We additionally show divergence of somatic mutations in COLO829 associated with differences in cell line lineage. We present this reference to the community as a standard for enabling interpretation and identification of somatic mutations across institutions and analytical pipelines.

  Study EGAS00001001385

• The ERASMUSMC-HEMA Data Access Committee controlling appeals for 3q26-rearranged acute myeloid leukemia datasets from the department of Hematology at Erasmus MC

  Dac EGAC00001000162

• TUM Experimental Neuroimmunology

  This DAC will decide about all data requests to human data deposited at EGA that was primarily produced at the Institute for Experimental Neuroimmunology at the Technical University Munich, Germany.

  Dac EGAC50000000093