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IG-MYC ALL - DNA and RNA sequencing

The dataset is composed by the raw RNA sequencing (n=6), targeted DNA sequencing (n=18) and whole exome sequencing (n=17) from 19 patients with IG-MYC-rearrangements.

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IG-MYC ALL Data Access Policy

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom the Newcastle University IG-MYC ALL Data Access Committee grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The Newcastle University IG-MYC ALL Data Access Committee and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. Newcastle University IG-MYC ALL Data Access Committee: Dr Lisa J Russell and Dr Simon Bomken at the Newcastle University , Wolfson Childhood Cancer Research Centre, Herschel Building, Brewery Lane, Newcastle upon Tyne, United Kingdom. 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines ( ) and the Toronto Statement ( This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) ( ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) ( ). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify the Newcastle University IG-MYC ALL Data Access Committee within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the Newcastle University IG-MYC ALL Data Access Committee prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the Newcastle University IG-MYC ALL Data Access Committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Newcastle University IG-MYC ALL Data Access Committee may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than the Newcastle University IG-MYC ALL Data Access Committee. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of England and Wales and shall be subject to the exclusive jurisdiction of the English courts. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for the Newcastle University IG-MYC ALL Data Access Committee Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) EGA Study ID: EGAS00001005111 Dataset details: The dataset is composed by the raw RNA-sequencing (n=6), targeted-sequencing (n=18) and whole exome sequencing (n=17) from patients with IG-MYC-rearrangements Name of project that created the dataset Molecular characterisation and clinical outcome of B-cell precursor acute lymphoblastic leukaemia with IG-MYC rearrangement Names of other data producers/collaborators Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA Specific limitations on areas of research The dataset should only be used for purposes of genetic studies in the field of haematological malignancies and is not adequate for other areas of research unless an adequate rational is provided. Minimum protection measures required The identity and anonymity of the subjects must be ensured at all times and findings relating to the health and wellbeing of these individuals should not be divulged without obtaining previous consent from them and the Newcastle University IG-MYC ALL Data Access Committee. File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY The Newcastle University IG-MYC ALL Data Access Committee intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. The Newcastle University IG-MYC ALL Data Access Committee anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until 6 months after these data were first made available on the relevant hosting database, unless the Newcastle University IG-MYC ALL Data Access Committee has provided written consent to earlier submission. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with the Newcastle University IG-MYC ALL Data Access Committee.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001005111 Cancer Genomics
ID File Type Size Located in
EGAF00005099413 fastq.gz 50.0 MB
EGAF00005099414 fastq.gz 50.9 MB
EGAF00005099415 fastq.gz 366.8 MB
EGAF00005099416 fastq.gz 366.8 MB
EGAF00005099417 fastq.gz 329.2 MB
EGAF00005099418 fastq.gz 331.1 MB
EGAF00005099419 fastq.gz 354.5 MB
EGAF00005099420 fastq.gz 358.9 MB
EGAF00005099421 fastq.gz 361.2 MB
EGAF00005099422 fastq.gz 376.8 MB
EGAF00005099423 fastq.gz 319.2 MB
EGAF00005099424 fastq.gz 333.8 MB
EGAF00005099425 fastq.gz 409.4 MB
EGAF00005099426 fastq.gz 411.9 MB
EGAF00005099427 fastq.gz 298.5 MB
EGAF00005099428 fastq.gz 302.9 MB
EGAF00005099429 fastq.gz 345.0 MB
EGAF00005099430 fastq.gz 347.3 MB
EGAF00005099431 fastq.gz 431.1 MB
EGAF00005099432 fastq.gz 442.1 MB
EGAF00005099433 fastq.gz 404.0 MB
EGAF00005099434 fastq.gz 436.1 MB
EGAF00005099435 fastq.gz 397.3 MB
EGAF00005099436 fastq.gz 404.8 MB
EGAF00005099437 fastq.gz 431.6 MB
EGAF00005099438 fastq.gz 490.8 MB
EGAF00005099439 fastq.gz 375.1 MB
EGAF00005099440 fastq.gz 379.5 MB
EGAF00005099441 fastq.gz 474.5 MB
EGAF00005099442 fastq.gz 495.3 MB
EGAF00005099443 fastq.gz 492.2 MB
EGAF00005099444 fastq.gz 496.6 MB
EGAF00005099445 fastq.gz 375.0 MB
EGAF00005099446 fastq.gz 379.9 MB
EGAF00005099447 fastq.gz 434.0 MB
EGAF00005099448 fastq.gz 437.6 MB
EGAF00005099449 fastq.gz 1.3 GB
EGAF00005099450 fastq.gz 1.3 GB
EGAF00005099451 fastq.gz 1.2 GB
EGAF00005099452 fastq.gz 1.2 GB
EGAF00005099453 fastq.gz 1.1 GB
EGAF00005099454 fastq.gz 1.1 GB
EGAF00005099455 fastq.gz 1.4 GB
EGAF00005099456 fastq.gz 1.4 GB
EGAF00005099457 fastq.gz 1.2 GB
EGAF00005099458 fastq.gz 1.2 GB
EGAF00005099459 fastq.gz 1.3 GB
EGAF00005099460 fastq.gz 1.3 GB
EGAF00005099461 fastq.gz 1.3 GB
EGAF00005099462 fastq.gz 1.3 GB
EGAF00005099463 fastq.gz 1.1 GB
EGAF00005099464 fastq.gz 1.1 GB
EGAF00005099465 fastq.gz 1.3 GB
EGAF00005099466 fastq.gz 1.4 GB
EGAF00005099467 fastq.gz 1.2 GB
EGAF00005099468 fastq.gz 1.3 GB
EGAF00005099469 fastq.gz 1.3 GB
EGAF00005099470 fastq.gz 1.3 GB
EGAF00005099471 fastq.gz 1.2 GB
EGAF00005099472 fastq.gz 1.2 GB
EGAF00005099473 fastq.gz 1.2 GB
EGAF00005099474 fastq.gz 1.2 GB
EGAF00005099475 fastq.gz 1.7 GB
EGAF00005099476 fastq.gz 1.7 GB
EGAF00005099477 fastq.gz 1.2 GB
EGAF00005099478 fastq.gz 1.2 GB
EGAF00005099479 fastq.gz 1.1 GB
EGAF00005099480 fastq.gz 1.1 GB
EGAF00005099481 fastq.gz 1.3 GB
EGAF00005099482 fastq.gz 1.3 GB
EGAF00005099483 fastq.gz 1.0 GB
EGAF00005099484 fastq.gz 1.0 GB
EGAF00005099485 fastq.gz 1.5 GB
EGAF00005099486 fastq.gz 1.5 GB
EGAF00005099487 fastq.gz 1.2 GB
EGAF00005099488 fastq.gz 1.3 GB
EGAF00005099489 fastq.gz 1.3 GB
EGAF00005099490 fastq.gz 1.3 GB
EGAF00005099491 fastq.gz 1.5 GB
EGAF00005099492 fastq.gz 1.5 GB
EGAF00005099493 fastq.gz 1.1 GB
EGAF00005099494 fastq.gz 1.1 GB
EGAF00005099495 fastq.gz 1.3 GB
EGAF00005099496 fastq.gz 1.3 GB
EGAF00005099497 fastq.gz 1.3 GB
EGAF00005099498 fastq.gz 1.3 GB
EGAF00005099499 fastq.gz 1.6 GB
EGAF00005099500 fastq.gz 1.7 GB
EGAF00005099501 fastq.gz 1.4 GB
EGAF00005099502 fastq.gz 1.4 GB
EGAF00005099503 fastq.gz 1.0 GB
EGAF00005099504 fastq.gz 1.1 GB
EGAF00005099505 fastq.gz 1.2 GB
EGAF00005099506 fastq.gz 1.2 GB
EGAF00005099507 fastq.gz 1.1 GB
EGAF00005099508 fastq.gz 1.1 GB
EGAF00005099509 fastq.gz 1.1 GB
EGAF00005099510 fastq.gz 1.1 GB
EGAF00005099511 fastq.gz 1.1 GB
EGAF00005099512 fastq.gz 1.1 GB
EGAF00005099513 fastq.gz 1.0 GB
EGAF00005099514 fastq.gz 1.0 GB
EGAF00005099515 fastq.gz 1.3 GB
EGAF00005099516 fastq.gz 1.4 GB
EGAF00005099517 fastq.gz 2.1 GB
EGAF00005099518 fastq.gz 2.1 GB
EGAF00005099519 fastq.gz 4.0 GB
EGAF00005099520 fastq.gz 4.0 GB
EGAF00005099521 fastq.gz 136.1 MB
EGAF00005099522 fastq.gz 138.9 MB
EGAF00005099523 fastq.gz 1.3 GB
EGAF00005099524 fastq.gz 1.3 GB
EGAF00005099525 fastq.gz 2.3 GB
EGAF00005099526 fastq.gz 2.4 GB
EGAF00005099527 fastq.gz 2.9 GB
EGAF00005099528 fastq.gz 2.9 GB
EGAF00005099529 fastq.gz 3.8 GB
EGAF00005099530 fastq.gz 4.0 GB
EGAF00005099531 fastq.gz 805.0 MB
EGAF00005099532 fastq.gz 810.0 MB
120 Files (133.7 GB)