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Pre-neoplastic somatic mutations including MYD88L265P in lymphoplasmacytic lymphoma

In this study, we sequenced multiple stages of the B-lineage in elderly individuals and patients with lymphoplasmacytic lymphoma to study whether mutations are accumulated in normal-cell counterparts prior to lymphoma

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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

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 Clínica Universidad de Navarra - Centro de Investigación Médica Aplicada (CUN-CIMA hereafter) 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: CUN-CIMA 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/computational 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. 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 (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). 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) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). 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 CUN-CIMA within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify CUN-CIMA prior to any significant changes to the protocol for the Project. 14. The User Institution will notify CUN-CIMA as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. CUN-CIMA 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 CUN-CIMA. 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. 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 CUN-CIMA 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) EGAxxxxxxxxx. In this study, we sequenced (through whole-exome sequencing) multiple stages of the B-lineage in elderly individuals and patients with lymphoplasmacytic lymphoma, a singular disease for studying lymphomagenesis because of high-prevalence of mutated MYD88. Name of project that created the dataset Pre-neoplastic somatic mutations including MYD88L265P in lymphoplasmacytic lymphoma Names of other data producers/collaborators Sara Rodriguez, Jon Celay, Ibai Goicoechea, Cristina Jimenez, Cirino Botta, Maria-José Garcia-Barchino, Juan-Jose Garces, Marta Larrayoz, Susana Santos, Diego Alignani, Amaia Vilas-Zornoza, Cristina Perez, Sonia Garate, Sarai Sarvide, Aitziber Lopez, Hans-Christian Reinhardt, Yolanda R. Carrasco, Isidro Sanchez-Garcia, Maria-Jose Larrayoz, Maria-Jose Calasanz, Carlos Panizo, Felipe Prosper, Jose-Maria Lamo-Espinosa, Marina Motta, Giuseppe Rossi, Antonio Sacco, Massimo Gentile, Sara Duarte, Helena Vitoria, Catarina Geraldes, Artur Paiva, Noemi Puig, Ramon Garcia-Sanz, Aldo M. Roccaro, Gema Fuerte, Jesus F. San Miguel, Jose-Angel Martinez-Climent and Bruno Paiva Specific limitations on areas of research To advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical/computational methods that may be applied to such research. Minimum protection measures required 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 CUN-CIMA 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. CUN-CIMA 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 12 months after these data were first made available on the relevant hosting database, unless CUN-CIMA 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 CUN-CIMA.

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
EGAS00001005656 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00005499215 fastq.gz 5.5 GB
EGAF00005499216 fastq.gz 5.9 GB
EGAF00005499217 fastq.gz 7.7 GB
EGAF00005499218 fastq.gz 8.2 GB
EGAF00005499219 fastq.gz 9.2 GB
EGAF00005499220 fastq.gz 9.6 GB
EGAF00005499221 fastq.gz 10.9 GB
EGAF00005499222 fastq.gz 11.7 GB
EGAF00005499223 fastq.gz 6.4 GB
EGAF00005499224 fastq.gz 6.8 GB
EGAF00005499225 fastq.gz 5.3 GB
EGAF00005499226 fastq.gz 5.7 GB
EGAF00005499227 fastq.gz 7.3 GB
EGAF00005499228 fastq.gz 7.9 GB
EGAF00005499229 fastq.gz 12.0 GB
EGAF00005499230 fastq.gz 12.5 GB
EGAF00005499231 fastq.gz 11.4 GB
EGAF00005499232 fastq.gz 11.9 GB
EGAF00005499233 fastq.gz 10.1 GB
EGAF00005499234 fastq.gz 10.6 GB
EGAF00005499235 fastq.gz 16.1 GB
EGAF00005499236 fastq.gz 16.9 GB
EGAF00005499237 fastq.gz 11.3 GB
EGAF00005499238 fastq.gz 11.9 GB
EGAF00005499239 fastq.gz 6.4 GB
EGAF00005499240 fastq.gz 6.7 GB
EGAF00005499241 fastq.gz 6.1 GB
EGAF00005499242 fastq.gz 6.5 GB
EGAF00005499243 fastq.gz 11.5 GB
EGAF00005499244 fastq.gz 12.1 GB
EGAF00005499245 fastq.gz 5.8 GB
EGAF00005499246 fastq.gz 6.2 GB
EGAF00005499247 fastq.gz 9.8 GB
EGAF00005499248 fastq.gz 10.3 GB
EGAF00005499249 fastq.gz 7.3 GB
EGAF00005499250 fastq.gz 7.7 GB
EGAF00005499251 fastq.gz 6.3 GB
EGAF00005499252 fastq.gz 6.7 GB
EGAF00005499253 fastq.gz 6.4 GB
EGAF00005499254 fastq.gz 6.8 GB
EGAF00005499255 fastq.gz 7.3 GB
EGAF00005499256 fastq.gz 7.8 GB
EGAF00005499257 fastq.gz 6.1 GB
EGAF00005499258 fastq.gz 6.5 GB
EGAF00005499259 fastq.gz 11.1 GB
EGAF00005499260 fastq.gz 11.6 GB
EGAF00005499261 fastq.gz 11.7 GB
EGAF00005499262 fastq.gz 12.2 GB
EGAF00005499263 fastq.gz 5.9 GB
EGAF00005499264 fastq.gz 6.2 GB
EGAF00005499265 fastq.gz 5.9 GB
EGAF00005499266 fastq.gz 6.2 GB
EGAF00005499267 fastq.gz 6.2 GB
EGAF00005499268 fastq.gz 6.6 GB
EGAF00005499269 fastq.gz 6.3 GB
EGAF00005499270 fastq.gz 6.6 GB
EGAF00005499271 fastq.gz 5.7 GB
EGAF00005499272 fastq.gz 6.1 GB
EGAF00005499273 fastq.gz 11.3 GB
EGAF00005499274 fastq.gz 11.9 GB
EGAF00005499275 fastq.gz 9.2 GB
EGAF00005499276 fastq.gz 9.6 GB
EGAF00005499277 fastq.gz 9.2 GB
EGAF00005499278 fastq.gz 9.6 GB
EGAF00005499279 fastq.gz 11.3 GB
EGAF00005499280 fastq.gz 11.9 GB
EGAF00005499281 fastq.gz 3.5 GB
EGAF00005499282 fastq.gz 3.7 GB
EGAF00005499283 fastq.gz 11.6 GB
EGAF00005499284 fastq.gz 12.1 GB
EGAF00005499285 fastq.gz 11.6 GB
EGAF00005499286 fastq.gz 12.3 GB
EGAF00005499287 fastq.gz 11.3 GB
EGAF00005499288 fastq.gz 11.8 GB
EGAF00005499289 fastq.gz 11.1 GB
EGAF00005499290 fastq.gz 11.6 GB
EGAF00005499291 fastq.gz 12.2 GB
EGAF00005499292 fastq.gz 12.7 GB
EGAF00005499293 fastq.gz 14.0 GB
EGAF00005499294 fastq.gz 14.7 GB
EGAF00005499295 fastq.gz 12.3 GB
EGAF00005499296 fastq.gz 12.9 GB
EGAF00005499297 fastq.gz 10.8 GB
EGAF00005499298 fastq.gz 11.2 GB
EGAF00005499299 fastq.gz 10.7 GB
EGAF00005499300 fastq.gz 11.2 GB
EGAF00005499301 fastq.gz 11.2 GB
EGAF00005499302 fastq.gz 11.7 GB
EGAF00005499303 fastq.gz 11.2 GB
EGAF00005499304 fastq.gz 11.8 GB
EGAF00005499305 fastq.gz 7.2 GB
EGAF00005499306 fastq.gz 7.6 GB
EGAF00005499307 fastq.gz 8.7 GB
EGAF00005499308 fastq.gz 9.3 GB
EGAF00005499309 fastq.gz 6.9 GB
EGAF00005499310 fastq.gz 7.3 GB
EGAF00005499311 fastq.gz 11.3 GB
EGAF00005499312 fastq.gz 11.9 GB
EGAF00005499313 fastq.gz 6.4 GB
EGAF00005499314 fastq.gz 6.8 GB
EGAF00005499315 fastq.gz 10.7 GB
EGAF00005499316 fastq.gz 11.1 GB
EGAF00005499317 fastq.gz 11.6 GB
EGAF00005499318 fastq.gz 12.2 GB
EGAF00005499319 fastq.gz 11.0 GB
EGAF00005499320 fastq.gz 11.5 GB
EGAF00005499321 fastq.gz 8.8 GB
EGAF00005499322 fastq.gz 9.2 GB
EGAF00005499323 fastq.gz 10.7 GB
EGAF00005499324 fastq.gz 11.1 GB
EGAF00005499325 fastq.gz 6.1 GB
EGAF00005499326 fastq.gz 6.5 GB
EGAF00005499327 fastq.gz 6.9 GB
EGAF00005499328 fastq.gz 7.3 GB
EGAF00005499329 fastq.gz 12.3 GB
EGAF00005499330 fastq.gz 12.8 GB
EGAF00005499331 fastq.gz 5.8 GB
EGAF00005499332 fastq.gz 6.3 GB
EGAF00005499333 fastq.gz 10.8 GB
EGAF00005499334 fastq.gz 11.5 GB
EGAF00005499335 fastq.gz 10.3 GB
EGAF00005499336 fastq.gz 10.6 GB
EGAF00005499337 fastq.gz 10.9 GB
EGAF00005499338 fastq.gz 11.7 GB
EGAF00005499339 fastq.gz 6.0 GB
EGAF00005499340 fastq.gz 6.3 GB
EGAF00005499341 fastq.gz 9.3 GB
EGAF00005499342 fastq.gz 9.7 GB
EGAF00005499343 fastq.gz 12.5 GB
EGAF00005499344 fastq.gz 13.2 GB
EGAF00005499345 fastq.gz 9.3 GB
EGAF00005499346 fastq.gz 9.7 GB
EGAF00005499347 fastq.gz 10.7 GB
EGAF00005499348 fastq.gz 11.2 GB
EGAF00005499349 fastq.gz 12.3 GB
EGAF00005499350 fastq.gz 12.9 GB
EGAF00005499351 fastq.gz 11.4 GB
EGAF00005499352 fastq.gz 11.9 GB
EGAF00005499353 fastq.gz 9.1 GB
EGAF00005499354 fastq.gz 9.5 GB
EGAF00005499355 fastq.gz 8.8 GB
EGAF00005499356 fastq.gz 9.2 GB
EGAF00005499357 fastq.gz 8.9 GB
EGAF00005499358 fastq.gz 9.2 GB
EGAF00005499359 fastq.gz 5.8 GB
EGAF00005499360 fastq.gz 6.1 GB
146 Files (1.4 TB)