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Longitudinal ctDNA in Uveal Melanoma

This dataset contains data from 11 uveal melanoma patients. Plasma samples were collected at baseline, 2-weeks, 3-, 6-, and 12-months post treatment (surgery/radiation). Samples underwent targeted panel, shallow whole genome, and cfMeDIP sequencing. A total of 46 plasma samples, 7 tumours, 11 buffy coats, and 10 healthy controls are included.

Request Access

This DAC is for the uveal melanoma study at the OICR/PMCC

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 Authorized Personnel: The individuals at the User Institution to whom the Data Access Committee (DAC) grants access to the Data. This includes the User, and those individuals under the direct supervision of the User, as well as any other individuals listed in Appendix II. Details of the initial Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access, as is outlined in the Appendix 1 attached hereto. Data Producers: The Principal Investigator responsible for the creation of this Data and other investigators responsible for the creation of this 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. Research Ethics Board Approval shall mean approval of the Project by the User Institution’s research ethics board or other research ethics board or independent review board for whom said User Institution obtains research ethics approval(s). User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. University Health Network: The University Health Network (UHN) is the largest clinical and research hospital in Canada. UHN is affiliated with the University of Toronto and is a member of the Toronto Academic Health Science Network. 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) within the Research Purposes, and only in accordance with Research Ethics Board Approval, and any conditions or restrictions imposed pursuant to such Research Ethics Board Approval. 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 breach the anonymity of the Research Participants, including agreeing to not attempt to re-identify or contact any Research Participant. 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 the Data. Despite the confidentiality of the Data, the User Institution may publish aggregate data and other results arising from use of the Data and may refer to the Data by reference to the accession number(s) as documented in Appendix I in further support of any publication resulting from use of said 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 re-identification. 4. The User Institution agrees not to link or combine these Data to other information or archived data in a way that could re-identify the Research Participants, even if access to that other 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 Authorized 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 and enter into a separate Data Access Agreement. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or provision 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 recognize the contribution of the Data Producers and include 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 analyzing 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. 11. The User Institution agrees to destroy/delete the Data held, once it is no longer being used for the Project, or in the event that the User departs the User Institution or otherwise can no longer complete the Project, with the proviso that the User Institution can retain a copy of the Data for archival purposes only in conformity with audit or legal requirements. 12. The User Institution will notify the DAC within 30 days of any changes or departures of the User, at which point the Project will terminate and the User Institution delete or destroy the Data (as per Section 11) unless otherwise agreed by the DAC. 13. The User Institution will notify the DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Either party may terminate this agreement by written notice to the other party. 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. 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 Authorized Personnel. The User Institution will procure that the Authorized Personnel comply with the terms of this agreement. 19. The Parties agree to remain silent on choice of law. Agreed for User Institution Signature: Name: Title: Date: User I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for The 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) Name of project that created the dataset Names of UHN Principal Investigator and other team members responsible for the Creation of the Data Specific limitations on areas of research (if any) as imposed by the Patient Consent and any further limitations imposed by Principal Investigator of Data Producer n/a Minimum protection measures required User Institution and Authorized Users cannot share the files with other external collaborators unless obtaining specific approval by the DAC and agreement between such external collaborator(s) and University Health Network. Raw Files shall not be uploaded in an open database. As per the Agreement, Research Ethics Board Approval of the Project under submission is required unless waived in writing by UHN. File access: Data can be held in unencrypted files on an institutional computer system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access. All Data must be held by User Institution behind a secure firewall. If Data is transferred using USB keys or other portable hard drives, the USB key or portable harddrive 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 In any publications based on these Data, please describe how the data has been 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 the underlying publication from which this data was derived (if relevant) in the standard form.

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
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
EGAF00006221129 1655859623531 7.6 GB
EGAF00006221130 1655858726203 5.6 GB
EGAF00006221131 1655858726203 7.0 GB
EGAF00006221132 1655859623531 7.3 GB
EGAF00006221133 1655860521665 7.1 GB
EGAF00006221134 1655859623531 6.6 GB
EGAF00006221135 1655860521665 7.1 GB
EGAF00006221136 1655856027900 4.8 GB
EGAF00006221137 1655859623531 6.6 GB
EGAF00006221138 1655857827913 7.4 GB
EGAF00006221139 1655858726203 7.9 GB
EGAF00006221140 1655858726203 9.7 GB
EGAF00006221141 1655860521665 9.2 GB
EGAF00006221142 1655856928141 4.5 GB
EGAF00006221143 1655856928141 3.8 GB
EGAF00006221144 1655860521665 7.7 GB
EGAF00006221145 1655858726203 3.7 GB
EGAF00006221146 1655859623531 6.5 GB
EGAF00006221147 1655858726203 5.2 GB
EGAF00006221148 1655857827913 3.8 GB
EGAF00006221149 1655857827913 3.9 GB
EGAF00006221150 1655858726203 5.3 GB
EGAF00006221151 1655859623531 6.1 GB
EGAF00006221152 1655860521665 4.9 GB
EGAF00006221153 1655859623531 7.3 GB
EGAF00006221154 1655857827913 8.7 GB
EGAF00006221155 1655859623531 5.5 GB
EGAF00006221156 1655859623531 4.3 GB
EGAF00006221157 1655858726203 4.5 GB
EGAF00006221158 1655858726203 4.4 GB
EGAF00006221159 1655858726203 5.1 GB
EGAF00006221160 1655856027900 4.0 GB
EGAF00006221161 1655858726203 4.8 GB
EGAF00006221162 1655856928141 4.5 GB
EGAF00006221163 1655860521665 7.1 GB
EGAF00006221164 1655858726203 4.0 GB
EGAF00006221165 1655859623531 7.4 GB
EGAF00006221166 1655859623531 5.6 GB
EGAF00006221167 1655857827913 3.9 GB
EGAF00006221168 1655857827913 2.9 GB
EGAF00006221169 1655859623531 3.6 GB
EGAF00006221170 1655857827913 7.4 GB
EGAF00006221171 1655860521665 5.2 GB
EGAF00006221172 1655857827913 4.9 GB
EGAF00006221173 1655858726203 4.8 GB
EGAF00006221174 1655857827913 5.1 GB
EGAF00006221175 1655857827913 5.1 GB
EGAF00006221176 1655860521665 8.1 GB
EGAF00006221177 1655856928141 4.0 GB
EGAF00006221178 1655856928141 3.6 GB
EGAF00006221179 1655856027900 2.9 GB
EGAF00006221180 1655860521665 4.2 GB
EGAF00006221181 1655858726203 3.9 GB
EGAF00006221182 1655856928141 1.5 GB
EGAF00006221183 1655856928141 1.1 GB
EGAF00006221184 1655855147348 1.0 GB
EGAF00006221185 1655856928141 1.4 GB
EGAF00006221186 1655856027900 1.0 GB
EGAF00006221187 1655856027900 562.8 MB
EGAF00006221188 1655857827913 1.6 GB
EGAF00006221189 1655857827913 1.2 GB
EGAF00006221190 1655857827913 2.7 GB
EGAF00006221191 1655856928141 1.3 GB
EGAF00006221192 1655857827913 986.3 MB
EGAF00006221193 1655856928141 871.3 MB
EGAF00006221194 1655857827913 1.9 GB
EGAF00006221195 1655858726203 1.4 GB
EGAF00006221196 1655857827913 1.7 GB
EGAF00006221197 1655856027900 1.3 GB
EGAF00006221198 1655856027902 1.3 GB
EGAF00006221199 1655856928141 1.0 GB
EGAF00006221200 1655857827913 1.8 GB
EGAF00006221201 1655857827913 1.9 GB
EGAF00006221202 1655857827913 1.4 GB
EGAF00006221203 1655856027902 1.8 GB
EGAF00006221204 1655856027900 1.8 GB
EGAF00006221205 1655856027900 650.9 MB
EGAF00006221206 1655856928141 1.9 GB
EGAF00006221207 1655856928141 1.6 GB
EGAF00006221208 1655857827913 1.6 GB
EGAF00006221209 1655857827913 2.0 GB
EGAF00006221210 1655856928141 1.2 GB
EGAF00006221211 1655856928141 1.7 GB
EGAF00006221212 1655856928141 1.3 GB
EGAF00006221213 1655856928141 1.5 GB
EGAF00006221214 1655856027900 2.4 GB
EGAF00006221215 1655858726203 1.6 GB
EGAF00006221216 1655856027900 1.9 GB
EGAF00006221217 1655857827913 1.9 GB
EGAF00006221218 1655858726203 1.7 GB
EGAF00006221219 1655858726203 2.5 GB
EGAF00006221220 1655857827913 1.4 GB
EGAF00006221221 1655858726203 2.4 GB
EGAF00006221222 1655856928141 442.7 MB
EGAF00006221223 1655857827913 1.7 GB
EGAF00006221224 1655856928141 1.8 GB
EGAF00006221225 1655856928141 889.5 MB
EGAF00006221226 1655858726203 1.8 GB
EGAF00006221227 1655856928141 2.7 GB
EGAF00006221228 1655858726203 2.6 GB
EGAF00006221229 1655857827913 1.8 GB
EGAF00006221230 1655858726203 3.8 GB
EGAF00006221231 1655856027900 488.4 MB
EGAF00006221232 1655857827913 1.1 GB
EGAF00006221233 1655857827913 2.5 GB
EGAF00006221234 1655858726203 1.7 GB
EGAF00006221235 1655857827913 2.7 GB
EGAF00006221236 1655857827913 2.5 GB
EGAF00006221237 1655857827913 2.6 GB
EGAF00006221238 1655856928141 990.1 MB
EGAF00006221239 1655856928141 731.3 MB
EGAF00006221240 1655858726203 3.1 GB
EGAF00006221241 1655859623531 3.1 GB
EGAF00006221242 1655858726203 2.8 GB
EGAF00006221243 1655859623531 2.8 GB
EGAF00006221244 1655858726203 2.8 GB
EGAF00006221245 1655857827913 910.5 MB
EGAF00006221246 1655857827913 2.1 GB
EGAF00006221247 1655857827913 1.4 GB
EGAF00006221248 1655858726203 1.3 GB
EGAF00006221249 1655856928141 1.4 GB
EGAF00006221250 1655858726203 2.7 GB
EGAF00006221251 1655858726203 2.6 GB
EGAF00006221252 1655859623531 2.6 GB
EGAF00006221253 1655856928141 1.9 GB
EGAF00006221254 1655857827913 2.5 GB
EGAF00006221255 1655859623531 2.2 GB
EGAF00006221256 1655858726203 4.7 GB
EGAF00006221257 1655857827913 2.4 GB
EGAF00006221258 1655858726203 2.1 GB
EGAF00006221259 1655857827913 1.9 GB
EGAF00006221260 1655857827913 2.3 GB
EGAF00006221261 1655860521665 5.7 GB
EGAF00006221262 1655858726203 1.8 GB
EGAF00006221263 1655857827913 5.2 GB
EGAF00006221264 1655858726203 2.2 GB
EGAF00006221265 1655859623531 4.1 GB
EGAF00006221266 1655858726203 3.7 GB
EGAF00006221267 1655858726203 4.0 GB
EGAF00006221268 1655860521665 3.6 GB
EGAF00006221269 1655859623531 4.4 GB
EGAF00006221270 1655858726203 6.6 GB
EGAF00006221271 1655858726203 3.6 GB
EGAF00006221272 1655858726203 5.7 GB
EGAF00006221273 1655859623531 7.2 GB
EGAF00006221274 1655858726203 3.5 GB
EGAF00006221275 1655860521665 6.1 GB
EGAF00006221276 1655860521665 9.3 GB
EGAF00006221277 1655859623531 3.5 GB
EGAF00006221278 1655858726203 4.0 GB
EGAF00006221279 1655859623531 4.8 GB
EGAF00006221280 1655857827913 4.6 GB
EGAF00006221281 1655857827913 6.0 GB
EGAF00006221282 1655857827913 5.2 GB
EGAF00006221283 1655857827913 3.4 GB
EGAF00006221284 1655860521665 5.4 GB
EGAF00006221285 1655858726203 4.0 GB
EGAF00006221286 1655858726203 5.0 GB
EGAF00006221287 1655859623531 5.3 GB
EGAF00006221288 1655859623531 2.3 GB
EGAF00006221289 1655859623531 4.3 GB
EGAF00006221290 1655859623531 2.6 GB
EGAF00006221291 1655860521665 4.8 GB
EGAF00006221292 1655859623531 2.4 GB
EGAF00006221293 1655859623531 5.9 GB
EGAF00006221294 1655858726203 3.2 GB
EGAF00006221295 1655859623531 5.2 GB
EGAF00006221296 1655859623531 5.0 GB
EGAF00006221297 1655859623531 3.2 GB
EGAF00006221298 1655858726203 5.5 GB
EGAF00006221299 1655859623531 6.4 GB
EGAF00006221300 1655858726203 4.1 GB
EGAF00006221301 1655859623531 5.2 GB
EGAF00006221302 1655859623531 5.0 GB
EGAF00006221303 1655860521666 3.8 GB
EGAF00006221304 1655859623531 4.3 GB
EGAF00006221305 1655859623531 6.6 GB
EGAF00006221306 1655860521665 5.2 GB
EGAF00006221307 1655860521665 4.3 GB
EGAF00006221308 1655859623531 3.9 GB
EGAF00006221309 1655859623531 4.3 GB
EGAF00006221310 1655859623531 3.7 GB
EGAF00006221311 1655859623531 4.4 GB
EGAF00006221312 1655859623531 5.4 GB
EGAF00006221313 1655858726203 3.5 GB
EGAF00006221314 1655860521665 5.5 GB
EGAF00006221315 1655858726203 4.8 GB
EGAF00006221316 1655860521665 4.9 GB
EGAF00006221317 1655860521665 4.6 GB
EGAF00006221318 1655859623531 5.7 GB
EGAF00006221319 1655858726203 5.1 GB
191 Files (713.8 GB)