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The spatio-temporal evolution of lymph node spread in early breast cancer

Set of multi-region sequenced breast cancer primary samples, lymph nodes and ctDNA. We collected samples from 11 breast cancer patients with lymph node involvement but no sign of distant metastasis. We performed a mix of whole-exome sequencing, targeted capture sequencing, and whole-genome sequencing of primary tumour samples and lymph nodes, as well as targeted capture sequencing of circulating tumour DNA.

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Multi-region sequencing of breast cancer samples by Sottoriva Lab

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 Institute of Cancer Research 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 Institute of Cancer Research 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. 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 that it, and its Authorised Personnel, are covered by and shall comply with the obligations contained in the Data Protection Act 1998 as amended from time to time, the General Data Protection Regulation EU 2016/679 ("GDPR") (when applicable) or equivalent national provisions no less onerous then those contained in the General Data Protection Regulation EU 2016/679. In particular, the Recipient and its Registered Users understand their duties under such legislation in relation to the handling of Data and the rights of Data Subjects. 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 The Institute of Cancer Research within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify The Institute of Cancer Research prior to any significant changes to the protocol for the Project. 14. The User Institution will notify The Institute of Cancer Research as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Institute of Cancer Research 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 Institute of Cancer Research. 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 Institute of Cancer Research Signature: Name: Title: Date: APPENDIX I - DATASET DETAILS APPENDIX II --PROJECT DETAILS APPENDIX III -- PUBLICATION POLICY APPENDIX I - DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) EGAS00001002947 63 whole-exome sequencing samples 80 targeted panel sequencing samples 114 whole-genome sequencing samples Name of project that created the dataset The spatio-temporal evolution of lymph node spread in early breast cancer Names of other data producers/collaborators none Specific limitations on areas of research Use of the data must be related to cancer. Use of the data includes methods development research (e.g., development of software or algorithms). Minimum protection measures required The User Institution agrees that it shall take all reasonable security precautions to keep the Data confidential; to guard against unauthorised or unlawful processing of the Data;, and to prevent accidental loss or destruction of, or damage to, the Data. Such precautions to be no less onerous than those applied in respect of the Recipient's own confidential information. 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. The internal hard drives of Laptops holding these data must be encrypted and 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 Institute of Cancer Research 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 Institute of Cancer Research 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 3 months after these data were first made available on the relevant hosting database, unless The Institute of Cancer Research 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 Institute of Cancer Research.

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
EGAS00001002947 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
EGAF00002010111 bam 22.8 GB
EGAF00002010112 bam 24.4 GB
EGAF00002010113 bam 22.4 GB
EGAF00002010114 bam 17.2 GB
EGAF00002010115 bam 22.8 GB
EGAF00002010116 bam 21.6 GB
EGAF00002010117 bam 22.0 GB
EGAF00002010118 bam 18.8 GB
EGAF00002010119 bam 18.9 GB
EGAF00002010120 bam 19.8 GB
EGAF00002010121 bam 19.2 GB
EGAF00002010122 bam 22.6 GB
EGAF00002010123 bam 19.7 GB
EGAF00002010124 bam 19.9 GB
EGAF00002010125 bam 19.4 GB
EGAF00002010126 bam 19.7 GB
EGAF00002010127 bam 21.4 GB
EGAF00002010128 bam 17.1 GB
EGAF00002010129 bam 17.0 GB
EGAF00002010130 bam 12.7 GB
EGAF00002010131 bam 14.2 GB
EGAF00002010132 bam 18.5 GB
EGAF00002010133 bam 22.5 GB
EGAF00002010134 bam 23.3 GB
EGAF00002010135 bam 14.7 GB
EGAF00002010136 bam 21.7 GB
EGAF00002010137 bam 26.9 GB
EGAF00002010138 bam 21.4 GB
EGAF00002010139 bam 14.0 GB
EGAF00002010140 bam 19.2 GB
EGAF00002010141 bam 22.2 GB
EGAF00002010142 bam 20.9 GB
EGAF00002010143 bam 12.8 GB
EGAF00002010144 bam 14.3 GB
EGAF00002010145 bam 26.4 GB
EGAF00002010146 bam 19.6 GB
EGAF00002010147 bam 16.7 GB
EGAF00002010148 bam 21.3 GB
EGAF00002010149 bam 17.2 GB
EGAF00002010150 bam 12.6 GB
EGAF00002010151 bam 17.5 GB
EGAF00002010152 bam 19.2 GB
EGAF00002010153 bam 17.3 GB
EGAF00002010154 bam 11.6 GB
EGAF00002010155 bam 13.2 GB
EGAF00002010156 bam 15.6 GB
EGAF00002010157 bam 10.5 GB
EGAF00002010158 bam 18.6 GB
EGAF00002010159 bam 12.6 GB
EGAF00002010160 bam 17.3 GB
EGAF00002010161 bam 20.3 GB
EGAF00002010162 bam 20.4 GB
EGAF00002010163 bam 15.4 GB
EGAF00002010164 bam 13.1 GB
EGAF00002010165 bam 16.7 GB
EGAF00002010166 bam 23.4 GB
EGAF00002010167 bam 17.9 GB
EGAF00002010168 bam 19.6 GB
EGAF00002010169 bam 15.7 GB
EGAF00002010170 bam 16.1 GB
EGAF00002010171 bam 17.2 GB
EGAF00002010172 bam 16.6 GB
EGAF00002010173 bam 17.0 GB
EGAF00002010174 bam 48.3 GB
EGAF00002010175 bam 61.8 GB
EGAF00002010176 bam 61.2 GB
EGAF00002010177 bam 58.0 GB
EGAF00002010178 bam 56.4 GB
EGAF00002010179 bam 60.5 GB
EGAF00002010180 bam 437.6 MB
EGAF00002010181 bam 1.4 GB
EGAF00002010182 bam 423.9 MB
EGAF00002010183 bam 325.7 MB
EGAF00002010184 bam 251.1 MB
EGAF00002010185 bam 809.8 MB
EGAF00002010186 bam 174.0 MB
EGAF00002010187 bam 259.6 MB
EGAF00002010188 bam 269.6 MB
EGAF00002010189 bam 258.3 MB
EGAF00002010190 bam 1.3 GB
EGAF00002010191 bam 365.4 MB
EGAF00002010192 bam 373.0 MB
EGAF00002010193 bam 709.5 MB
EGAF00002010194 bam 524.3 MB
EGAF00002010195 bam 208.7 MB
EGAF00002010196 bam 330.3 MB
EGAF00002010197 bam 553.1 MB
EGAF00002010198 bam 992.4 MB
EGAF00002010199 bam 342.4 MB
EGAF00002010200 bam 474.5 MB
EGAF00002010201 bam 1.2 GB
EGAF00002010202 bam 299.0 MB
EGAF00002010203 bam 1.1 GB
EGAF00002010204 bam 418.0 MB
EGAF00002010205 bam 260.8 MB
EGAF00002010206 bam 198.0 MB
EGAF00002010207 bam 296.6 MB
EGAF00002010208 bam 319.5 MB
EGAF00002010209 bam 335.0 MB
EGAF00002010210 bam 429.8 MB
EGAF00002010211 bam 311.3 MB
EGAF00002010212 bam 708.4 MB
EGAF00002010213 bam 374.0 MB
EGAF00002010214 bam 1.3 GB
EGAF00002010215 bam 1.3 GB
EGAF00002010216 bam 1.2 GB
EGAF00002010217 bam 407.1 MB
EGAF00002010218 bam 1.5 GB
EGAF00002010219 bam 1.8 GB
EGAF00002010220 bam 377.0 MB
EGAF00002010221 bam 615.8 MB
EGAF00002010222 bam 384.7 MB
EGAF00002010223 bam 279.4 MB
EGAF00002010224 bam 307.3 MB
EGAF00002010225 bam 254.5 MB
EGAF00002010226 bam 424.5 MB
EGAF00002010227 bam 225.4 MB
EGAF00002010228 bam 420.5 MB
EGAF00002010229 bam 353.1 MB
EGAF00002010230 bam 743.6 MB
EGAF00002010231 bam 389.8 MB
EGAF00002010232 bam 688.5 MB
EGAF00002010233 bam 448.5 MB
EGAF00002010234 bam 411.9 MB
EGAF00002010235 bam 597.7 MB
EGAF00002010236 bam 303.9 MB
EGAF00002010237 bam 833.7 MB
EGAF00002010238 bam 418.9 MB
EGAF00002010239 bam 257.0 MB
EGAF00002010240 bam 220.0 MB
EGAF00002010241 bam 237.0 MB
EGAF00002010242 bam 226.5 MB
EGAF00002010243 bam 253.1 MB
EGAF00002010244 bam 349.9 MB
EGAF00002010245 bam 413.2 MB
EGAF00002010246 bam 459.0 MB
EGAF00002010247 bam 424.7 MB
EGAF00002010248 bam 703.7 MB
EGAF00002010249 bam 1.1 GB
EGAF00002010250 bam 352.5 MB
EGAF00002010251 bam 441.1 MB
EGAF00002010252 bam 539.8 MB
EGAF00002010253 bam 702.5 MB
EGAF00002010254 bam 673.1 MB
EGAF00002010255 bam 732.8 MB
EGAF00002010256 bam 599.7 MB
EGAF00002010257 bam 273.7 MB
EGAF00002010258 bam 226.4 MB
EGAF00002010259 bam 247.6 MB
EGAF00002010260 bam 1.6 GB
EGAF00002010261 bam 378.9 MB
EGAF00002010262 bam 326.7 MB
EGAF00002010263 bam 555.4 MB
EGAF00002010264 bam 468.4 MB
EGAF00002010265 bam 454.0 MB
EGAF00002010266 bam 326.8 MB
EGAF00002010267 bam 490.4 MB
EGAF00002010268 bam 330.7 MB
EGAF00002010269 bam 1.2 GB
EGAF00002010270 bam 1.5 GB
EGAF00002010271 bam 445.4 MB
EGAF00002010272 bam 260.5 MB
EGAF00002010273 bam 364.0 MB
EGAF00002010274 bam 541.9 MB
EGAF00002010275 bam 996.5 MB
EGAF00002010276 bam 351.2 MB
EGAF00002010277 bam 402.0 MB
EGAF00002010278 bam 414.0 MB
EGAF00002010279 bam 394.6 MB
EGAF00002010280 bam 202.6 MB
EGAF00002010281 bam 238.0 MB
EGAF00002010282 bam 425.0 MB
EGAF00002010283 bam 196.7 MB
EGAF00002010284 bam 485.5 MB
EGAF00002010285 bam 409.9 MB
EGAF00002010286 bam 1.5 GB
EGAF00002010287 bam 638.3 MB
EGAF00002010288 bam 214.1 MB
EGAF00002010289 bam 248.1 MB
EGAF00002010290 bam 326.3 MB
EGAF00002010291 bam 379.6 MB
EGAF00002010292 bam 488.4 MB
EGAF00002010293 bam 587.6 MB
183 Files (1.6 TB)