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TOTHER3 dataset

This dataset contains the FASTQ and BAM files for TOTHER3 study. Targeted DNA-Seq experiment were realized with 49 samples. Since this data was obtained with a panel of genes protected by Intellectual Property (IP), these files only contain information to validate the results published and, in consequence, sensible data had to be specifically removed.

Request Access

TOTHER3 access policy

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. 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 Fundació de Recerca Clinic Hospital in Barcelona within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Fundació de Recerca Clinic Hospital in Barcelona prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Fundació de Recerca Clinic Hospital in Barcelona as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Fundació de Recerca Clinic Hospital in Barcelona 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 Fundació de Recerca Clinic Hospital in Barcelona. 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 Spain and shall be subject to the exclusive jurisdiction of the Spanish courts. APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details): - EGA Study ID 731. - Dataset contains FASTQ and BAM files from targeted DNA-Seq experiments of 49 breast cancer samples. Name of project that created the dataset: TOTHER3 Names of other data producers/collaborators: - Aleix Prat - Francisco J. Pardo-Palacios - Fara Brasó Maristany Specific limitations on areas of research: - Since this data was obtained with a panel of genes protected by Intellectual Property (IP), these files only contain information to validate published results and, in consequence, sensible data had to be specifically removed. 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 This information must be completed by the Requestor to request access for the dataset. 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 APPENDIX III – PUBLICATION POLICY Fundació de Recerca Clinic Hospital in Barcelona intends 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. Fundació de Recerca Clinic Hospital in Barcelona anticipates 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 Fundació de Recerca Clinic Hospital in Barcelona 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 Fundació de Recerca Clinic Hospital in Barcelona

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
EGAS50000000385 Cancer Genomics

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
EGAF50000126097 bai 1.4 MB
EGAF50000126098 bai 1.4 MB
EGAF50000126099 bam 179.1 MB
EGAF50000126100 bai 1.4 MB
EGAF50000126101 bai 1.5 MB
EGAF50000126102 bam 267.3 MB
EGAF50000126103 bai 1.4 MB
EGAF50000126104 bai 1.5 MB
EGAF50000126105 fastq.gz 176.1 MB
EGAF50000126106 fastq.gz 116.6 MB
EGAF50000126107 fastq.gz 101.4 MB
EGAF50000126108 fastq.gz 102.1 MB
EGAF50000126109 fastq.gz 131.0 MB
EGAF50000126110 fastq.gz 62.0 MB
EGAF50000126111 fastq.gz 102.9 MB
EGAF50000126112 fastq.gz 293.4 MB
EGAF50000126113 fastq.gz 210.8 MB
EGAF50000126114 fastq.gz 214.1 MB
EGAF50000126115 fastq.gz 214.1 MB
EGAF50000126116 bam 264.0 MB
EGAF50000126117 bai 1.5 MB
EGAF50000126118 bam 310.9 MB
EGAF50000126119 bai 1.5 MB
EGAF50000126120 bam 246.1 MB
EGAF50000126121 fastq.gz 28.7 MB
EGAF50000126122 fastq.gz 28.3 MB
EGAF50000126123 fastq.gz 182.5 MB
EGAF50000126124 fastq.gz 146.7 MB
EGAF50000126125 fastq.gz 71.8 MB
EGAF50000126126 fastq.gz 184.3 MB
EGAF50000126127 fastq.gz 51.6 MB
EGAF50000126128 bai 1.5 MB
EGAF50000126129 bam 309.0 MB
EGAF50000126130 bai 1.4 MB
EGAF50000126131 fastq.gz 265.1 MB
EGAF50000126132 fastq.gz 80.1 MB
EGAF50000126133 fastq.gz 241.9 MB
EGAF50000126134 fastq.gz 135.2 MB
EGAF50000126135 fastq.gz 136.8 MB
EGAF50000126136 fastq.gz 181.9 MB
EGAF50000126137 fastq.gz 180.0 MB
EGAF50000126138 fastq.gz 51.5 MB
EGAF50000126139 fastq.gz 178.9 MB
EGAF50000126140 fastq.gz 186.2 MB
EGAF50000126141 fastq.gz 130.5 MB
EGAF50000126142 fastq.gz 291.6 MB
EGAF50000126143 bam 202.1 MB
EGAF50000126144 bam 115.9 MB
EGAF50000126145 fastq.gz 245.0 MB
EGAF50000126146 fastq.gz 84.3 MB
EGAF50000126147 bam 117.0 MB
EGAF50000126148 bai 1.4 MB
EGAF50000126149 fastq.gz 210.4 MB
EGAF50000126150 fastq.gz 263.6 MB
EGAF50000126151 fastq.gz 76.1 MB
EGAF50000126152 fastq.gz 46.2 MB
EGAF50000126153 fastq.gz 209.7 MB
EGAF50000126154 fastq.gz 213.7 MB
EGAF50000126155 fastq.gz 180.7 MB
EGAF50000126156 fastq.gz 182.9 MB
EGAF50000126157 bai 1.5 MB
EGAF50000126158 bam 386.5 MB
EGAF50000126159 bai 1.5 MB
EGAF50000126160 bam 297.1 MB
EGAF50000126161 bai 1.4 MB
EGAF50000126162 bai 1.5 MB
EGAF50000126163 bam 103.2 MB
EGAF50000126164 bam 270.3 MB
EGAF50000126165 fastq.gz 75.8 MB
EGAF50000126166 fastq.gz 193.4 MB
EGAF50000126167 fastq.gz 45.2 MB
EGAF50000126168 fastq.gz 79.7 MB
EGAF50000126169 fastq.gz 268.9 MB
EGAF50000126170 fastq.gz 270.6 MB
EGAF50000126171 fastq.gz 68.9 MB
EGAF50000126172 fastq.gz 69.6 MB
EGAF50000126173 fastq.gz 85.1 MB
EGAF50000126174 fastq.gz 146.8 MB
EGAF50000126175 fastq.gz 144.6 MB
EGAF50000126176 bam 270.6 MB
EGAF50000126177 bam 47.1 MB
EGAF50000126178 bam 75.3 MB
EGAF50000126179 bai 1.5 MB
EGAF50000126180 bam 276.1 MB
EGAF50000126181 bam 221.4 MB
EGAF50000126182 bai 1.4 MB
EGAF50000126183 bai 1.5 MB
EGAF50000126184 bam 224.3 MB
EGAF50000126185 bai 1.5 MB
EGAF50000126186 bam 287.0 MB
EGAF50000126187 bai 1.5 MB
EGAF50000126188 bam 290.8 MB
EGAF50000126189 bai 1.4 MB
EGAF50000126190 bam 123.1 MB
EGAF50000126191 bai 1.4 MB
EGAF50000126192 bam 103.0 MB
EGAF50000126193 bai 1.4 MB
EGAF50000126194 bam 263.4 MB
EGAF50000126195 bai 1.5 MB
EGAF50000126196 bam 303.6 MB
EGAF50000126197 bai 1.4 MB
EGAF50000126198 bam 99.9 MB
EGAF50000126199 bai 1.5 MB
EGAF50000126200 bam 337.9 MB
EGAF50000126201 bai 1.5 MB
EGAF50000126202 bam 359.8 MB
EGAF50000126203 bai 1.4 MB
EGAF50000126204 bam 242.3 MB
EGAF50000126205 bai 1.4 MB
EGAF50000126206 bam 170.1 MB
EGAF50000126207 bai 1.4 MB
EGAF50000126208 bam 94.8 MB
EGAF50000126209 bai 1.5 MB
EGAF50000126210 bam 398.6 MB
EGAF50000126211 fastq.gz 194.8 MB
EGAF50000126212 fastq.gz 197.1 MB
EGAF50000126213 fastq.gz 51.8 MB
EGAF50000126214 fastq.gz 51.7 MB
EGAF50000126215 fastq.gz 221.4 MB
EGAF50000126216 fastq.gz 225.4 MB
EGAF50000126217 fastq.gz 207.4 MB
EGAF50000126218 fastq.gz 209.6 MB
EGAF50000126219 fastq.gz 156.5 MB
EGAF50000126220 fastq.gz 73.8 MB
EGAF50000126221 fastq.gz 74.4 MB
EGAF50000126222 fastq.gz 69.8 MB
EGAF50000126223 fastq.gz 147.0 MB
EGAF50000126224 fastq.gz 144.5 MB
EGAF50000126225 fastq.gz 205.0 MB
EGAF50000126226 fastq.gz 208.3 MB
EGAF50000126227 fastq.gz 36.4 MB
EGAF50000126228 fastq.gz 36.2 MB
EGAF50000126229 fastq.gz 139.5 MB
EGAF50000126230 fastq.gz 140.1 MB
EGAF50000126231 fastq.gz 230.4 MB
EGAF50000126232 fastq.gz 233.1 MB
EGAF50000126233 fastq.gz 106.6 MB
EGAF50000126234 fastq.gz 103.9 MB
EGAF50000126235 fastq.gz 128.4 MB
EGAF50000126236 fastq.gz 175.0 MB
EGAF50000126237 fastq.gz 114.9 MB
EGAF50000126238 fastq.gz 52.1 MB
EGAF50000126239 fastq.gz 195.1 MB
EGAF50000126240 bai 1.4 MB
EGAF50000126241 bai 1.4 MB
EGAF50000126242 bai 1.4 MB
EGAF50000126243 bam 68.9 MB
EGAF50000126244 bai 1.4 MB
EGAF50000126245 bam 196.2 MB
EGAF50000126246 bam 78.3 MB
EGAF50000126247 bai 1.4 MB
EGAF50000126248 bai 1.5 MB
EGAF50000126249 bam 278.9 MB
EGAF50000126250 bai 1.5 MB
EGAF50000126251 bam 281.5 MB
EGAF50000126252 bam 53.7 MB
EGAF50000126253 bai 1.4 MB
EGAF50000126254 bai 1.4 MB
EGAF50000126255 bai 1.5 MB
EGAF50000126256 bam 333.8 MB
EGAF50000126257 bai 1.4 MB
EGAF50000126258 bam 143.5 MB
EGAF50000126259 bai 1.4 MB
EGAF50000126260 bam 193.1 MB
EGAF50000126261 bai 1.4 MB
EGAF50000126262 bam 247.3 MB
EGAF50000126263 bai 1.4 MB
EGAF50000126264 bam 168.1 MB
EGAF50000126265 bam 70.3 MB
EGAF50000126266 bam 145.4 MB
EGAF50000126267 bai 1.4 MB
EGAF50000126268 bai 1.4 MB
EGAF50000126269 bam 82.1 MB
EGAF50000126270 bai 1.4 MB
EGAF50000126271 bam 140.0 MB
EGAF50000126272 fastq.gz 200.5 MB
EGAF50000126273 fastq.gz 135.2 MB
EGAF50000126274 fastq.gz 61.3 MB
EGAF50000126275 fastq.gz 101.6 MB
EGAF50000126276 fastq.gz 89.6 MB
EGAF50000126277 fastq.gz 91.2 MB
EGAF50000126278 fastq.gz 208.3 MB
EGAF50000126279 fastq.gz 211.2 MB
EGAF50000126280 fastq.gz 229.9 MB
EGAF50000126281 fastq.gz 201.2 MB
EGAF50000126282 fastq.gz 200.4 MB
EGAF50000126283 fastq.gz 155.1 MB
EGAF50000126284 fastq.gz 141.1 MB
EGAF50000126285 fastq.gz 193.0 MB
EGAF50000126286 bai 1.4 MB
EGAF50000126287 bam 197.9 MB
EGAF50000126288 bam 336.9 MB
EGAF50000126289 fastq.gz 220.1 MB
EGAF50000126290 fastq.gz 225.7 MB
EGAF50000126291 fastq.gz 228.5 MB
EGAF50000126292 fastq.gz 52.6 MB
196 Files (25.1 GB)