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Tagged-amplicon deep sequencing

This dataset contains a collection of tumour samples from high grade serous ovarian carcinoma patients with recurrent disease collected near the point of diagnosis as well as tumour samples collected after patient relapse upon or some time after study entry. Whole blood samples were also collected from patients at study entry for the purpose of germline variant detection. The majority of diagnosis samples were preserved in neutral buffered formalin whereas the majority of post-relapse samples were preserved in universal molecular fixative (UMFIX, Sakura Finetek USA, Inc). DNA was extracted and the tagged-amplicon deep sequencing assay was applied (TAm-Seq, Forshew et al. 2002, Sci Transl Med) with the aid of fluidigm access array technology. Targeted loci were sequenced at very high depths (typically >100X) for the detection of both somatic and germline variants. Sequenced reads were aligned to the GRCh37 reference genome (release hs37d5).

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The UK Translational Research in Ovarian Cancer (BriTROC) Consortium Data Access and Use Agreement for non personal data.

Between Ovarian Cancer Action, a company limited by guarantee (registered in England and Wales under number 5403443) and a charity (registered in England under number 1109743 and registered in Scotland under number SC043478) of 8 – 12 Camden High St, London NW1 0JH, and Cancer Research UK, a company limited by guarantee (registered in England and Wales under number 4325234) and a charity (registered in England under number 1089464 and registered in Scotland under number SC041666) of Angel Building, 407 St John Street, London, EC1V 4AD, United Kingdom (collectively referred to as the “Funders”), and the undersigned parties. This agreement governs the terms on which access will be granted to the genotype and expression data generated as a result of the activities of the BriTROC Consortium and deposited by members of the Consortium including the Funders. In signing this agreement, you are agreeing with the Funders to be bound by the terms and conditions set out in this agreement. NOW THEREFORE in consideration of the access to the Data provided by the Funders to User Institution, and for other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound hereby, the parties hereto agree as follows: Definitions: “Application” means an application made by an entity (including You) to request access to the Data for a specific project and/or purpose. “Consortium” means the UK Translational Research in Ovarian Cancer consortium, known as BriTROC. “Data Access Committee” means the committee established by BriTROC to consider Applications. “Data” means non personal data including all and any human genetic and raw expression data obtained from the Consortium (which is currently available through the European Genome-phenome Archive). “Data Subject” means a person, who has been informed of the purpose for which the Data was collected, is currently held, and the purposes for which it can and will be distributed and disclosed, and has given his/her informed consent thereto. All references to individual Data Subjects have been removed and the Data is no longer personal data. User means a researcher whose User Institution has signed this Data Access Agreement and has received acknowledgement of the acceptance of its Application. Publications means, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. User Institution means the organisation at which the User is employed, affiliated or enrolled. User Institution is referred to within this Agreement as “You” (and “Your” shall be construed accordingly). Terms and Conditions: 1. You agree to preserve, at all times, the confidentiality and privacy of information and Data pertaining to Data Subjects. In particular, you undertake not to use, or attempt to use the Data to compromise or otherwise breach or infringe the confidentiality and privacy of information on Data Subjects. 
2. You agree not to attempt to link the Data to any other data source on the same samples, link the Data to any person or otherwise identify any Data Subject from the Data. We have taken organisational and technical measures to ensure this cannot happen. 
3. You agree not to transfer or disclose the Data, in whole or part, to others, except to persons within the User Institution for the fulfilment of the Purpose as reasonably necessary for Data/safety monitoring or programme management. If you wish to disclose the Data to a collaborator outside the User Institution, the third party must make a separate Application for access to the Data and enter into a separate Agreement. 
4. You agree to use the Data for the advancement of medical research, and solely for the approved purpose and project described in Your Application and for no other purpose, which is attached hereto as Schedule “B” (the “Purpose”); provided that any use of the Data beyond the scope of the Purpose will require a new Application, approval and Agreement. You agree to destroy the raw data once the project is completed, and upon request of the Consortium, provide written certification of such destruction. 
5. You agree that Data may be reissued from time to time, with suitable versioning. If the reissue is at the request of sample donors and/or other ethical scrutiny, you will destroy earlier versions of the Data, and upon request of the Consortium, provide written certification of such destruction. 
6. You agree to acknowledge in any work or Publications based in whole or part on the Data, the published paper from which the Data derives, the version of the Data, and the role of the Consortium and the Funders, in accordance with the Publications Policy attached as Schedule “A”. 
7. You agree and acknowledge that the Consortium, its members, the original Data creators, depositors or copyright holders, or the Funders: 
a) bear no legal responsibility or liability for the accuracy or comprehensiveness of the Data, or from any use of the Data including further analysis or interpretation of such Data; and
b) shall have no liability for any direct or indirect, consequential, or incidental damages or losses whatsoever arising out of Your use of the Data, or from the unavailability of, or lack of access to, the Data for whatever reason; and 
c) disclaim any and all representations, conditions or warranties (either express, implied or statutory) regarding the Data, including accuracy of the Data or that the Data corresponds with a particular description or is fit for a particular purpose. 
8. You shall indemnify, hold harmless and defend each of the Funders, any members of the Consortium and their respective directors, officers, employees and agents against any and all claims (including all associated legal fees and disbursements actually incurred) arising out of this Agreement, including without limitation against any damages or losses, consequential or otherwise, arising in any manner at all from or out of Your use of the Data. Section 8 shall not apply to any public body or institution that is prevented by applicable laws from providing indemnification. 9. You understand and acknowledge that the Data is owned by the Funders and protected by copyright, database rights and other intellectual property rights owned by the Funders. You agree that you shall not reproduce or copy the Data, except as reasonably required to carry out the Purpose and for no other purpose, or sell all or any part of the Data in any circumstances. 
10. You recognise that nothing in this Agreement shall operate to transfer to You any ownership or intellectual property rights relating to the Data. 
11. You accept that this Agreement will terminate immediately upon any breach of this Agreement by You and You will be required to destroy or return any Data, and upon request, provide written certification of such destruction. For the avoidance of doubt clause 3, 7, 8, 14, 15 will continue to operate in full force and effect. 
12. You accept that it may be necessary for the Funders to alter the terms of this Agreement from time to time in order to address new concerns. In this event, one of the Funders or a representative of the Consortium will contact You to inform You of any changes and You agree that Your continued use of the Data shall be dependent on the parties entering into a new version of the Agreement. 
13. You agree that you will submit a report to the Consortium Data Access Committee, if requested, on completion of the Purpose. The Consortium Data Access Committee agrees to treat the report and all information, data, results, and conclusions contained within such report as confidential information belonging to the User Institution. 
14. You agree that the Data is protected by and subject to applicable international laws, which may include without limitation the UK Data Protection Act 1998 and that you are responsible for ensuring compliance with any such laws. The Funders (via the BriTROC Data Access Committee) reserve the right to request and inspect Your data security and management documentation to ensure the adequacy of data protection measures in countries that have no privacy legislation comparable with that contained herein. 
15. Part or all of any section of this Agreement that is indefinite, invalid, illegal or otherwise voidable or unenforceable may be severed and the balance of this agreement will continue in full force and effect. 
Schedule “A” Publications Policy Any use of Data must acknowledge BriTROC using the following wording: "This study makes use of data generated by the BriTROC consortium. Funding for the project was provided by Ovraian Cancer Action and Cancer Research UK." and cite the relevant primary BRITROC publications (Piskorz, Ennis, Macintyre et al, Ann. Oncol 2015) which is the source of the Data. Schedule “B”
Application form (approved by the Consortium 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
EGAS00001007292 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
EGAF00008097069 fq.gz 21.4 MB
EGAF00008097070 fq.gz 25.7 MB
EGAF00008097071 fq.gz 2.3 MB
EGAF00008097072 fq.gz 2.8 MB
EGAF00008097073 fq.gz 21.5 MB
EGAF00008097074 fq.gz 26.6 MB
EGAF00008097075 fq.gz 20.9 MB
EGAF00008097076 fq.gz 25.3 MB
EGAF00008097077 fq.gz 24.3 MB
EGAF00008097078 fq.gz 30.1 MB
EGAF00008097079 fq.gz 25.6 MB
EGAF00008097080 fq.gz 31.3 MB
EGAF00008097081 fq.gz 26.4 MB
EGAF00008097082 fq.gz 32.1 MB
EGAF00008097083 fq.gz 20.6 MB
EGAF00008097084 fq.gz 25.1 MB
EGAF00008097085 fq.gz 30.2 MB
EGAF00008097086 fq.gz 36.6 MB
EGAF00008097087 fq.gz 24.3 MB
EGAF00008097088 fq.gz 29.4 MB
EGAF00008097089 fq.gz 23.2 MB
EGAF00008097090 fq.gz 27.9 MB
EGAF00008097091 fq.gz 30.9 MB
EGAF00008097092 fq.gz 38.1 MB
EGAF00008097093 fq.gz 29.9 MB
EGAF00008097094 fq.gz 36.5 MB
EGAF00008097095 fq.gz 23.1 MB
EGAF00008097096 fq.gz 27.4 MB
EGAF00008097097 fq.gz 25.5 MB
EGAF00008097098 fq.gz 30.7 MB
EGAF00008097099 fq.gz 24.3 MB
EGAF00008097100 fq.gz 29.6 MB
EGAF00008097101 fq.gz 23.2 MB
EGAF00008097102 fq.gz 28.6 MB
EGAF00008097103 fq.gz 29.1 MB
EGAF00008097104 fq.gz 33.6 MB
EGAF00008097105 fq.gz 26.1 MB
EGAF00008097106 fq.gz 31.5 MB
EGAF00008097107 fq.gz 27.5 MB
EGAF00008097108 fq.gz 33.5 MB
EGAF00008097109 fq.gz 32.3 MB
EGAF00008097110 fq.gz 38.9 MB
EGAF00008097111 fq.gz 28.7 MB
EGAF00008097112 fq.gz 34.3 MB
EGAF00008097113 fq.gz 32.8 MB
EGAF00008097114 fq.gz 39.1 MB
EGAF00008097115 fq.gz 36.7 MB
EGAF00008097116 fq.gz 44.5 MB
EGAF00008097117 fq.gz 19.9 MB
EGAF00008097118 fq.gz 23.9 MB
EGAF00008097119 fq.gz 23.2 MB
EGAF00008097120 fq.gz 27.7 MB
EGAF00008097121 fq.gz 25.8 MB
EGAF00008097122 fq.gz 31.2 MB
EGAF00008097123 fq.gz 48.5 MB
EGAF00008097124 fq.gz 58.8 MB
EGAF00008097125 fq.gz 31.1 MB
EGAF00008097126 fq.gz 36.7 MB
EGAF00008097127 fq.gz 32.2 MB
EGAF00008097128 fq.gz 39.1 MB
EGAF00008097129 fq.gz 27.1 MB
EGAF00008097130 fq.gz 32.9 MB
EGAF00008097131 fq.gz 31.3 MB
EGAF00008097132 fq.gz 37.5 MB
EGAF00008097133 fq.gz 31.0 MB
EGAF00008097134 fq.gz 37.4 MB
EGAF00008097135 fq.gz 24.8 MB
EGAF00008097136 fq.gz 29.9 MB
EGAF00008097137 fq.gz 38.5 MB
EGAF00008097138 fq.gz 46.2 MB
EGAF00008097139 fq.gz 34.2 MB
EGAF00008097140 fq.gz 41.2 MB
EGAF00008097141 fq.gz 31.5 MB
EGAF00008097142 fq.gz 37.8 MB
EGAF00008097143 fq.gz 22.8 MB
EGAF00008097144 fq.gz 27.8 MB
EGAF00008097145 fq.gz 31.9 MB
EGAF00008097146 fq.gz 38.0 MB
EGAF00008097147 fq.gz 36.0 MB
EGAF00008097148 fq.gz 43.6 MB
EGAF00008097149 fq.gz 31.6 MB
EGAF00008097150 fq.gz 38.5 MB
EGAF00008097151 fq.gz 28.9 MB
EGAF00008097152 fq.gz 34.8 MB
EGAF00008097153 fq.gz 26.7 MB
EGAF00008097154 fq.gz 32.0 MB
EGAF00008097155 fq.gz 30.8 MB
EGAF00008097156 fq.gz 37.3 MB
EGAF00008097157 fq.gz 41.1 MB
EGAF00008097158 fq.gz 49.8 MB
EGAF00008097159 fq.gz 41.0 MB
EGAF00008097160 fq.gz 49.8 MB
EGAF00008097161 fq.gz 25.9 MB
EGAF00008097162 fq.gz 30.9 MB
EGAF00008097163 fq.gz 4.3 MB
EGAF00008097164 fq.gz 5.0 MB
EGAF00008097165 fq.gz 26.6 MB
EGAF00008097166 fq.gz 31.6 MB
EGAF00008097167 fq.gz 42.2 MB
EGAF00008097168 fq.gz 51.1 MB
EGAF00008097169 fq.gz 33.2 MB
EGAF00008097170 fq.gz 39.2 MB
EGAF00008097171 fq.gz 37.0 MB
EGAF00008097172 fq.gz 45.6 MB
EGAF00008097173 fq.gz 31.8 MB
EGAF00008097174 fq.gz 38.6 MB
EGAF00008097175 fq.gz 23.7 MB
EGAF00008097176 fq.gz 28.7 MB
EGAF00008097177 fq.gz 13.5 MB
EGAF00008097178 fq.gz 16.1 MB
EGAF00008097179 fq.gz 22.8 MB
EGAF00008097180 fq.gz 27.7 MB
EGAF00008097181 fq.gz 32.8 MB
EGAF00008097182 fq.gz 39.6 MB
EGAF00008097183 fq.gz 30.4 MB
EGAF00008097184 fq.gz 36.9 MB
EGAF00008097185 fq.gz 22.8 MB
EGAF00008097186 fq.gz 27.4 MB
EGAF00008097187 fq.gz 31.2 MB
EGAF00008097188 fq.gz 37.7 MB
EGAF00008097189 fq.gz 26.5 MB
EGAF00008097190 fq.gz 31.6 MB
EGAF00008097191 fq.gz 29.3 MB
EGAF00008097192 fq.gz 35.5 MB
EGAF00008097193 fq.gz 26.9 MB
EGAF00008097194 fq.gz 32.2 MB
EGAF00008097195 fq.gz 37.1 MB
EGAF00008097196 fq.gz 45.1 MB
EGAF00008097197 fq.gz 29.2 MB
EGAF00008097198 fq.gz 34.9 MB
EGAF00008097199 fq.gz 34.1 MB
EGAF00008097200 fq.gz 41.6 MB
EGAF00008097201 fq.gz 37.0 MB
EGAF00008097202 fq.gz 44.7 MB
EGAF00008097203 fq.gz 32.8 MB
EGAF00008097204 fq.gz 39.7 MB
EGAF00008097205 fq.gz 14.6 MB
EGAF00008097206 fq.gz 17.4 MB
EGAF00008097207 fq.gz 20.4 MB
EGAF00008097208 fq.gz 24.4 MB
EGAF00008097209 fq.gz 27.0 MB
EGAF00008097210 fq.gz 32.2 MB
EGAF00008097211 fq.gz 21.2 MB
EGAF00008097212 fq.gz 25.7 MB
EGAF00008097213 fq.gz 29.6 MB
EGAF00008097214 fq.gz 35.8 MB
EGAF00008097215 fq.gz 23.2 MB
EGAF00008097216 fq.gz 27.9 MB
EGAF00008097217 fq.gz 25.2 MB
EGAF00008097218 fq.gz 30.6 MB
EGAF00008097219 fq.gz 25.6 MB
EGAF00008097220 fq.gz 31.2 MB
EGAF00008097221 fq.gz 26.4 MB
EGAF00008097222 fq.gz 32.3 MB
EGAF00008097223 fq.gz 37.6 MB
EGAF00008097224 fq.gz 44.7 MB
EGAF00008097225 fq.gz 30.3 MB
EGAF00008097226 fq.gz 36.2 MB
EGAF00008097227 fq.gz 31.6 MB
EGAF00008097228 fq.gz 38.0 MB
EGAF00008097229 fq.gz 33.1 MB
EGAF00008097230 fq.gz 39.7 MB
EGAF00008097231 fq.gz 35.0 MB
EGAF00008097232 fq.gz 41.4 MB
EGAF00008097233 fq.gz 44.6 MB
EGAF00008097234 fq.gz 54.0 MB
EGAF00008097235 fq.gz 42.6 MB
EGAF00008097236 fq.gz 51.1 MB
EGAF00008097237 fq.gz 20.6 MB
EGAF00008097238 fq.gz 25.2 MB
EGAF00008097239 fq.gz 27.2 MB
EGAF00008097240 fq.gz 32.9 MB
EGAF00008097241 fq.gz 32.6 MB
EGAF00008097242 fq.gz 39.1 MB
EGAF00008097243 fq.gz 31.1 MB
EGAF00008097244 fq.gz 37.3 MB
EGAF00008097245 fq.gz 43.7 MB
EGAF00008097246 fq.gz 52.5 MB
EGAF00008097247 fq.gz 37.6 MB
EGAF00008097248 fq.gz 45.3 MB
EGAF00008097249 fq.gz 45.4 MB
EGAF00008097250 fq.gz 53.9 MB
EGAF00008097251 fq.gz 32.1 MB
EGAF00008097252 fq.gz 38.8 MB
EGAF00008097253 fq.gz 43.3 MB
EGAF00008097254 fq.gz 52.4 MB
EGAF00008097255 fq.gz 43.6 MB
EGAF00008097256 fq.gz 52.6 MB
EGAF00008097257 fq.gz 39.7 MB
EGAF00008097258 fq.gz 47.8 MB
EGAF00008097259 fq.gz 36.9 MB
EGAF00008097260 fq.gz 44.4 MB
EGAF00008097261 fq.gz 43.8 MB
EGAF00008097262 fq.gz 53.3 MB
EGAF00008097263 fq.gz 39.6 MB
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EGAF00008097265 fq.gz 39.6 MB
EGAF00008097266 fq.gz 48.1 MB
EGAF00008097267 fq.gz 38.8 MB
EGAF00008097268 fq.gz 46.4 MB
EGAF00008097269 fq.gz 39.8 MB
EGAF00008097270 fq.gz 48.1 MB
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EGAF00008097272 fq.gz 50.0 MB
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EGAF00008097279 fq.gz 40.0 MB
EGAF00008097280 fq.gz 47.7 MB
EGAF00008097281 fq.gz 37.1 MB
EGAF00008097282 fq.gz 44.4 MB
EGAF00008097283 fq.gz 37.2 MB
EGAF00008097284 fq.gz 45.5 MB
EGAF00008097285 fq.gz 45.6 MB
EGAF00008097286 fq.gz 54.8 MB
EGAF00008097287 fq.gz 48.2 MB
EGAF00008097288 fq.gz 58.7 MB
EGAF00008097289 fq.gz 53.4 MB
EGAF00008097290 fq.gz 63.4 MB
EGAF00008097291 fq.gz 41.6 MB
EGAF00008097292 fq.gz 50.5 MB
EGAF00008097293 fq.gz 14.8 MB
EGAF00008097294 fq.gz 17.8 MB
EGAF00008097295 fq.gz 40.7 MB
EGAF00008097296 fq.gz 49.1 MB
EGAF00008097297 fq.gz 44.8 MB
EGAF00008097298 fq.gz 54.0 MB
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EGAF00008097300 fq.gz 47.0 MB
EGAF00008097301 fq.gz 39.4 MB
EGAF00008097302 fq.gz 47.4 MB
EGAF00008097303 fq.gz 32.9 MB
EGAF00008097304 fq.gz 39.6 MB
EGAF00008097305 fq.gz 40.3 MB
EGAF00008097306 fq.gz 48.3 MB
EGAF00008097307 fq.gz 49.5 MB
EGAF00008097308 fq.gz 59.5 MB
EGAF00008097309 fq.gz 50.5 MB
EGAF00008097310 fq.gz 56.3 MB
EGAF00008097311 fq.gz 38.9 MB
EGAF00008097312 fq.gz 46.7 MB
EGAF00008097313 fq.gz 46.9 MB
EGAF00008097314 fq.gz 56.1 MB
EGAF00008097315 fq.gz 35.5 MB
EGAF00008097316 fq.gz 42.1 MB
EGAF00008097317 fq.gz 41.9 MB
EGAF00008097318 fq.gz 50.5 MB
EGAF00008097319 fq.gz 33.8 MB
EGAF00008097320 fq.gz 40.3 MB
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EGAF00008097378 fq.gz 57.2 MB
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EGAF00008097381 fq.gz 27.1 MB
EGAF00008097382 fq.gz 31.9 MB
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EGAF00008097388 fq.gz 59.4 MB
EGAF00008097389 fq.gz 49.1 MB
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EGAF00008097411 fq.gz 45.0 MB
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EGAF00008097413 fq.gz 10.9 MB
EGAF00008097414 fq.gz 14.0 MB
EGAF00008097415 fq.gz 41.4 MB
EGAF00008097416 fq.gz 49.6 MB
EGAF00008097417 fq.gz 54.6 MB
EGAF00008097418 fq.gz 64.2 MB
EGAF00008097419 fq.gz 36.8 MB
EGAF00008097420 fq.gz 44.9 MB
EGAF00008097421 fq.gz 39.8 MB
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6348 Files (389.2 GB)