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Tam-Seq of HGSOC samples for fixative comparison study

Targeted amplicon sequencing of samples as part of the study "Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples. The amplicon panel consists of 48 amplicons in TP53, PTEN, EGFR, PIK3CA, KRAS and BRAF genes as described previously [Forshew, STM 2012]. All libraries were pooled and quantify using DNA 1000 kit on Agilent 2100 Bioanalyzer and KAPA SYBR FAST ABI Prism qPCR Kit (KAPA Biosystems) on 7900HT Fast Real-Time PCR System (Applied Biosystems) according to the supplier's recommendations. Reads were aligned using bwa-mem v0.7.12-r1039 to the 1000 genomes version of human genome build GRCh37, retaining duplicate reads.

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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
EGAS00001001433 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
EGAF00001107014 bam 7.7 MB
EGAF00001107015 bam 3.1 MB
EGAF00001107016 bam 6.9 MB
EGAF00001107017 bam 7.8 MB
EGAF00001107018 bam 8.0 MB
EGAF00001107019 bam 1.4 MB
EGAF00001107020 bam 1.2 MB
EGAF00001107021 bam 1.6 MB
EGAF00001107022 bam 10.7 MB
EGAF00001107023 bam 20.3 MB
EGAF00001107024 bam 12.4 MB
EGAF00001107025 bam 32.0 MB
EGAF00001107026 bam 30.0 MB
EGAF00001107027 bam 9.5 MB
EGAF00001107028 bam 8.8 MB
EGAF00001107029 bam 8.4 MB
EGAF00001107030 bam 8.1 MB
EGAF00001107031 bam 6.1 MB
EGAF00001107032 bam 6.9 MB
EGAF00001107033 bam 12.4 MB
EGAF00001107034 bam 9.5 MB
EGAF00001107035 bam 8.5 MB
EGAF00001107036 bam 9.0 MB
EGAF00001107037 bam 10.0 MB
EGAF00001107038 bam 10.3 MB
EGAF00001107039 bam 8.2 MB
EGAF00001107040 bam 5.5 MB
EGAF00001107041 bam 7.5 MB
EGAF00001107042 bam 6.0 MB
EGAF00001107043 bam 6.4 MB
EGAF00001107044 bam 7.2 MB
EGAF00001107045 bam 5.0 MB
EGAF00001107046 bam 5.2 MB
EGAF00001107047 bam 4.2 MB
EGAF00001107048 bam 35.0 MB
EGAF00001107049 bam 3.0 MB
EGAF00001107050 bam 2.7 MB
EGAF00001107051 bam 6.6 MB
EGAF00001107052 bam 4.6 MB
EGAF00001107053 bam 1.9 MB
EGAF00001107054 bam 2.4 MB
EGAF00001107055 bam 1.8 MB
EGAF00001107056 bam 24.7 MB
EGAF00001107057 bam 20.2 MB
EGAF00001107058 bam 23.1 MB
EGAF00001107059 bam 34.3 MB
EGAF00001107060 bam 29.7 MB
EGAF00001107061 bam 35.0 MB
EGAF00001107062 bam 28.5 MB
EGAF00001107063 bam 8.9 MB
EGAF00001107064 bam 6.9 MB
EGAF00001107065 bam 9.3 MB
EGAF00001107066 bam 7.6 MB
EGAF00001107067 bam 8.5 MB
EGAF00001107068 bam 5.5 MB
EGAF00001107069 bam 8.5 MB
EGAF00001107070 bam 2.9 MB
EGAF00001107071 bam 6.2 MB
EGAF00001107072 bam 21.1 MB
EGAF00001107073 bam 15.8 MB
EGAF00001107074 bam 19.6 MB
EGAF00001107075 bam 16.0 MB
EGAF00001107076 bam 6.7 MB
EGAF00001107077 bam 6.9 MB
EGAF00001107078 bam 7.7 MB
EGAF00001107079 bam 6.5 MB
EGAF00001107080 bam 7.7 MB
EGAF00001107081 bam 6.7 MB
EGAF00001107082 bam 6.4 MB
EGAF00001107083 bam 7.8 MB
EGAF00001107084 bam 11.7 MB
EGAF00001107085 bam 3.2 MB
EGAF00001107086 bam 2.4 MB
EGAF00001107087 bam 2.8 MB
EGAF00001107088 bam 3.1 MB
EGAF00001107089 bam 3.1 MB
EGAF00001107090 bam 3.0 MB
EGAF00001107091 bam 10.7 MB
EGAF00001107092 bam 8.6 MB
EGAF00001107093 bam 9.0 MB
EGAF00001107094 bam 7.8 MB
EGAF00001107095 bam 7.2 MB
EGAF00001107096 bam 7.9 MB
EGAF00001107097 bam 6.7 MB
EGAF00001107098 bam 10.2 MB
EGAF00001107099 bam 8.5 MB
EGAF00001107100 bam 7.0 MB
EGAF00001107101 bam 6.5 MB
EGAF00001107102 bam 5.1 MB
EGAF00001107103 bam 7.5 MB
EGAF00001107104 bam 5.9 MB
EGAF00001107105 bam 10.0 MB
EGAF00001107106 bam 21.1 MB
EGAF00001107107 bam 18.5 MB
EGAF00001107108 bam 25.8 MB
EGAF00001107109 bam 21.8 MB
EGAF00001107110 bam 21.5 MB
EGAF00001107111 bam 13.3 MB
EGAF00001107112 bam 20.6 MB
EGAF00001107113 bam 7.1 MB
EGAF00001107114 bam 8.6 MB
EGAF00001107115 bam 7.1 MB
EGAF00001107116 bam 7.9 MB
EGAF00001107117 bam 7.1 MB
EGAF00001107118 bam 7.3 MB
EGAF00001107119 bam 6.6 MB
EGAF00001107120 bam 7.4 MB
EGAF00001107121 bam 9.2 MB
EGAF00001107122 bam 2.7 MB
EGAF00001107123 bam 2.1 MB
EGAF00001107124 bam 1.8 MB
EGAF00001107125 bam 2.0 MB
EGAF00001107126 bam 2.8 MB
EGAF00001107127 bam 2.7 MB
EGAF00001107128 bam 2.4 MB
EGAF00001107129 bam 1.2 MB
EGAF00001107130 bam 6.1 MB
EGAF00001107131 bam 7.7 MB
EGAF00001107132 bam 6.8 MB
EGAF00001107133 bam 6.3 MB
EGAF00001107134 bam 6.6 MB
EGAF00001107135 bam 6.5 MB
EGAF00001107136 bam 7.3 MB
EGAF00001107137 bam 7.0 MB
EGAF00001107138 bam 6.8 MB
EGAF00001107139 bam 8.6 MB
EGAF00001107140 bam 8.8 MB
EGAF00001107141 bam 9.0 MB
EGAF00001107142 bam 7.0 MB
EGAF00001107143 bam 7.2 MB
EGAF00001107144 bam 12.9 MB
EGAF00001107145 bam 11.5 MB
132 Files (1.3 GB)